Starting phenix.real_space_refine on Sat Mar 23 16:45:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg7_33810/03_2024/7yg7_33810.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg7_33810/03_2024/7yg7_33810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg7_33810/03_2024/7yg7_33810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg7_33810/03_2024/7yg7_33810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg7_33810/03_2024/7yg7_33810.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg7_33810/03_2024/7yg7_33810.pdb" } resolution = 3.7 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= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 187 5.16 5 C 23925 2.51 5 N 6281 2.21 5 O 7544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 127": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38035 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "B" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "C" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "D" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "E" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "F" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "G" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "H" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "I" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "J" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "K" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 18, 'TRANS': 395} Chain: "U" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1977 Classifications: {'RNA': 99} Modifications used: {'5*END': 1, 'rna2p_pyr': 13, 'rna3p_pyr': 86} Link IDs: {'rna2p': 13, 'rna3p': 85} Time building chain proxies: 19.42, per 1000 atoms: 0.51 Number of scatterers: 38035 At special positions: 0 Unit cell: (189.06, 189.06, 100.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 187 16.00 P 98 15.00 O 7544 8.00 N 6281 7.00 C 23925 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: 14.15 Conformation dependent library (CDL) restraints added in 6.2 seconds 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8514 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 11 sheets defined 46.9% alpha, 1.2% beta 0 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 10.91 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA A 209 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 210 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA A 314 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 382 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA B 130 " --> pdb=" O GLU B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 130' Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.610A pdb=" N ARG B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA B 209 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 210 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA B 227 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 382 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA C 130 " --> pdb=" O GLU C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 130' Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.502A pdb=" N HIS C 202 " --> pdb=" O MET C 198 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 210 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'C' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA C 227 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA C 314 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.547A pdb=" N TRP C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 382 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA D 130 " --> pdb=" O GLU D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 130' Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS D 202 " --> pdb=" O MET D 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA D 209 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D 210 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 219 Processing helix chain 'D' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA D 227 " --> pdb=" O CYS D 223 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA D 314 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 removed outlier: 3.735A pdb=" N ILE D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 382 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA E 130 " --> pdb=" O GLU E 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 130' Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.610A pdb=" N ARG E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 162 removed outlier: 3.844A pdb=" N MET E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 186 through 203 removed outlier: 3.502A pdb=" N HIS E 202 " --> pdb=" O MET E 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 210 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA E 227 " --> pdb=" O CYS E 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 236 " --> pdb=" O VAL E 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 299 through 306 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA E 314 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 382 removed outlier: 3.549A pdb=" N TRP E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 382 " --> pdb=" O TRP E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 399 Processing helix chain 'E' and resid 408 through 417 Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 63 through 76 Processing helix chain 'F' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA F 130 " --> pdb=" O GLU F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 127 through 130' Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.610A pdb=" N ARG F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS F 202 " --> pdb=" O MET F 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 203 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA F 209 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR F 210 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 219 Processing helix chain 'F' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA F 227 " --> pdb=" O CYS F 223 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 236 " --> pdb=" O VAL F 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA F 314 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 382 removed outlier: 3.549A pdb=" N TRP F 375 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 382 " --> pdb=" O TRP F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 399 Processing helix chain 'F' and resid 408 through 417 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA G 130 " --> pdb=" O GLU G 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 130' Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.612A pdb=" N ARG G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET G 155 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS G 202 " --> pdb=" O MET G 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR G 210 " --> pdb=" O ILE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 219 Processing helix chain 'G' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA G 227 " --> pdb=" O CYS G 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR G 236 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 237 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 249 through 260 Processing helix chain 'G' and resid 299 through 306 Processing helix chain 'G' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA G 314 " --> pdb=" O ALA G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 339 removed outlier: 3.735A pdb=" N ILE G 325 " --> pdb=" O ASP G 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 382 " --> pdb=" O TRP G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 399 Processing helix chain 'G' and resid 408 through 417 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA H 130 " --> pdb=" O GLU H 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 130' Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 162 removed outlier: 3.844A pdb=" N MET H 155 " --> pdb=" O ARG H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS H 202 " --> pdb=" O MET H 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR H 210 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 219 Processing helix chain 'H' and resid 223 through 237 removed outlier: 3.974A pdb=" N ALA H 227 " --> pdb=" O CYS H 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 236 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 237 " --> pdb=" O VAL H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 246 Processing helix chain 'H' and resid 249 through 260 Processing helix chain 'H' and resid 299 through 306 Processing helix chain 'H' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA H 314 " --> pdb=" O ALA H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP H 375 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 382 " --> pdb=" O TRP H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 399 Processing helix chain 'H' and resid 408 through 417 Processing helix chain 'I' and resid 45 through 55 Processing helix chain 'I' and resid 63 through 76 Processing helix chain 'I' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA I 130 " --> pdb=" O GLU I 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 162 removed outlier: 3.844A pdb=" N MET I 155 " --> pdb=" O ARG I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE I 203 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA I 209 " --> pdb=" O SER I 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR I 210 " --> pdb=" O ILE I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 219 Processing helix chain 'I' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA I 227 " --> pdb=" O CYS I 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 236 " --> pdb=" O VAL I 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY I 237 " --> pdb=" O VAL I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 246 Processing helix chain 'I' and resid 249 through 260 Processing helix chain 'I' and resid 299 through 306 Processing helix chain 'I' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA I 314 " --> pdb=" O ALA I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE I 325 " --> pdb=" O ASP I 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP I 375 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 382 " --> pdb=" O TRP I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 399 Processing helix chain 'I' and resid 408 through 417 Processing helix chain 'J' and resid 45 through 55 Processing helix chain 'J' and resid 63 through 76 Processing helix chain 'J' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA J 130 " --> pdb=" O GLU J 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 127 through 130' Processing helix chain 'J' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG J 141 " --> pdb=" O LEU J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET J 155 " --> pdb=" O ARG J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 186 through 203 removed outlier: 3.501A pdb=" N HIS J 202 " --> pdb=" O MET J 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 213 removed outlier: 3.533A pdb=" N ALA J 209 " --> pdb=" O SER J 206 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR J 210 " --> pdb=" O ILE J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 219 Processing helix chain 'J' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA J 227 " --> pdb=" O CYS J 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY J 237 " --> pdb=" O VAL J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 246 Processing helix chain 'J' and resid 249 through 260 Processing helix chain 'J' and resid 299 through 306 Processing helix chain 'J' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA J 314 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 339 removed outlier: 3.734A pdb=" N ILE J 325 " --> pdb=" O ASP J 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER J 339 " --> pdb=" O ALA J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 382 removed outlier: 3.549A pdb=" N TRP J 375 " --> pdb=" O SER J 371 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 382 " --> pdb=" O TRP J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 399 Processing helix chain 'J' and resid 408 through 417 Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 127 through 130 removed outlier: 3.842A pdb=" N ALA K 130 " --> pdb=" O GLU K 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 127 through 130' Processing helix chain 'K' and resid 131 through 144 removed outlier: 3.611A pdb=" N ARG K 141 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 162 removed outlier: 3.843A pdb=" N MET K 155 " --> pdb=" O ARG K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 186 through 203 removed outlier: 3.502A pdb=" N HIS K 202 " --> pdb=" O MET K 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 213 removed outlier: 3.532A pdb=" N ALA K 209 " --> pdb=" O SER K 206 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR K 210 " --> pdb=" O ILE K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 219 Processing helix chain 'K' and resid 223 through 237 removed outlier: 3.975A pdb=" N ALA K 227 " --> pdb=" O CYS K 223 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR K 236 " --> pdb=" O VAL K 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY K 237 " --> pdb=" O VAL K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 246 Processing helix chain 'K' and resid 249 through 260 Processing helix chain 'K' and resid 299 through 306 Processing helix chain 'K' and resid 310 through 314 removed outlier: 3.581A pdb=" N ALA K 314 " --> pdb=" O ALA K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 339 removed outlier: 3.735A pdb=" N ILE K 325 " --> pdb=" O ASP K 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER K 339 " --> pdb=" O ALA K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 382 removed outlier: 3.548A pdb=" N TRP K 375 " --> pdb=" O SER K 371 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL K 382 " --> pdb=" O TRP K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 399 Processing helix chain 'K' and resid 408 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP A 86 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 88 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP B 86 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 88 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP C 86 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 88 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP D 86 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 88 " --> pdb=" O HIS D 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 88 removed outlier: 6.951A pdb=" N TRP E 86 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER E 88 " --> pdb=" O HIS E 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP F 86 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER F 88 " --> pdb=" O HIS F 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP G 86 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 88 " --> pdb=" O HIS G 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP H 86 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER H 88 " --> pdb=" O HIS H 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP I 86 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER I 88 " --> pdb=" O HIS I 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 86 through 88 removed outlier: 6.951A pdb=" N TRP J 86 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER J 88 " --> pdb=" O HIS J 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 86 through 88 removed outlier: 6.952A pdb=" N TRP K 86 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER K 88 " --> pdb=" O HIS K 91 " (cutoff:3.500A) 1254 hydrogen bonds defined for protein. 3432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 10.13 Time building geometry restraints manager: 15.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7628 1.33 - 1.45: 9682 1.45 - 1.57: 21243 1.57 - 1.69: 196 1.69 - 1.81: 319 Bond restraints: 39068 Sorted by residual: bond pdb=" SD MET H 279 " pdb=" CE MET H 279 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.65e+00 bond pdb=" SD MET F 279 " pdb=" CE MET F 279 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.63e+00 bond pdb=" SD MET D 279 " pdb=" CE MET D 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" SD MET I 279 " pdb=" CE MET I 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" SD MET B 279 " pdb=" CE MET B 279 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.54e+00 ... (remaining 39063 not shown) Histogram of bond angle deviations from ideal: 96.56 - 104.07: 926 104.07 - 111.59: 16633 111.59 - 119.10: 15154 119.10 - 126.61: 19910 126.61 - 134.12: 741 Bond angle restraints: 53364 Sorted by residual: angle pdb=" C ARG F 353 " pdb=" N LYS F 354 " pdb=" CA LYS F 354 " ideal model delta sigma weight residual 121.80 130.22 -8.42 2.44e+00 1.68e-01 1.19e+01 angle pdb=" C ARG C 353 " pdb=" N LYS C 354 " pdb=" CA LYS C 354 " ideal model delta sigma weight residual 121.80 130.21 -8.41 2.44e+00 1.68e-01 1.19e+01 angle pdb=" C ARG B 353 " pdb=" N LYS B 354 " pdb=" CA LYS B 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 angle pdb=" C ARG I 353 " pdb=" N LYS I 354 " pdb=" CA LYS I 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 angle pdb=" C ARG A 353 " pdb=" N LYS A 354 " pdb=" CA LYS A 354 " ideal model delta sigma weight residual 121.80 130.20 -8.40 2.44e+00 1.68e-01 1.18e+01 ... (remaining 53359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 22475 34.72 - 69.44: 1157 69.44 - 104.16: 40 104.16 - 138.88: 4 138.88 - 173.60: 12 Dihedral angle restraints: 23688 sinusoidal: 10422 harmonic: 13266 Sorted by residual: dihedral pdb=" O4' U U 95 " pdb=" C1' U U 95 " pdb=" N1 U U 95 " pdb=" C2 U U 95 " ideal model delta sinusoidal sigma weight residual -160.00 13.60 -173.60 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U U 97 " pdb=" C1' U U 97 " pdb=" N1 U U 97 " pdb=" C2 U U 97 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U U 5 " pdb=" C1' U U 5 " pdb=" N1 U U 5 " pdb=" C2 U U 5 " ideal model delta sinusoidal sigma weight residual -160.00 12.68 -172.68 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 23685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4079 0.045 - 0.090: 1497 0.090 - 0.135: 297 0.135 - 0.180: 48 0.180 - 0.224: 40 Chirality restraints: 5961 Sorted by residual: chirality pdb=" CG LEU D 132 " pdb=" CB LEU D 132 " pdb=" CD1 LEU D 132 " pdb=" CD2 LEU D 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU C 132 " pdb=" CB LEU C 132 " pdb=" CD1 LEU C 132 " pdb=" CD2 LEU C 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU F 132 " pdb=" CB LEU F 132 " pdb=" CD1 LEU F 132 " pdb=" CD2 LEU F 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5958 not shown) Planarity restraints: 6479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 16 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO K 17 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 16 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO G 17 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO G 17 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 17 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 16 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO B 17 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.056 5.00e-02 4.00e+02 ... (remaining 6476 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 396 2.63 - 3.20: 32506 3.20 - 3.77: 58402 3.77 - 4.33: 79342 4.33 - 4.90: 126441 Nonbonded interactions: 297087 Sorted by model distance: nonbonded pdb=" O2' U U 38 " pdb=" O5' U U 39 " model vdw 2.065 2.440 nonbonded pdb=" O2' U U 38 " pdb=" O4' U U 39 " model vdw 2.221 2.440 nonbonded pdb=" O2' U U 41 " pdb=" OP1 U U 43 " model vdw 2.235 2.440 nonbonded pdb=" N THR A 289 " pdb=" OP2 U U 76 " model vdw 2.293 2.520 nonbonded pdb=" OH TYR F 150 " pdb=" OP2 U U 26 " model vdw 2.304 2.440 ... (remaining 297082 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.040 Extract box with map and model: 3.470 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 96.020 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.004 0.060 39068 Z= 0.290 Angle : 0.796 10.357 53364 Z= 0.415 Chirality : 0.050 0.224 5961 Planarity : 0.007 0.105 6479 Dihedral : 18.894 173.599 15174 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 1.00 % Allowed : 26.99 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 4532 helix: -1.01 (0.10), residues: 2002 sheet: None (None), residues: 0 loop : -2.37 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 183 HIS 0.002 0.001 HIS G 177 PHE 0.029 0.002 PHE B 180 TYR 0.054 0.003 TYR F 70 ARG 0.008 0.001 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 525 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 368 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7568 (mmmt) REVERT: C 37 ARG cc_start: 0.6995 (mmt90) cc_final: 0.6600 (mtm-85) REVERT: C 260 MET cc_start: 0.8099 (mmt) cc_final: 0.7638 (mmm) REVERT: C 342 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8870 (mt) REVERT: D 342 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8338 (mt) REVERT: D 396 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7951 (ttp-170) REVERT: E 342 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8728 (mt) REVERT: F 37 ARG cc_start: 0.6950 (mmt90) cc_final: 0.6678 (mtm-85) REVERT: F 342 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (mt) REVERT: F 368 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7396 (mmmt) REVERT: F 396 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7763 (ttp80) REVERT: G 342 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (mt) REVERT: H 9 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5851 (p0) REVERT: I 9 ASN cc_start: 0.6219 (OUTLIER) cc_final: 0.5775 (p0) REVERT: J 27 SER cc_start: 0.8028 (t) cc_final: 0.7681 (t) REVERT: J 200 TYR cc_start: 0.7360 (m-10) cc_final: 0.7141 (m-10) REVERT: J 259 MET cc_start: 0.8747 (ttp) cc_final: 0.8371 (ttp) REVERT: J 368 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7867 (mttm) REVERT: K 259 MET cc_start: 0.8590 (ttp) cc_final: 0.8365 (ttp) REVERT: K 319 GLU cc_start: 0.6497 (tt0) cc_final: 0.6254 (tt0) REVERT: K 368 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7713 (mmmt) outliers start: 39 outliers final: 4 residues processed: 536 average time/residue: 0.5260 time to fit residues: 445.9460 Evaluate side-chains 458 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 442 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 267 ASP Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain K residue 368 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 0.0370 chunk 348 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 360 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 219 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 417 optimal weight: 20.0000 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN G 66 HIS H 66 HIS H 384 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39068 Z= 0.154 Angle : 0.531 9.089 53364 Z= 0.282 Chirality : 0.042 0.319 5961 Planarity : 0.005 0.069 6479 Dihedral : 15.053 176.566 6579 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.27 % Allowed : 26.55 % Favored : 71.18 % 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: -1.75 (0.12), residues: 4532 helix: -0.08 (0.11), residues: 2101 sheet: None (None), residues: 0 loop : -2.24 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 86 HIS 0.003 0.001 HIS G 66 PHE 0.016 0.001 PHE J 211 TYR 0.040 0.002 TYR I 52 ARG 0.005 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 454 time to evaluate : 4.648 Fit side-chains REVERT: A 249 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.6932 (mt0) REVERT: A 332 MET cc_start: 0.8477 (ttt) cc_final: 0.8067 (ttt) REVERT: A 368 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7535 (mmmt) REVERT: B 60 LYS cc_start: 0.6427 (mmtm) cc_final: 0.6034 (mmtm) REVERT: B 249 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: C 249 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: C 381 ASP cc_start: 0.7530 (t70) cc_final: 0.7145 (t0) REVERT: D 60 LYS cc_start: 0.6842 (mmtm) cc_final: 0.6543 (mmtm) REVERT: D 249 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: E 63 ARG cc_start: 0.6348 (tpp-160) cc_final: 0.6086 (tpp-160) REVERT: E 249 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: E 342 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8760 (mt) REVERT: F 71 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7889 (mm) REVERT: F 249 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7058 (mt0) REVERT: F 260 MET cc_start: 0.8615 (mmt) cc_final: 0.8091 (mmt) REVERT: F 368 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7690 (mmmt) REVERT: G 24 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6186 (t0) REVERT: G 249 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8125 (mm-40) REVERT: H 199 PHE cc_start: 0.7685 (t80) cc_final: 0.7310 (t80) REVERT: H 249 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7819 (mm-40) REVERT: I 249 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: I 381 ASP cc_start: 0.7941 (t70) cc_final: 0.7599 (t0) REVERT: J 27 SER cc_start: 0.7844 (t) cc_final: 0.7499 (t) REVERT: J 100 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6980 (tt) REVERT: J 199 PHE cc_start: 0.7725 (t80) cc_final: 0.7307 (t80) REVERT: J 249 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: J 259 MET cc_start: 0.8722 (ttp) cc_final: 0.8392 (ttp) REVERT: J 368 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7958 (mttm) REVERT: J 390 MET cc_start: 0.9003 (mtp) cc_final: 0.8751 (mtm) REVERT: K 199 PHE cc_start: 0.7995 (t80) cc_final: 0.7523 (t80) REVERT: K 249 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7919 (mm-40) REVERT: K 259 MET cc_start: 0.8542 (ttp) cc_final: 0.8309 (ttp) REVERT: K 342 ILE cc_start: 0.9046 (mm) cc_final: 0.8718 (mt) REVERT: K 368 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8019 (mptt) outliers start: 88 outliers final: 21 residues processed: 527 average time/residue: 0.4610 time to fit residues: 403.4993 Evaluate side-chains 453 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 417 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 267 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 418 optimal weight: 0.9990 chunk 452 optimal weight: 10.0000 chunk 372 optimal weight: 0.5980 chunk 414 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 335 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN D 51 GLN E 51 GLN G 66 HIS H 66 HIS I 51 GLN I 292 ASN J 51 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 39068 Z= 0.306 Angle : 0.600 9.865 53364 Z= 0.316 Chirality : 0.046 0.327 5961 Planarity : 0.005 0.065 6479 Dihedral : 14.861 179.898 6543 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 3.35 % Allowed : 25.62 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.12), residues: 4532 helix: -0.10 (0.12), residues: 2112 sheet: None (None), residues: 0 loop : -2.22 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 298 HIS 0.003 0.001 HIS H 177 PHE 0.021 0.002 PHE G 295 TYR 0.031 0.002 TYR K 52 ARG 0.005 0.001 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 428 time to evaluate : 4.725 Fit side-chains REVERT: A 249 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: A 332 MET cc_start: 0.8557 (ttt) cc_final: 0.8114 (ttt) REVERT: A 368 LYS cc_start: 0.8362 (mmtm) cc_final: 0.7594 (mmmt) REVERT: B 60 LYS cc_start: 0.6483 (mmtm) cc_final: 0.6123 (mmtm) REVERT: B 70 TYR cc_start: 0.5972 (t80) cc_final: 0.5627 (t80) REVERT: B 249 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: C 16 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7990 (pp) REVERT: C 37 ARG cc_start: 0.7068 (mmt90) cc_final: 0.6779 (mtm-85) REVERT: C 70 TYR cc_start: 0.6832 (t80) cc_final: 0.6569 (t80) REVERT: C 81 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7012 (mm) REVERT: C 249 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: C 381 ASP cc_start: 0.7581 (t70) cc_final: 0.7323 (t0) REVERT: D 60 LYS cc_start: 0.6441 (mmtm) cc_final: 0.6083 (mmtm) REVERT: D 63 ARG cc_start: 0.6523 (tpp-160) cc_final: 0.6311 (tpp-160) REVERT: D 249 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8325 (mm-40) REVERT: D 343 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7855 (tt0) REVERT: E 249 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8149 (mm-40) REVERT: F 249 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: F 273 MET cc_start: 0.7132 (tmm) cc_final: 0.6876 (tmm) REVERT: F 343 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: F 368 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8012 (mmmt) REVERT: G 24 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6338 (t0) REVERT: G 249 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8264 (mm-40) REVERT: H 9 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6012 (p0) REVERT: H 249 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: J 249 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: J 279 MET cc_start: 0.7027 (mmt) cc_final: 0.6536 (mmm) REVERT: J 368 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8174 (mptt) REVERT: J 390 MET cc_start: 0.8979 (mtp) cc_final: 0.8692 (mtm) REVERT: K 70 TYR cc_start: 0.6373 (t80) cc_final: 0.6077 (t80) REVERT: K 249 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8416 (mm-40) REVERT: K 368 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8035 (mptt) outliers start: 130 outliers final: 75 residues processed: 537 average time/residue: 0.4641 time to fit residues: 416.5697 Evaluate side-chains 503 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 413 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 267 ASP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 199 optimal weight: 50.0000 chunk 281 optimal weight: 40.0000 chunk 419 optimal weight: 20.0000 chunk 444 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN G 66 HIS G 188 ASN G 415 GLN H 51 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 39068 Z= 0.378 Angle : 0.654 10.652 53364 Z= 0.347 Chirality : 0.048 0.342 5961 Planarity : 0.005 0.077 6479 Dihedral : 14.971 178.274 6539 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 5.69 % Allowed : 24.31 % Favored : 70.00 % 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: -1.94 (0.12), residues: 4532 helix: -0.30 (0.11), residues: 2134 sheet: None (None), residues: 0 loop : -2.28 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 298 HIS 0.004 0.001 HIS K 177 PHE 0.023 0.002 PHE F 29 TYR 0.036 0.002 TYR J 52 ARG 0.005 0.001 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 436 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6331 (t80) cc_final: 0.6048 (t80) REVERT: A 81 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6969 (mm) REVERT: A 343 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: A 368 LYS cc_start: 0.8356 (mmtm) cc_final: 0.7654 (mmmt) REVERT: B 60 LYS cc_start: 0.6359 (mmtm) cc_final: 0.6139 (mmtm) REVERT: B 70 TYR cc_start: 0.6203 (t80) cc_final: 0.5821 (t80) REVERT: B 81 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7111 (mm) REVERT: B 87 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7447 (t0) REVERT: B 249 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: C 81 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6937 (mm) REVERT: C 87 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: C 249 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: C 381 ASP cc_start: 0.7647 (t70) cc_final: 0.7397 (t0) REVERT: D 60 LYS cc_start: 0.6751 (mmtm) cc_final: 0.6414 (mmtm) REVERT: D 70 TYR cc_start: 0.6847 (t80) cc_final: 0.6618 (t80) REVERT: D 81 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6895 (mm) REVERT: D 105 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.4215 (mt) REVERT: D 249 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: D 343 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: E 70 TYR cc_start: 0.6647 (t80) cc_final: 0.6293 (t80) REVERT: E 249 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: F 70 TYR cc_start: 0.6290 (t80) cc_final: 0.6062 (t80) REVERT: F 81 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6844 (mm) REVERT: F 249 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: F 273 MET cc_start: 0.7533 (tmm) cc_final: 0.7295 (tmm) REVERT: F 343 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: F 368 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8127 (mmmt) REVERT: G 70 TYR cc_start: 0.6563 (t80) cc_final: 0.6246 (t80) REVERT: G 81 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6659 (mm) REVERT: G 87 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: G 105 LEU cc_start: 0.4774 (OUTLIER) cc_final: 0.4458 (mt) REVERT: H 70 TYR cc_start: 0.6496 (t80) cc_final: 0.6164 (t80) REVERT: H 81 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7562 (mm) REVERT: H 249 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7962 (mm-40) REVERT: I 70 TYR cc_start: 0.6450 (t80) cc_final: 0.6193 (t80) REVERT: I 81 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6723 (mm) REVERT: I 343 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: J 70 TYR cc_start: 0.6796 (t80) cc_final: 0.6543 (t80) REVERT: J 81 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6921 (mm) REVERT: J 105 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5610 (mt) REVERT: J 249 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: J 368 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8097 (mttm) REVERT: J 390 MET cc_start: 0.8995 (mtp) cc_final: 0.8713 (mtm) REVERT: K 81 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7007 (mm) REVERT: K 249 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8247 (mm-40) REVERT: K 368 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8103 (mptt) outliers start: 221 outliers final: 127 residues processed: 630 average time/residue: 0.4618 time to fit residues: 482.4182 Evaluate side-chains 561 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 406 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 181 ASP Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain I residue 369 ASN Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 195 CYS Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 369 ASN Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 331 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 379 optimal weight: 0.9980 chunk 307 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN E 231 HIS F 51 GLN K 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 39068 Z= 0.162 Angle : 0.539 10.047 53364 Z= 0.283 Chirality : 0.043 0.324 5961 Planarity : 0.004 0.083 6479 Dihedral : 14.600 179.141 6539 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 3.61 % Allowed : 26.22 % Favored : 70.18 % 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: -1.45 (0.12), residues: 4532 helix: 0.21 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.12 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 246 HIS 0.003 0.000 HIS K 177 PHE 0.014 0.001 PHE D 211 TYR 0.030 0.001 TYR J 52 ARG 0.007 0.000 ARG K 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 436 time to evaluate : 4.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7033 (mm) REVERT: A 249 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7064 (mt0) REVERT: A 332 MET cc_start: 0.8902 (ttt) cc_final: 0.8214 (ttt) REVERT: A 368 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7564 (mmmt) REVERT: B 81 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7209 (mm) REVERT: B 87 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7426 (t0) REVERT: B 249 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7685 (mp10) REVERT: C 87 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: C 249 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: C 343 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: C 381 ASP cc_start: 0.7559 (t70) cc_final: 0.7302 (t0) REVERT: D 60 LYS cc_start: 0.6929 (mmtm) cc_final: 0.6312 (mmtm) REVERT: D 81 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6960 (mm) REVERT: D 107 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.5269 (ptp-170) REVERT: D 249 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8246 (mm-40) REVERT: E 52 TYR cc_start: 0.6976 (m-80) cc_final: 0.6730 (m-80) REVERT: E 105 LEU cc_start: 0.5188 (OUTLIER) cc_final: 0.4732 (mt) REVERT: E 249 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: F 70 TYR cc_start: 0.6321 (t80) cc_final: 0.5963 (t80) REVERT: F 81 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6861 (mm) REVERT: F 105 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4826 (mt) REVERT: F 249 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: F 259 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8282 (ttm) REVERT: F 368 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8146 (mmmt) REVERT: G 24 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6105 (t0) REVERT: G 81 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6721 (mm) REVERT: G 87 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: G 211 PHE cc_start: 0.7959 (m-80) cc_final: 0.7669 (m-80) REVERT: G 249 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (mm-40) REVERT: H 70 TYR cc_start: 0.6373 (t80) cc_final: 0.6045 (t80) REVERT: H 81 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7594 (mm) REVERT: H 105 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4651 (mt) REVERT: H 249 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: I 70 TYR cc_start: 0.6612 (t80) cc_final: 0.6382 (t80) REVERT: I 81 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6724 (mm) REVERT: I 105 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4568 (mt) REVERT: I 249 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: J 81 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6951 (mm) REVERT: J 279 MET cc_start: 0.6976 (mmt) cc_final: 0.6539 (mmm) REVERT: J 368 LYS cc_start: 0.8593 (mmtt) cc_final: 0.7781 (mmmt) REVERT: J 390 MET cc_start: 0.8990 (mtp) cc_final: 0.8713 (mtm) REVERT: K 81 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7029 (mm) REVERT: K 249 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8184 (mm-40) REVERT: K 332 MET cc_start: 0.8727 (ttt) cc_final: 0.8465 (ttt) REVERT: K 368 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8055 (mptt) outliers start: 140 outliers final: 54 residues processed: 555 average time/residue: 0.4696 time to fit residues: 430.7534 Evaluate side-chains 493 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 409 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 332 MET Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 259 MET Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 8.9990 chunk 400 optimal weight: 0.9990 chunk 87 optimal weight: 0.0000 chunk 261 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 445 optimal weight: 0.8980 chunk 369 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 39068 Z= 0.137 Angle : 0.522 9.788 53364 Z= 0.271 Chirality : 0.041 0.314 5961 Planarity : 0.004 0.080 6479 Dihedral : 14.158 175.507 6539 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.96 % Allowed : 26.65 % Favored : 70.38 % 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 (0.13), residues: 4532 helix: 0.52 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.05 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.003 0.000 HIS I 66 PHE 0.011 0.001 PHE J 211 TYR 0.047 0.001 TYR K 52 ARG 0.007 0.000 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 449 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6891 (mm) REVERT: A 249 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6905 (mt0) REVERT: A 332 MET cc_start: 0.8861 (ttt) cc_final: 0.8328 (ttt) REVERT: A 368 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7494 (mmmt) REVERT: B 81 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7269 (mm) REVERT: B 87 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7315 (t0) REVERT: B 249 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: C 81 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7014 (mm) REVERT: C 249 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: C 343 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: C 381 ASP cc_start: 0.7511 (t70) cc_final: 0.7178 (t0) REVERT: D 60 LYS cc_start: 0.7057 (mmtm) cc_final: 0.6727 (mmtm) REVERT: D 81 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6940 (mm) REVERT: D 107 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.5324 (ptp-170) REVERT: D 249 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7965 (mm-40) REVERT: E 52 TYR cc_start: 0.6862 (m-80) cc_final: 0.6640 (m-80) REVERT: E 105 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.4750 (mt) REVERT: E 249 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: F 81 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6847 (mm) REVERT: F 249 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6977 (mt0) REVERT: F 259 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8242 (ttm) REVERT: G 8 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.5051 (t) REVERT: G 24 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6288 (t0) REVERT: G 81 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.6923 (mm) REVERT: G 87 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: H 81 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7549 (mm) REVERT: H 105 LEU cc_start: 0.4679 (OUTLIER) cc_final: 0.4205 (mt) REVERT: H 107 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.4806 (ptp-170) REVERT: H 249 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7822 (mm-40) REVERT: I 81 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6763 (mm) REVERT: I 249 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: J 81 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6925 (mm) REVERT: J 249 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: J 279 MET cc_start: 0.6867 (mmt) cc_final: 0.6609 (mmt) REVERT: J 368 LYS cc_start: 0.8538 (mmtt) cc_final: 0.7755 (mmmt) REVERT: J 382 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8222 (m) REVERT: J 390 MET cc_start: 0.9000 (mtp) cc_final: 0.8721 (mtm) REVERT: K 81 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6985 (mm) REVERT: K 200 TYR cc_start: 0.7141 (m-10) cc_final: 0.6894 (m-10) REVERT: K 249 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: K 332 MET cc_start: 0.8706 (ttt) cc_final: 0.8438 (ttt) REVERT: K 368 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8037 (mptt) outliers start: 115 outliers final: 53 residues processed: 543 average time/residue: 0.4660 time to fit residues: 418.1810 Evaluate side-chains 502 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 418 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 259 MET Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 325 optimal weight: 0.9980 chunk 251 optimal weight: 0.0770 chunk 374 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 443 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39068 Z= 0.199 Angle : 0.552 9.487 53364 Z= 0.287 Chirality : 0.043 0.304 5961 Planarity : 0.004 0.072 6479 Dihedral : 14.141 175.031 6539 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.37 % Allowed : 26.42 % Favored : 70.20 % 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: -1.25 (0.12), residues: 4532 helix: 0.40 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.04 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 298 HIS 0.004 0.001 HIS I 66 PHE 0.024 0.001 PHE J 211 TYR 0.039 0.002 TYR B 70 ARG 0.006 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 432 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6859 (mm) REVERT: A 249 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: A 332 MET cc_start: 0.8851 (ttt) cc_final: 0.8416 (ttt) REVERT: A 368 LYS cc_start: 0.8345 (mmtm) cc_final: 0.7502 (mmmt) REVERT: B 60 LYS cc_start: 0.6600 (mmtm) cc_final: 0.6335 (mmtm) REVERT: B 81 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7236 (mm) REVERT: B 87 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7335 (t0) REVERT: B 249 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: C 81 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.6997 (mm) REVERT: C 87 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: C 105 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4607 (mt) REVERT: C 249 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: C 343 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: C 381 ASP cc_start: 0.7550 (t70) cc_final: 0.7229 (t0) REVERT: D 60 LYS cc_start: 0.7055 (mmtm) cc_final: 0.6775 (mmtm) REVERT: D 81 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6938 (mm) REVERT: D 107 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5355 (ptp-170) REVERT: D 249 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8234 (mm-40) REVERT: D 343 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7784 (tt0) REVERT: E 105 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4749 (mt) REVERT: E 180 PHE cc_start: 0.6990 (p90) cc_final: 0.6758 (p90) REVERT: E 249 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7752 (mm-40) REVERT: F 81 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6848 (mm) REVERT: F 105 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.4948 (mt) REVERT: F 249 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: G 8 THR cc_start: 0.5428 (OUTLIER) cc_final: 0.5068 (t) REVERT: G 24 ASP cc_start: 0.6578 (OUTLIER) cc_final: 0.6242 (t0) REVERT: G 81 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.6966 (mm) REVERT: G 87 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: G 249 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8201 (mm-40) REVERT: G 279 MET cc_start: 0.7019 (mmt) cc_final: 0.6709 (mmp) REVERT: H 70 TYR cc_start: 0.6280 (t80) cc_final: 0.5779 (t80) REVERT: H 81 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7481 (mm) REVERT: H 105 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4657 (mt) REVERT: H 249 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8011 (mm-40) REVERT: I 8 THR cc_start: 0.4665 (OUTLIER) cc_final: 0.4401 (t) REVERT: I 9 ASN cc_start: 0.5705 (OUTLIER) cc_final: 0.5290 (p0) REVERT: I 81 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6726 (mm) REVERT: I 105 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4651 (mt) REVERT: I 249 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: I 343 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: J 81 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6999 (mm) REVERT: J 105 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5472 (mt) REVERT: J 249 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: J 279 MET cc_start: 0.6941 (mmt) cc_final: 0.6727 (mmt) REVERT: J 368 LYS cc_start: 0.8512 (mmtt) cc_final: 0.7792 (mmmt) REVERT: J 382 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8255 (m) REVERT: J 390 MET cc_start: 0.9015 (mtp) cc_final: 0.8747 (mtm) REVERT: K 81 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6957 (mm) REVERT: K 200 TYR cc_start: 0.7173 (m-10) cc_final: 0.6933 (m-10) REVERT: K 249 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8155 (mm-40) REVERT: K 342 ILE cc_start: 0.9060 (mm) cc_final: 0.8715 (mt) REVERT: K 368 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7977 (mptt) outliers start: 131 outliers final: 77 residues processed: 541 average time/residue: 0.4801 time to fit residues: 427.0370 Evaluate side-chains 529 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 414 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 343 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 267 ASP Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 302 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 348 optimal weight: 0.0060 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39068 Z= 0.157 Angle : 0.537 9.154 53364 Z= 0.278 Chirality : 0.042 0.302 5961 Planarity : 0.004 0.069 6479 Dihedral : 13.958 173.706 6539 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.12 % Allowed : 26.86 % Favored : 70.02 % 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: -1.13 (0.13), residues: 4532 helix: 0.57 (0.12), residues: 2079 sheet: None (None), residues: 0 loop : -2.03 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 169 HIS 0.002 0.000 HIS C 66 PHE 0.026 0.001 PHE J 203 TYR 0.038 0.001 TYR K 70 ARG 0.006 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 441 time to evaluate : 4.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8159 (m) cc_final: 0.7945 (m) REVERT: A 81 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6869 (mm) REVERT: A 249 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7083 (mt0) REVERT: A 332 MET cc_start: 0.8833 (ttt) cc_final: 0.8443 (ttt) REVERT: A 368 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7445 (mmmt) REVERT: B 81 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7236 (mm) REVERT: B 87 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7305 (t0) REVERT: B 249 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: C 81 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7101 (mm) REVERT: C 87 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: C 249 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: C 343 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: D 60 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6772 (mmtm) REVERT: D 81 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6890 (mm) REVERT: D 107 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.5188 (ptp-170) REVERT: D 249 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: E 105 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4750 (mt) REVERT: E 249 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7656 (mm-40) REVERT: E 319 GLU cc_start: 0.6847 (tt0) cc_final: 0.6609 (tt0) REVERT: F 81 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6841 (mm) REVERT: F 105 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4965 (mt) REVERT: F 249 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: G 8 THR cc_start: 0.5269 (OUTLIER) cc_final: 0.4957 (t) REVERT: G 24 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6252 (t0) REVERT: G 81 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6962 (mm) REVERT: G 87 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: G 249 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: H 70 TYR cc_start: 0.6116 (t80) cc_final: 0.5814 (t80) REVERT: H 81 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7461 (mm) REVERT: H 105 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4468 (mt) REVERT: H 249 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7942 (mm-40) REVERT: I 8 THR cc_start: 0.4552 (OUTLIER) cc_final: 0.4233 (t) REVERT: I 9 ASN cc_start: 0.5643 (OUTLIER) cc_final: 0.5335 (p0) REVERT: I 81 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6711 (mm) REVERT: I 105 LEU cc_start: 0.4924 (OUTLIER) cc_final: 0.4645 (mt) REVERT: I 249 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: J 81 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6858 (mm) REVERT: J 249 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7316 (mt0) REVERT: J 279 MET cc_start: 0.6891 (mmt) cc_final: 0.6648 (mmt) REVERT: J 368 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7643 (mmmt) REVERT: J 382 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8256 (m) REVERT: J 390 MET cc_start: 0.9016 (mtp) cc_final: 0.8741 (mtm) REVERT: K 81 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6960 (mm) REVERT: K 249 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8072 (mm-40) REVERT: K 332 MET cc_start: 0.8700 (ttt) cc_final: 0.8432 (ttt) REVERT: K 368 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7970 (mptt) outliers start: 121 outliers final: 75 residues processed: 543 average time/residue: 0.4733 time to fit residues: 420.6780 Evaluate side-chains 525 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 415 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 259 MET Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 195 CYS Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 3.9990 chunk 424 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 413 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 324 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 373 optimal weight: 4.9990 chunk 390 optimal weight: 6.9990 chunk 411 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39068 Z= 0.253 Angle : 0.589 10.166 53364 Z= 0.307 Chirality : 0.044 0.318 5961 Planarity : 0.004 0.068 6479 Dihedral : 14.127 174.602 6539 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 3.53 % Allowed : 26.63 % Favored : 69.84 % 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: -1.37 (0.12), residues: 4532 helix: 0.26 (0.12), residues: 2112 sheet: None (None), residues: 0 loop : -2.07 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 298 HIS 0.003 0.001 HIS H 177 PHE 0.024 0.002 PHE J 211 TYR 0.038 0.002 TYR H 52 ARG 0.006 0.000 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 430 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8224 (m) cc_final: 0.8019 (m) REVERT: A 81 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6859 (mm) REVERT: A 249 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: A 332 MET cc_start: 0.8857 (ttt) cc_final: 0.8450 (ttt) REVERT: A 343 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7785 (tt0) REVERT: A 368 LYS cc_start: 0.8319 (mmtm) cc_final: 0.7459 (mmmt) REVERT: B 70 TYR cc_start: 0.5955 (t80) cc_final: 0.5661 (t80) REVERT: B 81 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7196 (mm) REVERT: B 87 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7355 (t0) REVERT: B 105 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.3950 (mt) REVERT: B 249 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: B 318 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7604 (p0) REVERT: C 81 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6914 (mm) REVERT: C 87 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7104 (m-30) REVERT: C 105 LEU cc_start: 0.4948 (OUTLIER) cc_final: 0.4446 (mt) REVERT: C 249 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: C 343 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: C 381 ASP cc_start: 0.7597 (t70) cc_final: 0.7282 (t0) REVERT: D 60 LYS cc_start: 0.7154 (mmtm) cc_final: 0.6936 (mmtm) REVERT: D 81 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6898 (mm) REVERT: D 107 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.5368 (ptp-170) REVERT: D 249 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8332 (mm-40) REVERT: D 343 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7785 (tt0) REVERT: E 105 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.4922 (mt) REVERT: E 249 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: F 81 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6817 (mm) REVERT: F 105 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.4928 (mt) REVERT: F 249 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7316 (mt0) REVERT: G 8 THR cc_start: 0.5410 (OUTLIER) cc_final: 0.5069 (t) REVERT: G 81 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6928 (mm) REVERT: G 87 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: G 249 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8260 (mm-40) REVERT: H 70 TYR cc_start: 0.6166 (t80) cc_final: 0.5721 (t80) REVERT: H 81 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7456 (mm) REVERT: H 105 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4770 (mt) REVERT: H 249 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: I 8 THR cc_start: 0.4707 (OUTLIER) cc_final: 0.4460 (t) REVERT: I 9 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5239 (p0) REVERT: I 81 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6687 (mm) REVERT: I 249 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: I 279 MET cc_start: 0.6966 (mmt) cc_final: 0.6736 (mmt) REVERT: I 343 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7554 (tt0) REVERT: J 27 SER cc_start: 0.7909 (t) cc_final: 0.7642 (t) REVERT: J 81 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6831 (mm) REVERT: J 105 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5576 (mt) REVERT: J 368 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7714 (mmtt) REVERT: J 382 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8254 (m) REVERT: J 390 MET cc_start: 0.9015 (mtp) cc_final: 0.8757 (mtm) REVERT: K 81 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6930 (mm) REVERT: K 199 PHE cc_start: 0.8157 (t80) cc_final: 0.7834 (t80) REVERT: K 249 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: K 342 ILE cc_start: 0.9042 (mm) cc_final: 0.8691 (mt) REVERT: K 368 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7996 (mptt) outliers start: 137 outliers final: 91 residues processed: 546 average time/residue: 0.4750 time to fit residues: 425.5701 Evaluate side-chains 543 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 416 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain I residue 408 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 195 CYS Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 1.9990 chunk 436 optimal weight: 0.4980 chunk 266 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 458 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 364 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39068 Z= 0.205 Angle : 0.573 10.391 53364 Z= 0.299 Chirality : 0.043 0.320 5961 Planarity : 0.004 0.074 6479 Dihedral : 14.049 173.391 6539 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.30 % Allowed : 27.27 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4532 helix: 0.36 (0.12), residues: 2090 sheet: None (None), residues: 0 loop : -2.04 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 169 HIS 0.003 0.001 HIS C 177 PHE 0.023 0.001 PHE J 211 TYR 0.041 0.002 TYR H 52 ARG 0.006 0.000 ARG B 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 414 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6879 (mm) REVERT: A 249 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7048 (mt0) REVERT: A 332 MET cc_start: 0.8848 (ttt) cc_final: 0.8439 (ttt) REVERT: A 343 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7667 (tt0) REVERT: A 368 LYS cc_start: 0.8302 (mmtm) cc_final: 0.7431 (mmmt) REVERT: B 81 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7229 (mm) REVERT: B 87 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7340 (t0) REVERT: B 249 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: B 279 MET cc_start: 0.7011 (mmt) cc_final: 0.6759 (mmm) REVERT: C 81 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6845 (mm) REVERT: C 87 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: C 105 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4565 (mt) REVERT: C 249 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: C 343 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: C 381 ASP cc_start: 0.7584 (t70) cc_final: 0.7261 (t0) REVERT: D 60 LYS cc_start: 0.7122 (mmtm) cc_final: 0.5368 (mmmt) REVERT: D 81 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6897 (mm) REVERT: D 107 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5320 (ptp-170) REVERT: D 249 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8254 (mm-40) REVERT: E 105 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.4926 (mt) REVERT: E 249 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8035 (mm-40) REVERT: F 81 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6795 (mm) REVERT: F 105 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.5003 (mt) REVERT: F 249 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7285 (mt0) REVERT: G 8 THR cc_start: 0.5282 (OUTLIER) cc_final: 0.4956 (t) REVERT: G 81 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6935 (mm) REVERT: G 87 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: G 249 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8218 (mm-40) REVERT: G 279 MET cc_start: 0.7094 (mmt) cc_final: 0.6801 (mmp) REVERT: H 37 ARG cc_start: 0.7269 (mpt-90) cc_final: 0.7026 (mmt90) REVERT: H 70 TYR cc_start: 0.6166 (t80) cc_final: 0.5776 (t80) REVERT: H 81 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7467 (mm) REVERT: H 105 LEU cc_start: 0.5067 (OUTLIER) cc_final: 0.4763 (mt) REVERT: H 249 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: I 8 THR cc_start: 0.4618 (OUTLIER) cc_final: 0.4314 (t) REVERT: I 9 ASN cc_start: 0.5579 (OUTLIER) cc_final: 0.5166 (p0) REVERT: I 81 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6677 (mm) REVERT: I 249 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: I 279 MET cc_start: 0.6933 (mmt) cc_final: 0.6713 (mmt) REVERT: I 343 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7490 (tt0) REVERT: J 81 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6904 (mm) REVERT: J 105 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5577 (mt) REVERT: J 249 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: J 279 MET cc_start: 0.6878 (mmt) cc_final: 0.6513 (mmm) REVERT: J 368 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7651 (mmmt) REVERT: J 382 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8259 (m) REVERT: J 390 MET cc_start: 0.9009 (mtp) cc_final: 0.8741 (mtm) REVERT: K 81 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6951 (mm) REVERT: K 199 PHE cc_start: 0.8055 (t80) cc_final: 0.7786 (t80) REVERT: K 249 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8174 (mm-40) REVERT: K 368 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7990 (mptt) outliers start: 128 outliers final: 87 residues processed: 523 average time/residue: 0.4877 time to fit residues: 420.2226 Evaluate side-chains 530 residues out of total 3883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 408 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 235 ILE Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 ASN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 195 CYS Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 373 VAL Chi-restraints excluded: chain J residue 382 VAL Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain K residue 107 ARG Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 181 ASP Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 0.4980 chunk 388 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 336 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 365 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 375 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.172755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.149895 restraints weight = 46786.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.145767 restraints weight = 67271.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.143556 restraints weight = 78152.157| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39068 Z= 0.216 Angle : 0.580 10.486 53364 Z= 0.301 Chirality : 0.043 0.318 5961 Planarity : 0.004 0.073 6479 Dihedral : 14.012 173.083 6539 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 3.40 % Allowed : 27.07 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 4532 helix: 0.30 (0.12), residues: 2101 sheet: None (None), residues: 0 loop : -2.04 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 298 HIS 0.002 0.001 HIS E 177 PHE 0.022 0.001 PHE J 211 TYR 0.040 0.002 TYR H 52 ARG 0.006 0.000 ARG B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7433.10 seconds wall clock time: 137 minutes 16.07 seconds (8236.07 seconds total)