Starting phenix.real_space_refine on Mon Feb 19 12:15:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/02_2024/7utj_26772_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/02_2024/7utj_26772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/02_2024/7utj_26772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/02_2024/7utj_26772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/02_2024/7utj_26772_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utj_26772/02_2024/7utj_26772_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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 12 5.49 5 Mg 6 5.21 5 S 216 5.16 5 C 15462 2.51 5 N 4200 2.21 5 O 4695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "G ASP 711": "OD1" <-> "OD2" Residue "G ASP 757": "OD1" <-> "OD2" Residue "G TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 865": "OE1" <-> "OE2" Residue "H ASP 711": "OD1" <-> "OD2" Residue "H ASP 757": "OD1" <-> "OD2" Residue "H TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 865": "OE1" <-> "OE2" Residue "I ASP 711": "OD1" <-> "OD2" Residue "I ASP 757": "OD1" <-> "OD2" Residue "I TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 865": "OE1" <-> "OE2" Residue "K ASP 711": "OD1" <-> "OD2" Residue "K ASP 757": "OD1" <-> "OD2" Residue "K TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 865": "OE1" <-> "OE2" Residue "L ASP 711": "OD1" <-> "OD2" Residue "L ASP 757": "OD1" <-> "OD2" Residue "L TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 865": "OE1" <-> "OE2" Residue "Z ASP 711": "OD1" <-> "OD2" Residue "Z ASP 757": "OD1" <-> "OD2" Residue "Z TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 865": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24591 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "H" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "I" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "K" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "L" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "Z" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1179 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.51, per 1000 atoms: 0.55 Number of scatterers: 24591 At special positions: 0 Unit cell: (122.831, 101.091, 219.574, 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 216 16.00 P 12 15.00 Mg 6 11.99 O 4695 8.00 N 4200 7.00 C 15462 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=0, symmetry=0 Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 4.9 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 24 sheets defined 51.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.779A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.847A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 261 Proline residue: A 258 - end of helix removed outlier: 4.818A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 5.630A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 Proline residue: A 367 - end of helix removed outlier: 5.271A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.779A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 81 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 126 Processing helix chain 'B' and resid 137 through 144 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: 3.848A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.705A 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 253 through 261 Proline residue: B 258 - end of helix removed outlier: 4.817A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 5.630A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.271A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.780A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.847A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 261 Proline residue: C 258 - end of helix removed outlier: 4.817A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 5.629A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.271A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.780A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 81 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 126 Processing helix chain 'D' and resid 137 through 144 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: 3.847A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.706A 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 253 through 261 Proline residue: D 258 - end of helix removed outlier: 4.817A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 5.630A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 373 Proline residue: D 367 - end of helix removed outlier: 5.270A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.779A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 81 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 126 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.847A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 253 through 261 Proline residue: E 258 - end of helix removed outlier: 4.818A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 5.629A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 373 Proline residue: E 367 - end of helix removed outlier: 5.270A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.779A pdb=" N SER F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 81 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 126 Processing helix chain 'F' and resid 137 through 144 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: 3.847A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.705A 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 253 through 261 Proline residue: F 258 - end of helix removed outlier: 4.818A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 347 removed outlier: 5.630A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 373 Proline residue: F 367 - end of helix removed outlier: 5.271A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 711 through 730 Processing helix chain 'G' and resid 739 through 765 Processing helix chain 'G' and resid 773 through 803 Processing helix chain 'G' and resid 812 through 842 removed outlier: 4.002A pdb=" N SER G 817 " --> pdb=" O ASP G 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU G 818 " --> pdb=" O SER G 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 852 No H-bonds generated for 'chain 'G' and resid 849 through 852' Processing helix chain 'H' and resid 711 through 730 Processing helix chain 'H' and resid 739 through 765 Processing helix chain 'H' and resid 773 through 803 Processing helix chain 'H' and resid 812 through 842 removed outlier: 4.002A pdb=" N SER H 817 " --> pdb=" O ASP H 813 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU H 818 " --> pdb=" O SER H 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 849 through 852 No H-bonds generated for 'chain 'H' and resid 849 through 852' Processing helix chain 'I' and resid 711 through 730 Processing helix chain 'I' and resid 739 through 765 Processing helix chain 'I' and resid 773 through 803 Processing helix chain 'I' and resid 812 through 842 removed outlier: 4.002A pdb=" N SER I 817 " --> pdb=" O ASP I 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU I 818 " --> pdb=" O SER I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 849 through 852 No H-bonds generated for 'chain 'I' and resid 849 through 852' Processing helix chain 'K' and resid 711 through 730 Processing helix chain 'K' and resid 739 through 765 Processing helix chain 'K' and resid 773 through 803 Processing helix chain 'K' and resid 812 through 842 removed outlier: 4.002A pdb=" N SER K 817 " --> pdb=" O ASP K 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 849 through 852 No H-bonds generated for 'chain 'K' and resid 849 through 852' Processing helix chain 'L' and resid 711 through 730 Processing helix chain 'L' and resid 739 through 765 Processing helix chain 'L' and resid 773 through 803 Processing helix chain 'L' and resid 812 through 842 removed outlier: 4.002A pdb=" N SER L 817 " --> pdb=" O ASP L 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 849 through 852 No H-bonds generated for 'chain 'L' and resid 849 through 852' Processing helix chain 'Z' and resid 711 through 730 Processing helix chain 'Z' and resid 739 through 765 Processing helix chain 'Z' and resid 773 through 803 Processing helix chain 'Z' and resid 812 through 842 removed outlier: 4.002A pdb=" N SER Z 817 " --> pdb=" O ASP Z 813 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU Z 818 " --> pdb=" O SER Z 814 " (cutoff:3.500A) Processing helix chain 'Z' and resid 849 through 852 No H-bonds generated for 'chain 'Z' and resid 849 through 852' Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.696A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.196A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.696A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.196A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.697A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.196A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.697A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.196A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.697A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.197A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.696A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 34 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.195A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 238 through 241 1170 hydrogen bonds defined for protein. 3204 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: 7.60 Time building geometry restraints manager: 11.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4558 1.32 - 1.45: 5837 1.45 - 1.57: 14235 1.57 - 1.69: 18 1.69 - 1.82: 372 Bond restraints: 25020 Sorted by residual: bond pdb=" N VAL B 159 " pdb=" CA VAL B 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.041 1.18e-02 7.18e+03 1.20e+01 ... (remaining 25015 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.30: 607 105.30 - 112.99: 13738 112.99 - 120.68: 11591 120.68 - 128.37: 7735 128.37 - 136.06: 169 Bond angle restraints: 33840 Sorted by residual: angle pdb=" CA LEU Z 790 " pdb=" C LEU Z 790 " pdb=" O LEU Z 790 " ideal model delta sigma weight residual 120.55 115.33 5.22 1.06e+00 8.90e-01 2.43e+01 angle pdb=" N GLN I 789 " pdb=" CA GLN I 789 " pdb=" C GLN I 789 " ideal model delta sigma weight residual 111.28 107.19 4.09 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA ASP E 157 " pdb=" CB ASP E 157 " pdb=" CG ASP E 157 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" N GLN Z 789 " pdb=" CA GLN Z 789 " pdb=" C GLN Z 789 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN K 789 " pdb=" CA GLN K 789 " pdb=" C GLN K 789 " ideal model delta sigma weight residual 111.28 107.50 3.78 1.09e+00 8.42e-01 1.20e+01 ... (remaining 33835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 14441 27.20 - 54.39: 717 54.39 - 81.59: 124 81.59 - 108.78: 6 108.78 - 135.98: 18 Dihedral angle restraints: 15306 sinusoidal: 6156 harmonic: 9150 Sorted by residual: dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.98 -135.98 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.97 -135.97 1 2.00e+01 2.50e-03 4.13e+01 ... (remaining 15303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2586 0.052 - 0.104: 970 0.104 - 0.156: 203 0.156 - 0.208: 62 0.208 - 0.260: 13 Chirality restraints: 3834 Sorted by residual: chirality pdb=" CA LEU A 153 " pdb=" N LEU A 153 " pdb=" C LEU A 153 " pdb=" CB LEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU D 153 " pdb=" N LEU D 153 " pdb=" C LEU D 153 " pdb=" CB LEU D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU C 153 " pdb=" N LEU C 153 " pdb=" C LEU C 153 " pdb=" CB LEU C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3831 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Z 790 " -0.022 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" C LEU Z 790 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU Z 790 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN Z 791 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 156 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY D 156 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY D 156 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 157 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 156 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.027 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 118 2.52 - 3.12: 18492 3.12 - 3.71: 38915 3.71 - 4.31: 59864 4.31 - 4.90: 97448 Nonbonded interactions: 214837 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.927 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.955 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.957 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.973 2.170 ... (remaining 214832 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.340 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 67.560 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.009 0.065 25020 Z= 0.606 Angle : 0.915 7.122 33840 Z= 0.525 Chirality : 0.059 0.260 3834 Planarity : 0.005 0.046 4290 Dihedral : 16.795 135.978 9414 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.88 % Allowed : 4.15 % Favored : 91.97 % 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: 0.03 (0.15), residues: 3102 helix: 0.43 (0.12), residues: 1626 sheet: -0.11 (0.25), residues: 408 loop : -0.34 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 859 HIS 0.008 0.002 HIS E 161 PHE 0.007 0.001 PHE B 127 TYR 0.009 0.001 TYR F 53 ARG 0.006 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 432 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7964 (mm110) cc_final: 0.7312 (mm110) REVERT: A 325 MET cc_start: 0.8575 (mmp) cc_final: 0.7939 (mmp) REVERT: B 206 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7759 (ttp-170) REVERT: B 211 ASP cc_start: 0.7587 (t0) cc_final: 0.7335 (t0) REVERT: B 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8503 (mmm) REVERT: B 325 MET cc_start: 0.8799 (mmp) cc_final: 0.8182 (mmp) REVERT: C 82 MET cc_start: 0.8755 (tpt) cc_final: 0.8465 (tpp) REVERT: C 211 ASP cc_start: 0.7858 (t0) cc_final: 0.7596 (t0) REVERT: C 325 MET cc_start: 0.9009 (mmp) cc_final: 0.8750 (mmp) REVERT: D 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8547 (mmm) REVERT: D 326 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6052 (ptpt) REVERT: E 325 MET cc_start: 0.8817 (mmp) cc_final: 0.8525 (mmp) REVERT: E 326 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5636 (ptmm) REVERT: F 12 ASN cc_start: 0.7886 (m110) cc_final: 0.7566 (m110) REVERT: F 47 MET cc_start: 0.6726 (mmm) cc_final: 0.6338 (mmp) REVERT: F 206 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6688 (ttp80) REVERT: F 269 MET cc_start: 0.8846 (mtp) cc_final: 0.8547 (mtm) REVERT: G 717 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6527 (ttmt) REVERT: G 719 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: G 816 MET cc_start: 0.7436 (tpt) cc_final: 0.7186 (tpt) REVERT: G 834 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6838 (tptt) REVERT: H 715 LEU cc_start: 0.7340 (tp) cc_final: 0.7115 (tt) REVERT: I 826 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.7011 (mmm) REVERT: K 721 MET cc_start: 0.6388 (mmp) cc_final: 0.5343 (ptt) REVERT: L 744 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m) REVERT: L 795 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6486 (tmtt) REVERT: Z 719 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: Z 792 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (mt) outliers start: 103 outliers final: 12 residues processed: 481 average time/residue: 1.6441 time to fit residues: 888.4632 Evaluate side-chains 320 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 298 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 717 LYS Chi-restraints excluded: chain G residue 719 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain I residue 826 MET Chi-restraints excluded: chain L residue 744 SER Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 719 MET Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain Z residue 792 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.7980 chunk 236 optimal weight: 0.0170 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 10.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 314 GLN D 353 GLN E 92 ASN I 824 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 25020 Z= 0.166 Angle : 0.556 7.957 33840 Z= 0.279 Chirality : 0.042 0.132 3834 Planarity : 0.004 0.038 4290 Dihedral : 10.158 143.715 3516 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 10.75 % Favored : 87.25 % 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: 0.71 (0.15), residues: 3102 helix: 0.99 (0.13), residues: 1620 sheet: 0.15 (0.24), residues: 402 loop : -0.01 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 859 HIS 0.004 0.001 HIS E 161 PHE 0.008 0.001 PHE C 127 TYR 0.010 0.001 TYR D 143 ARG 0.003 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 338 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7918 (mm110) cc_final: 0.7284 (mm110) REVERT: A 206 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7740 (ttp-170) REVERT: A 314 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: A 325 MET cc_start: 0.8382 (mmp) cc_final: 0.7858 (mmp) REVERT: A 364 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 211 ASP cc_start: 0.7529 (t0) cc_final: 0.7237 (t0) REVERT: C 12 ASN cc_start: 0.8157 (m110) cc_final: 0.7868 (m-40) REVERT: C 72 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: C 82 MET cc_start: 0.8793 (tpt) cc_final: 0.8561 (tpt) REVERT: C 206 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7610 (ttp-110) REVERT: C 325 MET cc_start: 0.8674 (mmp) cc_final: 0.8307 (mmp) REVERT: C 328 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7832 (tttp) REVERT: C 372 ARG cc_start: 0.8146 (ptp-170) cc_final: 0.7770 (ptt180) REVERT: D 121 GLN cc_start: 0.8549 (tt0) cc_final: 0.8271 (tt0) REVERT: D 305 MET cc_start: 0.8897 (mmm) cc_final: 0.8521 (mmm) REVERT: D 325 MET cc_start: 0.8684 (mmp) cc_final: 0.8383 (mmp) REVERT: D 328 LYS cc_start: 0.8183 (tttp) cc_final: 0.7850 (tmtt) REVERT: E 314 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: E 325 MET cc_start: 0.8766 (mmp) cc_final: 0.8447 (mmp) REVERT: E 355 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7510 (mtt) REVERT: F 47 MET cc_start: 0.6865 (mmm) cc_final: 0.6555 (mmp) REVERT: G 717 LYS cc_start: 0.7220 (mtpt) cc_final: 0.6888 (mttm) REVERT: G 816 MET cc_start: 0.7613 (tpt) cc_final: 0.7308 (tpt) REVERT: G 834 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6868 (tptt) REVERT: H 719 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7360 (mtp) REVERT: H 756 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.6958 (tpp) REVERT: I 719 MET cc_start: 0.6917 (mtp) cc_final: 0.6677 (mtp) REVERT: I 826 MET cc_start: 0.7452 (tpt) cc_final: 0.7142 (mmm) REVERT: K 721 MET cc_start: 0.6276 (mmp) cc_final: 0.5395 (ptt) REVERT: L 795 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6447 (tmtt) REVERT: Z 719 MET cc_start: 0.8083 (mtm) cc_final: 0.7857 (mtp) REVERT: Z 721 MET cc_start: 0.6314 (tpp) cc_final: 0.6073 (tpt) outliers start: 53 outliers final: 11 residues processed: 364 average time/residue: 1.6483 time to fit residues: 674.4484 Evaluate side-chains 312 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 291 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 834 LYS Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 719 MET Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 792 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 0.0020 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN E 162 ASN F 162 ASN H 710 ASN I 824 ASN K 791 ASN L 718 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 25020 Z= 0.573 Angle : 0.685 8.810 33840 Z= 0.342 Chirality : 0.049 0.152 3834 Planarity : 0.005 0.044 4290 Dihedral : 9.952 139.020 3475 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.39 % Allowed : 11.27 % Favored : 85.33 % 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: 0.65 (0.15), residues: 3102 helix: 0.97 (0.13), residues: 1548 sheet: 0.17 (0.24), residues: 408 loop : -0.03 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 340 HIS 0.010 0.002 HIS F 161 PHE 0.013 0.002 PHE C 21 TYR 0.015 0.002 TYR C 188 ARG 0.007 0.001 ARG L 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 295 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7642 (mtt-85) REVERT: A 49 GLN cc_start: 0.8018 (mm110) cc_final: 0.7300 (mm110) REVERT: A 314 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: B 72 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: B 252 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8607 (p0) REVERT: B 299 MET cc_start: 0.8504 (mtm) cc_final: 0.8257 (mtm) REVERT: B 328 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8185 (tttp) REVERT: B 355 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: C 72 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: C 82 MET cc_start: 0.8794 (tpt) cc_final: 0.8389 (tpt) REVERT: C 206 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7695 (ttp-110) REVERT: C 314 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: C 328 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7945 (tttp) REVERT: C 372 ARG cc_start: 0.8257 (ptp-170) cc_final: 0.7953 (ptt180) REVERT: D 121 GLN cc_start: 0.8562 (tt0) cc_final: 0.8331 (tt0) REVERT: D 284 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8631 (mttp) REVERT: D 305 MET cc_start: 0.8925 (mmm) cc_final: 0.8536 (mmm) REVERT: D 328 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8035 (tmtt) REVERT: E 314 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: E 325 MET cc_start: 0.8508 (mmp) cc_final: 0.8168 (mmp) REVERT: E 355 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: F 44 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: F 47 MET cc_start: 0.7013 (mmm) cc_final: 0.6742 (mmp) REVERT: F 153 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8365 (tp) REVERT: F 314 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: G 723 MET cc_start: 0.7340 (tmm) cc_final: 0.6729 (tpp) REVERT: G 816 MET cc_start: 0.7677 (tpt) cc_final: 0.7337 (tpt) REVERT: H 715 LEU cc_start: 0.7245 (tp) cc_final: 0.6827 (tp) REVERT: H 719 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7455 (mtp) REVERT: H 756 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8172 (tpt) REVERT: I 826 MET cc_start: 0.7464 (tpt) cc_final: 0.7230 (mmm) REVERT: I 845 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5525 (mtmt) REVERT: K 721 MET cc_start: 0.6517 (mmt) cc_final: 0.5562 (ptt) REVERT: L 795 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6145 (tmtt) REVERT: L 861 MET cc_start: 0.6363 (mmt) cc_final: 0.5979 (mmt) REVERT: Z 721 MET cc_start: 0.6286 (tpp) cc_final: 0.6076 (tpt) outliers start: 90 outliers final: 23 residues processed: 344 average time/residue: 1.6284 time to fit residues: 630.1064 Evaluate side-chains 328 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 285 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain H residue 719 MET Chi-restraints excluded: chain H residue 756 MET Chi-restraints excluded: chain H residue 792 ILE Chi-restraints excluded: chain I residue 845 LYS Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 30.0000 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 284 optimal weight: 20.0000 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN G 710 ASN G 718 GLN G 801 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25020 Z= 0.227 Angle : 0.547 9.413 33840 Z= 0.271 Chirality : 0.042 0.135 3834 Planarity : 0.004 0.039 4290 Dihedral : 9.602 146.385 3469 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.22 % Allowed : 13.31 % Favored : 84.46 % 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: 1.05 (0.15), residues: 3102 helix: 1.22 (0.13), residues: 1560 sheet: 0.28 (0.24), residues: 408 loop : 0.30 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.006 0.001 HIS D 161 PHE 0.009 0.001 PHE C 31 TYR 0.008 0.001 TYR C 69 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 296 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7562 (mtt-85) REVERT: A 314 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: B 72 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: B 328 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8113 (tttp) REVERT: B 355 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: C 12 ASN cc_start: 0.8211 (m110) cc_final: 0.7874 (m-40) REVERT: C 72 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: C 206 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7581 (ttp-110) REVERT: C 328 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7920 (tttp) REVERT: D 121 GLN cc_start: 0.8532 (tt0) cc_final: 0.8297 (tt0) REVERT: D 305 MET cc_start: 0.8919 (mmm) cc_final: 0.8520 (mmm) REVERT: D 325 MET cc_start: 0.8855 (mmp) cc_final: 0.8095 (mmp) REVERT: D 328 LYS cc_start: 0.8272 (tttp) cc_final: 0.7925 (tmtt) REVERT: E 277 THR cc_start: 0.8885 (m) cc_final: 0.8631 (m) REVERT: E 314 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: E 355 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7422 (mtt) REVERT: E 364 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: F 153 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8385 (tp) REVERT: G 723 MET cc_start: 0.7303 (tmm) cc_final: 0.6715 (tpt) REVERT: G 816 MET cc_start: 0.7594 (tpt) cc_final: 0.7212 (tpt) REVERT: I 826 MET cc_start: 0.7430 (tpt) cc_final: 0.7226 (mmm) REVERT: K 721 MET cc_start: 0.6360 (mmt) cc_final: 0.5570 (ptt) REVERT: L 723 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5596 (tmm) REVERT: L 795 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6176 (tmtt) REVERT: L 861 MET cc_start: 0.6210 (mmt) cc_final: 0.5849 (mmt) REVERT: Z 721 MET cc_start: 0.6178 (tpp) cc_final: 0.5968 (tpt) outliers start: 59 outliers final: 21 residues processed: 326 average time/residue: 1.7045 time to fit residues: 625.4539 Evaluate side-chains 322 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 288 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 724 MET Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 723 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.3980 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 153 optimal weight: 0.0060 chunk 270 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25020 Z= 0.278 Angle : 0.567 11.378 33840 Z= 0.277 Chirality : 0.042 0.140 3834 Planarity : 0.004 0.039 4290 Dihedral : 9.515 150.454 3469 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.19 % Allowed : 14.29 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3102 helix: 1.27 (0.13), residues: 1560 sheet: 0.28 (0.24), residues: 408 loop : 0.35 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.009 0.001 PHE C 31 TYR 0.009 0.001 TYR E 133 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 298 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7674 (mtt-85) REVERT: A 314 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: B 72 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7238 (tp30) REVERT: B 299 MET cc_start: 0.8532 (mtm) cc_final: 0.8234 (mtm) REVERT: B 328 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8136 (tttp) REVERT: B 355 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8055 (mtm) REVERT: C 12 ASN cc_start: 0.8199 (m110) cc_final: 0.7833 (m-40) REVERT: C 72 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: C 206 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7586 (ttp-110) REVERT: C 328 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7986 (tttp) REVERT: D 121 GLN cc_start: 0.8538 (tt0) cc_final: 0.8304 (tt0) REVERT: D 305 MET cc_start: 0.8921 (mmm) cc_final: 0.8547 (mmm) REVERT: D 325 MET cc_start: 0.8831 (mmp) cc_final: 0.8088 (mmp) REVERT: D 328 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7994 (tmtt) REVERT: E 277 THR cc_start: 0.8903 (m) cc_final: 0.8654 (m) REVERT: E 314 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: E 355 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7418 (mtt) REVERT: E 364 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: F 153 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8396 (tp) REVERT: G 723 MET cc_start: 0.7357 (tmm) cc_final: 0.6773 (tpt) REVERT: G 816 MET cc_start: 0.7691 (tpt) cc_final: 0.7284 (tpt) REVERT: H 758 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6828 (mtpt) REVERT: K 721 MET cc_start: 0.6156 (mmt) cc_final: 0.5631 (ptt) REVERT: L 723 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.5521 (tmm) REVERT: L 776 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7541 (tt) REVERT: L 795 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6266 (tmtt) REVERT: L 861 MET cc_start: 0.6196 (mmt) cc_final: 0.5884 (mmt) REVERT: Z 721 MET cc_start: 0.6219 (tpp) cc_final: 0.6003 (tpt) outliers start: 58 outliers final: 24 residues processed: 332 average time/residue: 1.6330 time to fit residues: 612.1560 Evaluate side-chains 329 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 289 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 792 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain H residue 758 LYS Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 723 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 59 optimal weight: 0.0870 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 718 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 25020 Z= 0.144 Angle : 0.513 9.402 33840 Z= 0.247 Chirality : 0.040 0.133 3834 Planarity : 0.004 0.040 4290 Dihedral : 9.161 150.926 3469 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.77 % Allowed : 15.12 % Favored : 83.11 % 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: 1.31 (0.16), residues: 3102 helix: 1.35 (0.13), residues: 1602 sheet: 0.43 (0.25), residues: 408 loop : 0.52 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS E 161 PHE 0.007 0.001 PHE C 31 TYR 0.009 0.001 TYR B 69 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 306 time to evaluate : 3.111 Fit side-chains REVERT: A 28 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7661 (mtt-85) REVERT: A 206 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7802 (ttp-170) REVERT: B 299 MET cc_start: 0.8501 (mtm) cc_final: 0.8249 (mtm) REVERT: C 72 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: C 206 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7579 (ttp-110) REVERT: C 314 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: D 121 GLN cc_start: 0.8542 (tt0) cc_final: 0.8308 (tt0) REVERT: D 305 MET cc_start: 0.8901 (mmm) cc_final: 0.8514 (mmm) REVERT: D 325 MET cc_start: 0.8756 (mmp) cc_final: 0.8081 (mmp) REVERT: D 328 LYS cc_start: 0.8281 (tttp) cc_final: 0.7889 (tmtt) REVERT: E 107 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: F 153 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8451 (tp) REVERT: F 314 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: G 723 MET cc_start: 0.7217 (tmm) cc_final: 0.6664 (tpt) REVERT: G 816 MET cc_start: 0.7674 (tpt) cc_final: 0.7303 (tpt) REVERT: H 724 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6200 (tpp) REVERT: K 712 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6556 (pt) REVERT: K 721 MET cc_start: 0.5882 (mmt) cc_final: 0.5592 (ptt) REVERT: L 795 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6402 (tmtt) REVERT: L 861 MET cc_start: 0.6125 (mmt) cc_final: 0.5789 (mmt) REVERT: Z 721 MET cc_start: 0.6199 (tpp) cc_final: 0.5895 (tpt) outliers start: 47 outliers final: 17 residues processed: 332 average time/residue: 1.6181 time to fit residues: 606.0417 Evaluate side-chains 319 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 293 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 0.1980 chunk 220 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 254 optimal weight: 20.0000 chunk 168 optimal weight: 0.7980 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25020 Z= 0.211 Angle : 0.536 11.486 33840 Z= 0.258 Chirality : 0.041 0.135 3834 Planarity : 0.004 0.040 4290 Dihedral : 9.105 154.146 3467 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 15.84 % Favored : 82.62 % 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: 1.34 (0.15), residues: 3102 helix: 1.36 (0.13), residues: 1602 sheet: 0.43 (0.25), residues: 408 loop : 0.57 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.006 0.001 HIS E 161 PHE 0.008 0.001 PHE C 31 TYR 0.007 0.001 TYR D 143 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 303 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7646 (mtt-85) REVERT: B 299 MET cc_start: 0.8505 (mtm) cc_final: 0.8259 (mtm) REVERT: B 326 LYS cc_start: 0.8028 (tppt) cc_final: 0.7313 (ttmt) REVERT: C 72 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 206 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7609 (ttp-110) REVERT: C 314 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: D 121 GLN cc_start: 0.8536 (tt0) cc_final: 0.8242 (tt0) REVERT: D 305 MET cc_start: 0.8903 (mmm) cc_final: 0.8514 (mmm) REVERT: D 325 MET cc_start: 0.8722 (mmp) cc_final: 0.8037 (mmp) REVERT: D 328 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7897 (tmtt) REVERT: E 107 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: E 277 THR cc_start: 0.8893 (m) cc_final: 0.8614 (m) REVERT: E 314 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: F 153 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8417 (tp) REVERT: F 314 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: F 364 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: G 723 MET cc_start: 0.7181 (tmm) cc_final: 0.6634 (tpt) REVERT: G 816 MET cc_start: 0.7679 (tpt) cc_final: 0.7264 (tpt) REVERT: H 724 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6216 (tpp) REVERT: I 726 MET cc_start: 0.7182 (mtt) cc_final: 0.6953 (ttm) REVERT: K 721 MET cc_start: 0.5888 (mmt) cc_final: 0.5600 (ptt) REVERT: L 795 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6376 (tmtt) REVERT: L 861 MET cc_start: 0.6178 (mmt) cc_final: 0.5820 (mmt) REVERT: Z 721 MET cc_start: 0.6202 (tpp) cc_final: 0.5888 (tpt) outliers start: 41 outliers final: 18 residues processed: 325 average time/residue: 1.6193 time to fit residues: 594.0153 Evaluate side-chains 322 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 776 LEU Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 236 optimal weight: 0.0070 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25020 Z= 0.267 Angle : 0.561 11.030 33840 Z= 0.271 Chirality : 0.042 0.138 3834 Planarity : 0.004 0.039 4290 Dihedral : 9.133 160.840 3467 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.81 % Allowed : 15.65 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3102 helix: 1.26 (0.13), residues: 1608 sheet: 0.37 (0.25), residues: 408 loop : 0.57 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.007 0.001 HIS C 161 PHE 0.009 0.001 PHE C 31 TYR 0.008 0.001 TYR E 133 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 3.044 Fit side-chains REVERT: A 28 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7693 (mtt180) REVERT: B 299 MET cc_start: 0.8507 (mtm) cc_final: 0.8246 (mtm) REVERT: B 326 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7361 (ttmt) REVERT: C 72 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: C 206 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7633 (ttp-110) REVERT: C 241 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: C 314 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: D 121 GLN cc_start: 0.8475 (tt0) cc_final: 0.8221 (tt0) REVERT: D 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8531 (mmm) REVERT: D 325 MET cc_start: 0.8701 (mmp) cc_final: 0.8243 (mmp) REVERT: D 328 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7935 (tmtt) REVERT: E 277 THR cc_start: 0.8912 (m) cc_final: 0.8643 (m) REVERT: E 314 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: F 44 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7284 (mtp) REVERT: F 153 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8407 (tp) REVERT: F 314 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: F 364 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: G 723 MET cc_start: 0.7177 (tmm) cc_final: 0.6634 (tpt) REVERT: G 816 MET cc_start: 0.7622 (tpt) cc_final: 0.7209 (tpt) REVERT: G 827 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7730 (t0) REVERT: H 724 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.6235 (tpp) REVERT: K 721 MET cc_start: 0.5891 (mmt) cc_final: 0.5601 (ptt) REVERT: L 795 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6371 (tmtt) REVERT: L 861 MET cc_start: 0.6049 (mmt) cc_final: 0.5700 (mmt) REVERT: Z 721 MET cc_start: 0.6342 (tpp) cc_final: 0.6032 (tpt) outliers start: 48 outliers final: 20 residues processed: 331 average time/residue: 1.6427 time to fit residues: 613.3788 Evaluate side-chains 327 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 293 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 827 ASN Chi-restraints excluded: chain H residue 724 MET Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 280 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN H 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25020 Z= 0.259 Angle : 0.561 11.440 33840 Z= 0.271 Chirality : 0.042 0.141 3834 Planarity : 0.004 0.040 4290 Dihedral : 9.114 165.682 3467 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.62 % Allowed : 16.18 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.15), residues: 3102 helix: 1.26 (0.13), residues: 1608 sheet: 0.35 (0.25), residues: 408 loop : 0.57 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.006 0.001 HIS E 161 PHE 0.009 0.001 PHE C 31 TYR 0.008 0.001 TYR E 133 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 2.916 Fit side-chains REVERT: A 28 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7766 (mtt-85) REVERT: B 326 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7395 (ttmt) REVERT: B 328 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8121 (tttp) REVERT: C 72 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: C 206 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7628 (ttp-110) REVERT: C 241 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: C 314 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: D 121 GLN cc_start: 0.8459 (tt0) cc_final: 0.8225 (tt0) REVERT: D 305 MET cc_start: 0.8916 (mmm) cc_final: 0.8537 (mmm) REVERT: D 325 MET cc_start: 0.8672 (mmp) cc_final: 0.8223 (mmp) REVERT: D 326 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7988 (mptt) REVERT: D 328 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7970 (tmtt) REVERT: E 277 THR cc_start: 0.8913 (m) cc_final: 0.8640 (m) REVERT: E 314 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: F 44 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7125 (mtp) REVERT: F 153 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8408 (tp) REVERT: F 314 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: F 364 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: G 723 MET cc_start: 0.7195 (tmm) cc_final: 0.6656 (tpt) REVERT: G 816 MET cc_start: 0.7631 (tpt) cc_final: 0.7186 (tpt) REVERT: K 721 MET cc_start: 0.5889 (mmt) cc_final: 0.5602 (ptt) REVERT: L 795 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6430 (tmtt) REVERT: L 861 MET cc_start: 0.6007 (mmt) cc_final: 0.5741 (mmt) REVERT: Z 721 MET cc_start: 0.6344 (tpp) cc_final: 0.6032 (tpt) outliers start: 43 outliers final: 20 residues processed: 324 average time/residue: 1.5883 time to fit residues: 581.9243 Evaluate side-chains 327 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 294 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 180 optimal weight: 0.0770 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 12 ASN F 101 HIS H 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25020 Z= 0.295 Angle : 0.579 11.893 33840 Z= 0.280 Chirality : 0.043 0.146 3834 Planarity : 0.004 0.042 4290 Dihedral : 9.160 170.455 3467 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.36 % Allowed : 16.52 % Favored : 82.13 % 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: 1.16 (0.15), residues: 3102 helix: 1.20 (0.13), residues: 1608 sheet: 0.30 (0.25), residues: 408 loop : 0.53 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 PHE 0.011 0.001 PHE B 223 TYR 0.009 0.001 TYR E 133 ARG 0.007 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 297 time to evaluate : 3.111 Fit side-chains REVERT: A 28 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7763 (mtt-85) REVERT: B 326 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7449 (ttmt) REVERT: B 328 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8112 (tttp) REVERT: C 72 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: C 206 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7658 (ttp-110) REVERT: C 241 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 314 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: D 121 GLN cc_start: 0.8470 (tt0) cc_final: 0.8234 (tt0) REVERT: D 305 MET cc_start: 0.8913 (mmm) cc_final: 0.8527 (mmm) REVERT: D 325 MET cc_start: 0.8652 (mmp) cc_final: 0.8196 (mmp) REVERT: D 326 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8043 (mptt) REVERT: D 328 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8019 (tmtt) REVERT: E 277 THR cc_start: 0.8912 (m) cc_final: 0.8643 (m) REVERT: E 314 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: F 153 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8416 (tp) REVERT: F 314 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: F 364 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: G 723 MET cc_start: 0.7182 (tmm) cc_final: 0.6632 (tpt) REVERT: G 816 MET cc_start: 0.7644 (tpt) cc_final: 0.7200 (tpt) REVERT: K 721 MET cc_start: 0.6044 (mmt) cc_final: 0.5688 (ptt) REVERT: L 795 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6363 (tmtt) REVERT: Z 721 MET cc_start: 0.6373 (tpp) cc_final: 0.6058 (tpt) outliers start: 36 outliers final: 20 residues processed: 320 average time/residue: 1.6324 time to fit residues: 590.4040 Evaluate side-chains 327 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 295 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain K residue 712 ILE Chi-restraints excluded: chain L residue 795 LYS Chi-restraints excluded: chain Z residue 776 LEU Chi-restraints excluded: chain Z residue 840 SER Chi-restraints excluded: chain Z residue 861 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 12 ASN H 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102585 restraints weight = 25876.720| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.54 r_work: 0.2849 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25020 Z= 0.276 Angle : 0.570 12.792 33840 Z= 0.275 Chirality : 0.042 0.142 3834 Planarity : 0.004 0.048 4290 Dihedral : 9.159 174.309 3467 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.55 % Allowed : 16.52 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3102 helix: 1.22 (0.13), residues: 1608 sheet: 0.30 (0.25), residues: 408 loop : 0.54 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 PHE 0.010 0.001 PHE B 223 TYR 0.008 0.001 TYR E 133 ARG 0.007 0.000 ARG E 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9988.56 seconds wall clock time: 178 minutes 18.76 seconds (10698.76 seconds total)