Starting phenix.real_space_refine on Tue Mar 19 01:36:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzm_26915/03_2024/7uzm_26915.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzm_26915/03_2024/7uzm_26915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzm_26915/03_2024/7uzm_26915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzm_26915/03_2024/7uzm_26915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzm_26915/03_2024/7uzm_26915.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzm_26915/03_2024/7uzm_26915.pdb" } resolution = 3.24 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= 0.039 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14352 2.51 5 N 3996 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 475": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E GLU 475": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F GLU 475": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22752 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3787 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 11.22, per 1000 atoms: 0.49 Number of scatterers: 22752 At special positions: 0 Unit cell: (119.88, 112.32, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4296 8.00 N 3996 7.00 C 14352 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: 9.16 Conformation dependent library (CDL) restraints added in 4.3 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 59.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.631A pdb=" N VAL A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.611A pdb=" N SER A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.659A pdb=" N VAL A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 553 Processing helix chain 'B' and resid 65 through 89 removed outlier: 3.631A pdb=" N VAL B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 267 through 285 removed outlier: 4.413A pdb=" N THR B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 478 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.771A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 553 Processing helix chain 'C' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.736A pdb=" N MET C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.559A pdb=" N MET C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.909A pdb=" N ARG C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 553 Processing helix chain 'D' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 212 Processing helix chain 'D' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 267 through 285 removed outlier: 4.415A pdb=" N THR D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.561A pdb=" N MET D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 478 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 3.771A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 553 Processing helix chain 'E' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.611A pdb=" N SER E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.659A pdb=" N VAL E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 212 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 324 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 391 through 396 removed outlier: 3.911A pdb=" N ARG E 395 " --> pdb=" O SER E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 421 Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 478 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 553 Processing helix chain 'F' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 212 Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.736A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 267 through 285 removed outlier: 4.413A pdb=" N THR F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 370 through 374 Processing helix chain 'F' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG F 395 " --> pdb=" O SER F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 421 Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 478 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 553 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.687A pdb=" N GLY A 149 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY E 149 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE A 304 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY A 331 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 306 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 224 removed outlier: 3.687A pdb=" N GLY B 149 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 149 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366 removed outlier: 6.692A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 401 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 224 removed outlier: 3.688A pdb=" N GLY C 149 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 149 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE C 304 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY C 331 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL C 306 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 401 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.692A pdb=" N PHE D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE F 304 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY F 331 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL F 306 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 4050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7631 1.34 - 1.46: 3653 1.46 - 1.58: 11767 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 23231 Sorted by residual: bond pdb=" C THR C 144 " pdb=" N PRO C 145 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.01e-02 9.80e+03 6.96e+00 bond pdb=" C THR F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.78e+00 bond pdb=" C THR E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.69e+00 bond pdb=" C THR B 144 " pdb=" N PRO B 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.63e+00 bond pdb=" C THR A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 1.333 1.359 -0.025 1.01e-02 9.80e+03 6.23e+00 ... (remaining 23226 not shown) Histogram of bond angle deviations from ideal: 99.97 - 107.31: 840 107.31 - 114.64: 13490 114.64 - 121.98: 12718 121.98 - 129.31: 4215 129.31 - 136.65: 150 Bond angle restraints: 31413 Sorted by residual: angle pdb=" N HIS F 142 " pdb=" CA HIS F 142 " pdb=" C HIS F 142 " ideal model delta sigma weight residual 111.07 102.28 8.79 1.07e+00 8.73e-01 6.75e+01 angle pdb=" N HIS C 142 " pdb=" CA HIS C 142 " pdb=" C HIS C 142 " ideal model delta sigma weight residual 111.07 102.37 8.70 1.07e+00 8.73e-01 6.61e+01 angle pdb=" N HIS B 142 " pdb=" CA HIS B 142 " pdb=" C HIS B 142 " ideal model delta sigma weight residual 111.07 102.56 8.51 1.07e+00 8.73e-01 6.32e+01 angle pdb=" N HIS E 142 " pdb=" CA HIS E 142 " pdb=" C HIS E 142 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N HIS D 142 " pdb=" CA HIS D 142 " pdb=" C HIS D 142 " ideal model delta sigma weight residual 111.28 102.99 8.29 1.09e+00 8.42e-01 5.79e+01 ... (remaining 31408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 12662 16.11 - 32.21: 1032 32.21 - 48.32: 152 48.32 - 64.42: 42 64.42 - 80.52: 18 Dihedral angle restraints: 13906 sinusoidal: 5482 harmonic: 8424 Sorted by residual: dihedral pdb=" CA SER F 270 " pdb=" C SER F 270 " pdb=" N ALA F 271 " pdb=" CA ALA F 271 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER D 270 " pdb=" C SER D 270 " pdb=" N ALA D 271 " pdb=" CA ALA D 271 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER B 270 " pdb=" C SER B 270 " pdb=" N ALA B 271 " pdb=" CA ALA B 271 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 13903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2782 0.054 - 0.107: 555 0.107 - 0.161: 79 0.161 - 0.215: 4 0.215 - 0.268: 12 Chirality restraints: 3432 Sorted by residual: chirality pdb=" CA GLU D 552 " pdb=" N GLU D 552 " pdb=" C GLU D 552 " pdb=" CB GLU D 552 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLU A 552 " pdb=" N GLU A 552 " pdb=" C GLU A 552 " pdb=" CB GLU A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 401 " pdb=" CA ILE C 401 " pdb=" CG1 ILE C 401 " pdb=" CG2 ILE C 401 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3429 not shown) Planarity restraints: 4121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 141 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C GLN D 141 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN D 141 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS D 142 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 141 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLN A 141 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 141 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 142 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 258 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 259 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.025 5.00e-02 4.00e+02 ... (remaining 4118 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7478 2.84 - 3.36: 23379 3.36 - 3.87: 38561 3.87 - 4.39: 43906 4.39 - 4.90: 73975 Nonbonded interactions: 187299 Sorted by model distance: nonbonded pdb=" OD1 ASN E 392 " pdb=" NH2 ARG E 395 " model vdw 2.329 2.520 nonbonded pdb=" OD1 ASN C 392 " pdb=" NH2 ARG C 395 " model vdw 2.329 2.520 nonbonded pdb=" OD1 ASN D 392 " pdb=" NH2 ARG D 395 " model vdw 2.329 2.520 nonbonded pdb=" OD1 ASN F 392 " pdb=" NH2 ARG F 395 " model vdw 2.329 2.520 nonbonded pdb=" OD1 ASN A 392 " pdb=" NH2 ARG A 395 " model vdw 2.330 2.520 ... (remaining 187294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'B' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'C' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'D' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'E' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.290 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 59.770 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 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 : 0.003 0.031 23231 Z= 0.182 Angle : 0.636 11.648 31413 Z= 0.381 Chirality : 0.044 0.268 3432 Planarity : 0.004 0.045 4121 Dihedral : 12.389 80.525 8542 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.59 (0.15), residues: 2952 helix: 2.27 (0.13), residues: 1542 sheet: 0.11 (0.25), residues: 372 loop : -0.43 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 338 HIS 0.003 0.001 HIS F 315 PHE 0.017 0.002 PHE B 67 TYR 0.010 0.001 TYR B 240 ARG 0.005 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.7857 (tp) cc_final: 0.7549 (tp) REVERT: A 326 LYS cc_start: 0.7187 (ptpp) cc_final: 0.6966 (ptmt) REVERT: A 349 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7166 (mt-10) REVERT: A 412 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8336 (pm20) REVERT: A 471 GLN cc_start: 0.7407 (tt0) cc_final: 0.6808 (tp40) REVERT: A 495 ASP cc_start: 0.7209 (m-30) cc_final: 0.6934 (m-30) REVERT: B 238 ASP cc_start: 0.7071 (t0) cc_final: 0.6845 (t0) REVERT: B 309 PHE cc_start: 0.4447 (t80) cc_final: 0.4074 (t80) REVERT: B 412 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8305 (pm20) REVERT: B 468 MET cc_start: 0.6197 (ttp) cc_final: 0.5929 (ttp) REVERT: B 472 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 495 ASP cc_start: 0.7035 (m-30) cc_final: 0.6566 (m-30) REVERT: B 550 TYR cc_start: 0.8209 (t80) cc_final: 0.7896 (t80) REVERT: C 188 ILE cc_start: 0.7507 (tp) cc_final: 0.7095 (tp) REVERT: C 204 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7822 (tpt90) REVERT: C 215 ILE cc_start: 0.8551 (tt) cc_final: 0.8331 (tt) REVERT: C 314 LEU cc_start: 0.8258 (tp) cc_final: 0.7845 (tp) REVERT: C 349 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7251 (mt-10) REVERT: C 412 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8416 (pm20) REVERT: C 495 ASP cc_start: 0.7208 (m-30) cc_final: 0.6913 (m-30) REVERT: D 258 LYS cc_start: 0.7355 (mttt) cc_final: 0.7119 (mtpp) REVERT: D 314 LEU cc_start: 0.7761 (tp) cc_final: 0.7328 (tp) REVERT: D 349 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7147 (mt-10) REVERT: D 412 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8494 (pm20) REVERT: D 471 GLN cc_start: 0.7496 (tt0) cc_final: 0.6905 (tp40) REVERT: D 495 ASP cc_start: 0.7221 (m-30) cc_final: 0.6962 (m-30) REVERT: E 170 TYR cc_start: 0.7180 (m-10) cc_final: 0.6969 (m-10) REVERT: E 238 ASP cc_start: 0.7103 (t0) cc_final: 0.6885 (t0) REVERT: E 309 PHE cc_start: 0.4480 (t80) cc_final: 0.4105 (t80) REVERT: E 317 MET cc_start: 0.6802 (ptm) cc_final: 0.6596 (ptt) REVERT: E 412 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8288 (pm20) REVERT: E 495 ASP cc_start: 0.6955 (m-30) cc_final: 0.6584 (m-30) REVERT: E 550 TYR cc_start: 0.8195 (t80) cc_final: 0.7893 (t80) REVERT: F 188 ILE cc_start: 0.7585 (tp) cc_final: 0.7260 (tp) REVERT: F 204 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7927 (tpt90) REVERT: F 215 ILE cc_start: 0.8559 (tt) cc_final: 0.8332 (tt) REVERT: F 314 LEU cc_start: 0.8252 (tp) cc_final: 0.7856 (tp) REVERT: F 317 MET cc_start: 0.6908 (ptm) cc_final: 0.6707 (ptt) REVERT: F 347 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8564 (tm-30) REVERT: F 349 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7131 (mt-10) REVERT: F 412 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8375 (mp0) REVERT: F 495 ASP cc_start: 0.7231 (m-30) cc_final: 0.6992 (m-30) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.3923 time to fit residues: 356.2331 Evaluate side-chains 362 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 230 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 445 ASN B 262 GLN B 421 ASN C 262 GLN D 262 GLN E 262 GLN E 421 ASN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23231 Z= 0.177 Angle : 0.539 8.809 31413 Z= 0.281 Chirality : 0.043 0.205 3432 Planarity : 0.004 0.033 4121 Dihedral : 4.144 15.624 3228 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.48 % Allowed : 9.91 % Favored : 87.61 % 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: 1.68 (0.16), residues: 2952 helix: 2.41 (0.13), residues: 1590 sheet: 0.14 (0.25), residues: 366 loop : -0.65 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 338 HIS 0.006 0.001 HIS A 142 PHE 0.028 0.002 PHE C 304 TYR 0.016 0.001 TYR D 528 ARG 0.005 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 391 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 HIS cc_start: 0.8290 (t-170) cc_final: 0.7942 (t-170) REVERT: A 262 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7139 (mm110) REVERT: A 266 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6533 (m-70) REVERT: A 281 GLU cc_start: 0.7247 (tp30) cc_final: 0.6737 (tp30) REVERT: A 338 TRP cc_start: 0.7670 (t-100) cc_final: 0.7316 (t-100) REVERT: A 349 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7219 (mt-10) REVERT: A 399 LYS cc_start: 0.7676 (mmmt) cc_final: 0.6984 (mttm) REVERT: A 495 ASP cc_start: 0.7350 (m-30) cc_final: 0.7119 (m-30) REVERT: B 143 ARG cc_start: 0.7545 (mmm160) cc_final: 0.5742 (mpt-90) REVERT: B 326 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7001 (mttp) REVERT: B 349 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7039 (mp0) REVERT: B 399 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7367 (mttm) REVERT: B 468 MET cc_start: 0.6267 (ttp) cc_final: 0.5915 (ttp) REVERT: B 472 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 495 ASP cc_start: 0.7103 (m-30) cc_final: 0.6657 (m-30) REVERT: C 207 MET cc_start: 0.7616 (mtm) cc_final: 0.7411 (mtm) REVERT: C 252 HIS cc_start: 0.8304 (t-170) cc_final: 0.8061 (t-170) REVERT: C 281 GLU cc_start: 0.7017 (tp30) cc_final: 0.6668 (tp30) REVERT: C 282 ASN cc_start: 0.7851 (m-40) cc_final: 0.7551 (m110) REVERT: C 349 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7215 (mt-10) REVERT: C 373 GLU cc_start: 0.7252 (mp0) cc_final: 0.6981 (mp0) REVERT: C 399 LYS cc_start: 0.7425 (mmmt) cc_final: 0.6805 (mttm) REVERT: C 495 ASP cc_start: 0.7492 (m-30) cc_final: 0.7220 (m-30) REVERT: D 252 HIS cc_start: 0.8308 (t-170) cc_final: 0.8074 (t-170) REVERT: D 262 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: D 266 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6567 (m-70) REVERT: D 281 GLU cc_start: 0.6928 (tp30) cc_final: 0.6573 (tp30) REVERT: D 338 TRP cc_start: 0.7720 (t-100) cc_final: 0.7492 (t-100) REVERT: D 349 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7199 (mt-10) REVERT: D 399 LYS cc_start: 0.7750 (mmmt) cc_final: 0.6991 (mttt) REVERT: D 495 ASP cc_start: 0.7322 (m-30) cc_final: 0.7106 (m-30) REVERT: E 143 ARG cc_start: 0.7672 (mmm160) cc_final: 0.5862 (mpt-90) REVERT: E 258 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7580 (mttt) REVERT: E 262 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: E 317 MET cc_start: 0.6891 (ptm) cc_final: 0.6671 (ptt) REVERT: E 349 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7047 (mp0) REVERT: E 399 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7345 (mttm) REVERT: E 472 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6998 (mm-30) REVERT: E 495 ASP cc_start: 0.7156 (m-30) cc_final: 0.6704 (m-30) REVERT: F 252 HIS cc_start: 0.8255 (t-170) cc_final: 0.8034 (t-170) REVERT: F 281 GLU cc_start: 0.7005 (tp30) cc_final: 0.6685 (tp30) REVERT: F 282 ASN cc_start: 0.7816 (m-40) cc_final: 0.7454 (m110) REVERT: F 314 LEU cc_start: 0.7948 (tp) cc_final: 0.7412 (tp) REVERT: F 347 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8547 (tm-30) REVERT: F 349 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7187 (mt-10) REVERT: F 373 GLU cc_start: 0.7342 (mp0) cc_final: 0.7087 (mp0) REVERT: F 399 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6672 (tttm) REVERT: F 472 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6885 (mm-30) outliers start: 59 outliers final: 24 residues processed: 425 average time/residue: 0.3597 time to fit residues: 232.2210 Evaluate side-chains 363 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 333 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 222 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 288 optimal weight: 0.1980 chunk 238 optimal weight: 0.6980 chunk 265 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN B 189 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN C 189 ASN C 262 GLN D 189 ASN E 189 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 262 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23231 Z= 0.225 Angle : 0.556 10.382 31413 Z= 0.287 Chirality : 0.044 0.207 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.191 19.512 3228 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.60 % Allowed : 12.85 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 2952 helix: 2.19 (0.13), residues: 1596 sheet: 0.28 (0.27), residues: 366 loop : -0.87 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 442 HIS 0.007 0.001 HIS F 142 PHE 0.023 0.002 PHE F 214 TYR 0.015 0.002 TYR B 528 ARG 0.005 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 341 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6461 (m-10) cc_final: 0.5654 (m-10) REVERT: A 266 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6661 (m-70) REVERT: A 281 GLU cc_start: 0.7211 (tp30) cc_final: 0.6665 (tp30) REVERT: A 326 LYS cc_start: 0.8223 (mttp) cc_final: 0.7388 (ptmt) REVERT: A 338 TRP cc_start: 0.7583 (t-100) cc_final: 0.7191 (t-100) REVERT: A 349 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7182 (mt-10) REVERT: A 399 LYS cc_start: 0.7561 (mmmt) cc_final: 0.7053 (mttm) REVERT: A 495 ASP cc_start: 0.7384 (m-30) cc_final: 0.7052 (m-30) REVERT: B 326 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7417 (mtpt) REVERT: B 399 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7463 (mttm) REVERT: B 472 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 495 ASP cc_start: 0.7241 (m-30) cc_final: 0.6774 (m-30) REVERT: C 207 MET cc_start: 0.7672 (mtm) cc_final: 0.7413 (mtm) REVERT: C 252 HIS cc_start: 0.8255 (t-170) cc_final: 0.7994 (t-170) REVERT: C 281 GLU cc_start: 0.7026 (tp30) cc_final: 0.6665 (tp30) REVERT: C 282 ASN cc_start: 0.7979 (m-40) cc_final: 0.7566 (m110) REVERT: C 317 MET cc_start: 0.6995 (ptp) cc_final: 0.6722 (ptp) REVERT: C 349 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7208 (mt-10) REVERT: C 495 ASP cc_start: 0.7624 (m-30) cc_final: 0.7361 (m-30) REVERT: D 66 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5383 (m-80) REVERT: D 67 PHE cc_start: 0.6585 (m-10) cc_final: 0.5715 (m-10) REVERT: D 133 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7210 (mp0) REVERT: D 266 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6482 (m-70) REVERT: D 281 GLU cc_start: 0.6812 (tp30) cc_final: 0.6409 (tp30) REVERT: D 282 ASN cc_start: 0.7881 (m-40) cc_final: 0.7495 (m110) REVERT: D 326 LYS cc_start: 0.8398 (mttp) cc_final: 0.7556 (ptmt) REVERT: D 338 TRP cc_start: 0.7702 (t-100) cc_final: 0.7458 (t-100) REVERT: D 349 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7229 (mt-10) REVERT: D 399 LYS cc_start: 0.7624 (mmmt) cc_final: 0.7014 (mttt) REVERT: D 495 ASP cc_start: 0.7321 (m-30) cc_final: 0.6990 (m-30) REVERT: E 258 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7644 (mttt) REVERT: E 317 MET cc_start: 0.6841 (ptm) cc_final: 0.6627 (ptt) REVERT: E 399 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7451 (mttm) REVERT: E 472 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7044 (mm-30) REVERT: E 495 ASP cc_start: 0.7250 (m-30) cc_final: 0.6808 (m-30) REVERT: F 252 HIS cc_start: 0.8234 (t-170) cc_final: 0.7978 (t-170) REVERT: F 281 GLU cc_start: 0.7073 (tp30) cc_final: 0.6685 (tp30) REVERT: F 282 ASN cc_start: 0.7989 (m-40) cc_final: 0.7533 (m110) REVERT: F 326 LYS cc_start: 0.7267 (ptmt) cc_final: 0.6512 (mtmt) REVERT: F 347 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8527 (tm-30) REVERT: F 349 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7210 (mt-10) REVERT: F 472 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6940 (mm-30) outliers start: 62 outliers final: 47 residues processed: 369 average time/residue: 0.3539 time to fit residues: 200.2186 Evaluate side-chains 362 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 311 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.2980 chunk 201 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 262 GLN E 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23231 Z= 0.189 Angle : 0.525 10.326 31413 Z= 0.266 Chirality : 0.042 0.153 3432 Planarity : 0.004 0.029 4121 Dihedral : 4.097 19.829 3228 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.32 % Allowed : 14.87 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.15), residues: 2952 helix: 2.26 (0.13), residues: 1596 sheet: 0.23 (0.27), residues: 366 loop : -0.92 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 338 HIS 0.006 0.001 HIS A 142 PHE 0.017 0.002 PHE C 67 TYR 0.012 0.001 TYR B 528 ARG 0.005 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 349 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6275 (m-10) cc_final: 0.5566 (m-10) REVERT: A 262 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: A 266 HIS cc_start: 0.6778 (OUTLIER) cc_final: 0.6451 (m-70) REVERT: A 281 GLU cc_start: 0.7111 (tp30) cc_final: 0.6586 (tp30) REVERT: A 282 ASN cc_start: 0.7963 (m-40) cc_final: 0.7461 (m110) REVERT: A 326 LYS cc_start: 0.8225 (mttp) cc_final: 0.7382 (ptmt) REVERT: A 338 TRP cc_start: 0.7554 (t-100) cc_final: 0.7151 (t-100) REVERT: A 349 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7218 (mt-10) REVERT: A 399 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6968 (mttm) REVERT: A 495 ASP cc_start: 0.7399 (m-30) cc_final: 0.7021 (m-30) REVERT: B 262 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7181 (mm-40) REVERT: B 295 MET cc_start: 0.7054 (ttp) cc_final: 0.6835 (ttt) REVERT: B 326 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7502 (mtpt) REVERT: B 349 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7092 (mt-10) REVERT: B 399 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7408 (mttm) REVERT: B 472 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 495 ASP cc_start: 0.7266 (m-30) cc_final: 0.6778 (m-30) REVERT: C 67 PHE cc_start: 0.6243 (m-10) cc_final: 0.5264 (t80) REVERT: C 252 HIS cc_start: 0.8258 (t-170) cc_final: 0.7984 (t-170) REVERT: C 282 ASN cc_start: 0.8009 (m-40) cc_final: 0.7516 (m110) REVERT: C 295 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6685 (ptt) REVERT: C 349 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7168 (mt-10) REVERT: C 399 LYS cc_start: 0.7425 (mmmt) cc_final: 0.7049 (mttm) REVERT: C 495 ASP cc_start: 0.7658 (m-30) cc_final: 0.7419 (m-30) REVERT: D 67 PHE cc_start: 0.6201 (m-10) cc_final: 0.5490 (m-10) REVERT: D 133 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7249 (mp0) REVERT: D 262 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: D 266 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.6457 (m-70) REVERT: D 281 GLU cc_start: 0.6818 (tp30) cc_final: 0.6448 (tp30) REVERT: D 282 ASN cc_start: 0.7892 (m-40) cc_final: 0.7455 (m110) REVERT: D 326 LYS cc_start: 0.8389 (mttp) cc_final: 0.7470 (ptmt) REVERT: D 338 TRP cc_start: 0.7672 (t-100) cc_final: 0.7388 (t-100) REVERT: D 349 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7186 (mt-10) REVERT: D 399 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7095 (mttm) REVERT: D 495 ASP cc_start: 0.7339 (m-30) cc_final: 0.6981 (m-30) REVERT: E 262 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7151 (mm-40) REVERT: E 349 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7077 (mp0) REVERT: E 399 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7467 (mttm) REVERT: E 472 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7044 (mm-30) REVERT: E 495 ASP cc_start: 0.7262 (m-30) cc_final: 0.6803 (m-30) REVERT: F 252 HIS cc_start: 0.8250 (t-170) cc_final: 0.7979 (t-170) REVERT: F 281 GLU cc_start: 0.7035 (tp30) cc_final: 0.6527 (tp30) REVERT: F 282 ASN cc_start: 0.7999 (m-40) cc_final: 0.7516 (m110) REVERT: F 326 LYS cc_start: 0.7229 (ptmt) cc_final: 0.6479 (mtmt) REVERT: F 347 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8531 (tm-30) REVERT: F 349 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7278 (mt-10) REVERT: F 399 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7057 (mttm) outliers start: 79 outliers final: 56 residues processed: 387 average time/residue: 0.3276 time to fit residues: 200.6410 Evaluate side-chains 378 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 315 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 211 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 262 GLN D 262 GLN E 262 GLN E 445 ASN F 262 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23231 Z= 0.185 Angle : 0.515 10.359 31413 Z= 0.262 Chirality : 0.042 0.147 3432 Planarity : 0.004 0.030 4121 Dihedral : 4.051 19.391 3228 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.86 % Allowed : 15.29 % Favored : 80.85 % 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: 1.46 (0.15), residues: 2952 helix: 2.30 (0.13), residues: 1596 sheet: 0.16 (0.26), residues: 366 loop : -0.97 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 338 HIS 0.006 0.001 HIS D 142 PHE 0.017 0.002 PHE C 67 TYR 0.011 0.001 TYR B 528 ARG 0.007 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 333 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6043 (m-10) cc_final: 0.5426 (m-10) REVERT: A 133 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7262 (mp0) REVERT: A 266 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.6365 (m-70) REVERT: A 281 GLU cc_start: 0.7025 (tp30) cc_final: 0.6431 (tp30) REVERT: A 282 ASN cc_start: 0.7916 (m-40) cc_final: 0.7358 (m110) REVERT: A 326 LYS cc_start: 0.8375 (mttp) cc_final: 0.7554 (ptmt) REVERT: A 338 TRP cc_start: 0.7540 (t-100) cc_final: 0.7168 (t-100) REVERT: A 399 LYS cc_start: 0.7500 (mmmt) cc_final: 0.6971 (mttm) REVERT: A 495 ASP cc_start: 0.7427 (m-30) cc_final: 0.7032 (m-30) REVERT: B 67 PHE cc_start: 0.6274 (m-10) cc_final: 0.5295 (t80) REVERT: B 295 MET cc_start: 0.7065 (ttp) cc_final: 0.6860 (ttt) REVERT: B 326 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7502 (mtpt) REVERT: B 399 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7409 (mttm) REVERT: B 472 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 495 ASP cc_start: 0.7238 (m-30) cc_final: 0.6735 (m-30) REVERT: C 252 HIS cc_start: 0.8279 (t-170) cc_final: 0.7998 (t-170) REVERT: C 262 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: C 282 ASN cc_start: 0.7946 (m-40) cc_final: 0.7509 (t0) REVERT: C 295 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6686 (ptt) REVERT: C 349 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7174 (mt-10) REVERT: C 387 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6505 (mm110) REVERT: C 399 LYS cc_start: 0.7459 (mmmt) cc_final: 0.7113 (mttm) REVERT: C 495 ASP cc_start: 0.7650 (m-30) cc_final: 0.7392 (m-30) REVERT: D 67 PHE cc_start: 0.6130 (m-80) cc_final: 0.5478 (m-10) REVERT: D 69 MET cc_start: 0.7125 (mtt) cc_final: 0.6776 (mtt) REVERT: D 133 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7257 (mp0) REVERT: D 266 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6425 (m-70) REVERT: D 281 GLU cc_start: 0.6881 (tp30) cc_final: 0.6447 (tp30) REVERT: D 282 ASN cc_start: 0.7843 (m-40) cc_final: 0.7425 (m110) REVERT: D 311 ASN cc_start: 0.6815 (p0) cc_final: 0.6139 (m-40) REVERT: D 338 TRP cc_start: 0.7652 (t-100) cc_final: 0.7307 (t-100) REVERT: D 349 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7195 (mt-10) REVERT: D 495 ASP cc_start: 0.7376 (m-30) cc_final: 0.6998 (m-30) REVERT: E 67 PHE cc_start: 0.6309 (m-10) cc_final: 0.5307 (t80) REVERT: E 99 ARG cc_start: 0.6925 (mmm-85) cc_final: 0.6292 (mmm-85) REVERT: E 349 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7085 (mp0) REVERT: E 399 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7401 (mttm) REVERT: E 472 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6999 (mm-30) REVERT: E 495 ASP cc_start: 0.7274 (m-30) cc_final: 0.6804 (m-30) REVERT: F 67 PHE cc_start: 0.6262 (m-10) cc_final: 0.5236 (t80) REVERT: F 252 HIS cc_start: 0.8235 (t-170) cc_final: 0.7957 (t-170) REVERT: F 282 ASN cc_start: 0.7971 (m-40) cc_final: 0.7440 (m110) REVERT: F 326 LYS cc_start: 0.7246 (ptmt) cc_final: 0.6524 (mtmt) REVERT: F 347 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8574 (tm-30) REVERT: F 349 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7378 (mp0) REVERT: F 387 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6605 (mm110) REVERT: F 399 LYS cc_start: 0.7383 (mmmt) cc_final: 0.7044 (mttt) REVERT: F 412 GLU cc_start: 0.7949 (pm20) cc_final: 0.7280 (tm-30) outliers start: 92 outliers final: 65 residues processed: 380 average time/residue: 0.3311 time to fit residues: 198.4345 Evaluate side-chains 377 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 306 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 262 GLN D 262 GLN E 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23231 Z= 0.207 Angle : 0.525 10.367 31413 Z= 0.269 Chirality : 0.043 0.150 3432 Planarity : 0.004 0.033 4121 Dihedral : 4.128 19.194 3228 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.86 % Allowed : 15.67 % Favored : 80.47 % 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 (0.15), residues: 2952 helix: 2.27 (0.13), residues: 1596 sheet: 0.09 (0.26), residues: 366 loop : -1.07 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 442 HIS 0.005 0.001 HIS A 142 PHE 0.018 0.002 PHE F 417 TYR 0.011 0.001 TYR E 550 ARG 0.006 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 311 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6054 (m-80) cc_final: 0.5419 (m-10) REVERT: A 133 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7257 (mp0) REVERT: A 262 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: A 266 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6430 (m-70) REVERT: A 281 GLU cc_start: 0.6994 (tp30) cc_final: 0.6672 (tp30) REVERT: A 326 LYS cc_start: 0.8382 (mttp) cc_final: 0.7527 (ptmt) REVERT: A 338 TRP cc_start: 0.7503 (t-100) cc_final: 0.7177 (t-100) REVERT: A 399 LYS cc_start: 0.7473 (mmmt) cc_final: 0.6943 (mttm) REVERT: A 495 ASP cc_start: 0.7432 (m-30) cc_final: 0.7014 (m-30) REVERT: B 67 PHE cc_start: 0.6235 (m-10) cc_final: 0.5244 (t80) REVERT: B 99 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6430 (mmm-85) REVERT: B 248 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6611 (p0) REVERT: B 326 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7481 (mtpt) REVERT: B 349 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7060 (mp0) REVERT: B 399 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7401 (mttm) REVERT: B 472 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7098 (mm-30) REVERT: B 495 ASP cc_start: 0.7260 (m-30) cc_final: 0.6739 (m-30) REVERT: C 66 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: C 67 PHE cc_start: 0.6022 (m-10) cc_final: 0.5315 (t80) REVERT: C 252 HIS cc_start: 0.8065 (t-170) cc_final: 0.7714 (t-170) REVERT: C 282 ASN cc_start: 0.7855 (m-40) cc_final: 0.7421 (t0) REVERT: C 295 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6759 (ptt) REVERT: C 349 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7195 (mt-10) REVERT: C 399 LYS cc_start: 0.7470 (mmmt) cc_final: 0.7120 (mttt) REVERT: C 412 GLU cc_start: 0.7710 (pm20) cc_final: 0.7199 (tm-30) REVERT: C 533 ASP cc_start: 0.8095 (t0) cc_final: 0.7157 (t0) REVERT: D 67 PHE cc_start: 0.6060 (m-80) cc_final: 0.5440 (m-10) REVERT: D 69 MET cc_start: 0.7218 (mtt) cc_final: 0.6797 (mtt) REVERT: D 133 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7240 (mp0) REVERT: D 262 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: D 266 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6397 (m-70) REVERT: D 281 GLU cc_start: 0.6888 (tp30) cc_final: 0.6617 (tp30) REVERT: D 282 ASN cc_start: 0.7739 (m-40) cc_final: 0.7349 (m110) REVERT: D 311 ASN cc_start: 0.6817 (p0) cc_final: 0.6243 (m-40) REVERT: D 338 TRP cc_start: 0.7538 (t-100) cc_final: 0.7230 (t-100) REVERT: D 349 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7229 (mt-10) REVERT: D 399 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7016 (mttt) REVERT: D 495 ASP cc_start: 0.7422 (m-30) cc_final: 0.7012 (m-30) REVERT: E 67 PHE cc_start: 0.6267 (m-10) cc_final: 0.5260 (t80) REVERT: E 99 ARG cc_start: 0.6974 (mmm-85) cc_final: 0.6376 (mmm-85) REVERT: E 248 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6642 (p0) REVERT: E 399 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7404 (mttm) REVERT: E 472 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7113 (mm-30) REVERT: E 495 ASP cc_start: 0.7288 (m-30) cc_final: 0.6810 (m-30) REVERT: F 67 PHE cc_start: 0.6051 (m-10) cc_final: 0.5263 (t80) REVERT: F 252 HIS cc_start: 0.8099 (t-170) cc_final: 0.7787 (t-170) REVERT: F 282 ASN cc_start: 0.7836 (m-40) cc_final: 0.7293 (m110) REVERT: F 326 LYS cc_start: 0.7287 (ptmt) cc_final: 0.6632 (mtmt) REVERT: F 347 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8588 (tm-30) REVERT: F 349 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7330 (mp0) REVERT: F 387 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6734 (mm110) REVERT: F 399 LYS cc_start: 0.7472 (mmmt) cc_final: 0.7127 (mttt) REVERT: F 533 ASP cc_start: 0.8078 (t0) cc_final: 0.7127 (t0) outliers start: 92 outliers final: 65 residues processed: 359 average time/residue: 0.3272 time to fit residues: 186.3381 Evaluate side-chains 374 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 300 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 158 optimal weight: 0.0270 chunk 283 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 262 GLN D 262 GLN E 262 GLN F 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23231 Z= 0.184 Angle : 0.508 10.247 31413 Z= 0.260 Chirality : 0.043 0.218 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.064 19.209 3228 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.16 % Allowed : 15.71 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.15), residues: 2952 helix: 2.39 (0.13), residues: 1560 sheet: -0.07 (0.26), residues: 378 loop : -0.90 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 129 HIS 0.004 0.001 HIS D 142 PHE 0.015 0.001 PHE F 417 TYR 0.009 0.001 TYR B 528 ARG 0.006 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 321 time to evaluate : 2.604 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5941 (m-80) cc_final: 0.5348 (m-10) REVERT: A 133 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7259 (mp0) REVERT: A 262 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7177 (mm110) REVERT: A 266 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6416 (m-70) REVERT: A 281 GLU cc_start: 0.6781 (tp30) cc_final: 0.6504 (tp30) REVERT: A 282 ASN cc_start: 0.7863 (m-40) cc_final: 0.7270 (m110) REVERT: A 326 LYS cc_start: 0.8376 (mttp) cc_final: 0.7528 (ptmt) REVERT: A 338 TRP cc_start: 0.7402 (t-100) cc_final: 0.7112 (t-100) REVERT: A 399 LYS cc_start: 0.7459 (mmmt) cc_final: 0.6943 (mttm) REVERT: A 495 ASP cc_start: 0.7430 (m-30) cc_final: 0.7003 (m-30) REVERT: A 530 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 67 PHE cc_start: 0.5936 (m-10) cc_final: 0.5102 (t80) REVERT: B 99 ARG cc_start: 0.6955 (mmm-85) cc_final: 0.6365 (mmm-85) REVERT: B 248 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6755 (p0) REVERT: B 282 ASN cc_start: 0.7727 (m-40) cc_final: 0.7238 (m110) REVERT: B 326 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7316 (mtpt) REVERT: B 349 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7108 (mp0) REVERT: B 399 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7460 (mttm) REVERT: B 472 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 485 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7655 (tp) REVERT: B 495 ASP cc_start: 0.7267 (m-30) cc_final: 0.6739 (m-30) REVERT: B 530 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7742 (mt) REVERT: B 533 ASP cc_start: 0.8062 (t0) cc_final: 0.7470 (t0) REVERT: C 67 PHE cc_start: 0.6015 (m-10) cc_final: 0.5422 (t80) REVERT: C 252 HIS cc_start: 0.8118 (t-170) cc_final: 0.7770 (t-170) REVERT: C 282 ASN cc_start: 0.7879 (m-40) cc_final: 0.7484 (t0) REVERT: C 349 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7197 (mt-10) REVERT: C 399 LYS cc_start: 0.7418 (mmmt) cc_final: 0.7013 (mttt) REVERT: C 530 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7608 (mt) REVERT: C 533 ASP cc_start: 0.8106 (t0) cc_final: 0.7203 (t0) REVERT: D 67 PHE cc_start: 0.6113 (m-80) cc_final: 0.5491 (m-10) REVERT: D 133 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7282 (mp0) REVERT: D 262 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7052 (mm110) REVERT: D 266 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6412 (m-70) REVERT: D 281 GLU cc_start: 0.6815 (tp30) cc_final: 0.6614 (tp30) REVERT: D 282 ASN cc_start: 0.7725 (m-40) cc_final: 0.7310 (m110) REVERT: D 311 ASN cc_start: 0.6791 (p0) cc_final: 0.6245 (m-40) REVERT: D 338 TRP cc_start: 0.7504 (t-100) cc_final: 0.7162 (t-100) REVERT: D 349 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7251 (mt-10) REVERT: D 399 LYS cc_start: 0.7542 (mmmt) cc_final: 0.7057 (mttt) REVERT: D 495 ASP cc_start: 0.7418 (m-30) cc_final: 0.7003 (m-30) REVERT: D 533 ASP cc_start: 0.8175 (t0) cc_final: 0.7729 (t0) REVERT: E 67 PHE cc_start: 0.5987 (m-10) cc_final: 0.5142 (t80) REVERT: E 99 ARG cc_start: 0.6932 (mmm-85) cc_final: 0.6317 (mmm-85) REVERT: E 326 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7180 (ttpt) REVERT: E 349 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7151 (mp0) REVERT: E 399 LYS cc_start: 0.7710 (mmmt) cc_final: 0.7448 (mttm) REVERT: E 472 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6891 (mm-30) REVERT: E 495 ASP cc_start: 0.7281 (m-30) cc_final: 0.6801 (m-30) REVERT: E 533 ASP cc_start: 0.8061 (t0) cc_final: 0.7428 (t0) REVERT: F 67 PHE cc_start: 0.6022 (m-10) cc_final: 0.5321 (t80) REVERT: F 252 HIS cc_start: 0.8091 (t-170) cc_final: 0.7771 (t-170) REVERT: F 282 ASN cc_start: 0.7818 (m-40) cc_final: 0.7403 (t0) REVERT: F 326 LYS cc_start: 0.7290 (ptmt) cc_final: 0.6634 (mtmt) REVERT: F 347 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8578 (tm-30) REVERT: F 349 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7362 (mp0) REVERT: F 387 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6757 (mm110) REVERT: F 530 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7594 (mt) REVERT: F 533 ASP cc_start: 0.8101 (t0) cc_final: 0.7205 (t0) outliers start: 99 outliers final: 77 residues processed: 375 average time/residue: 0.3211 time to fit residues: 191.9608 Evaluate side-chains 394 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 306 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Chi-restraints excluded: chain F residue 530 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 180 optimal weight: 0.0570 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 0.0170 chunk 26 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 262 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN F 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23231 Z= 0.216 Angle : 0.528 10.150 31413 Z= 0.271 Chirality : 0.043 0.234 3432 Planarity : 0.004 0.035 4121 Dihedral : 4.095 19.078 3228 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.45 % Allowed : 15.83 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.15), residues: 2952 helix: 2.32 (0.13), residues: 1560 sheet: -0.00 (0.26), residues: 366 loop : -1.00 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 129 HIS 0.004 0.001 HIS A 142 PHE 0.016 0.002 PHE C 214 TYR 0.011 0.001 TYR C 170 ARG 0.006 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 306 time to evaluate : 2.619 Fit side-chains REVERT: A 67 PHE cc_start: 0.5957 (m-80) cc_final: 0.5381 (m-10) REVERT: A 133 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7285 (mp0) REVERT: A 262 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 266 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6363 (m-70) REVERT: A 281 GLU cc_start: 0.6885 (tp30) cc_final: 0.6582 (tp30) REVERT: A 326 LYS cc_start: 0.8437 (mttp) cc_final: 0.7542 (ptmt) REVERT: A 338 TRP cc_start: 0.7389 (t-100) cc_final: 0.7125 (t-100) REVERT: A 399 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6980 (mttm) REVERT: A 495 ASP cc_start: 0.7454 (m-30) cc_final: 0.7006 (m-30) REVERT: A 530 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 67 PHE cc_start: 0.5853 (m-10) cc_final: 0.4933 (m-10) REVERT: B 99 ARG cc_start: 0.6941 (mmm-85) cc_final: 0.6337 (mmm-85) REVERT: B 248 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6744 (p0) REVERT: B 282 ASN cc_start: 0.7698 (m-40) cc_final: 0.7216 (m110) REVERT: B 326 LYS cc_start: 0.7487 (mtpt) cc_final: 0.7269 (mtpt) REVERT: B 349 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7109 (mp0) REVERT: B 399 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7434 (mttm) REVERT: B 472 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7087 (mm-30) REVERT: B 485 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7660 (tp) REVERT: B 495 ASP cc_start: 0.7275 (m-30) cc_final: 0.6748 (m-30) REVERT: B 530 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7758 (mt) REVERT: B 533 ASP cc_start: 0.8070 (t0) cc_final: 0.7474 (t0) REVERT: C 66 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5930 (m-10) REVERT: C 67 PHE cc_start: 0.5991 (m-10) cc_final: 0.5430 (t80) REVERT: C 252 HIS cc_start: 0.8108 (t-170) cc_final: 0.7747 (t-170) REVERT: C 282 ASN cc_start: 0.7860 (m-40) cc_final: 0.7412 (t0) REVERT: C 349 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7303 (mt-10) REVERT: C 399 LYS cc_start: 0.7456 (mmmt) cc_final: 0.7107 (mttt) REVERT: C 530 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7606 (mt) REVERT: C 533 ASP cc_start: 0.8105 (t0) cc_final: 0.7238 (t0) REVERT: D 67 PHE cc_start: 0.6056 (m-80) cc_final: 0.5437 (m-10) REVERT: D 76 ARG cc_start: 0.7423 (mtp85) cc_final: 0.7128 (mtp180) REVERT: D 133 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7266 (mp0) REVERT: D 262 GLN cc_start: 0.7442 (mm-40) cc_final: 0.6779 (mp10) REVERT: D 266 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6354 (m-70) REVERT: D 281 GLU cc_start: 0.6801 (tp30) cc_final: 0.6241 (tp30) REVERT: D 282 ASN cc_start: 0.7763 (m-40) cc_final: 0.7332 (m110) REVERT: D 311 ASN cc_start: 0.6800 (p0) cc_final: 0.6295 (m-40) REVERT: D 326 LYS cc_start: 0.8393 (mttp) cc_final: 0.7424 (ptmt) REVERT: D 338 TRP cc_start: 0.7423 (t-100) cc_final: 0.7092 (t-100) REVERT: D 349 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7251 (mt-10) REVERT: D 399 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7140 (mttm) REVERT: D 495 ASP cc_start: 0.7426 (m-30) cc_final: 0.7002 (m-30) REVERT: D 530 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7703 (mt) REVERT: D 533 ASP cc_start: 0.8191 (t0) cc_final: 0.7727 (t0) REVERT: E 67 PHE cc_start: 0.5886 (m-10) cc_final: 0.4958 (m-10) REVERT: E 99 ARG cc_start: 0.6907 (mmm-85) cc_final: 0.6292 (mmm-85) REVERT: E 326 LYS cc_start: 0.7448 (mtpt) cc_final: 0.7172 (ttpt) REVERT: E 349 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7145 (mt-10) REVERT: E 399 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7496 (mttm) REVERT: E 472 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7091 (mm-30) REVERT: E 485 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7672 (tp) REVERT: E 495 ASP cc_start: 0.7287 (m-30) cc_final: 0.6805 (m-30) REVERT: E 530 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7742 (mt) REVERT: E 533 ASP cc_start: 0.8068 (t0) cc_final: 0.7473 (t0) REVERT: F 67 PHE cc_start: 0.6017 (m-10) cc_final: 0.5325 (t80) REVERT: F 116 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7898 (tt) REVERT: F 252 HIS cc_start: 0.8140 (t-170) cc_final: 0.7789 (t-170) REVERT: F 282 ASN cc_start: 0.7836 (m-40) cc_final: 0.7410 (t0) REVERT: F 326 LYS cc_start: 0.7314 (ptmt) cc_final: 0.6653 (mtmt) REVERT: F 347 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8596 (tm-30) REVERT: F 349 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7352 (mp0) REVERT: F 387 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6736 (mm-40) REVERT: F 399 LYS cc_start: 0.7506 (mmmt) cc_final: 0.7024 (mttt) REVERT: F 530 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7579 (mt) REVERT: F 533 ASP cc_start: 0.8095 (t0) cc_final: 0.7229 (t0) outliers start: 106 outliers final: 74 residues processed: 365 average time/residue: 0.3236 time to fit residues: 187.8287 Evaluate side-chains 387 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 298 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Chi-restraints excluded: chain F residue 530 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 264 optimal weight: 0.1980 chunk 158 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 262 GLN D 262 GLN E 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 23231 Z= 0.162 Angle : 0.504 10.196 31413 Z= 0.256 Chirality : 0.042 0.215 3432 Planarity : 0.003 0.034 4121 Dihedral : 3.954 19.260 3228 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.91 % Allowed : 16.30 % Favored : 79.80 % 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: 1.49 (0.15), residues: 2952 helix: 2.43 (0.13), residues: 1560 sheet: -0.09 (0.26), residues: 378 loop : -0.93 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 129 HIS 0.004 0.001 HIS D 142 PHE 0.012 0.001 PHE C 67 TYR 0.009 0.001 TYR B 528 ARG 0.007 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 320 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5882 (m-80) cc_final: 0.5297 (m-10) REVERT: A 133 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7278 (mp0) REVERT: A 262 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: A 266 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.6430 (m-70) REVERT: A 281 GLU cc_start: 0.6735 (tp30) cc_final: 0.6469 (tp30) REVERT: A 282 ASN cc_start: 0.7846 (m-40) cc_final: 0.7193 (m110) REVERT: A 326 LYS cc_start: 0.8374 (mttp) cc_final: 0.7522 (ptmt) REVERT: A 338 TRP cc_start: 0.7342 (t-100) cc_final: 0.7096 (t-100) REVERT: A 399 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6976 (mttm) REVERT: A 495 ASP cc_start: 0.7347 (m-30) cc_final: 0.6912 (m-30) REVERT: A 530 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7715 (mt) REVERT: A 533 ASP cc_start: 0.8156 (t0) cc_final: 0.7653 (t0) REVERT: B 67 PHE cc_start: 0.5734 (m-10) cc_final: 0.4911 (m-10) REVERT: B 99 ARG cc_start: 0.6972 (mmm-85) cc_final: 0.6337 (mmm-85) REVERT: B 282 ASN cc_start: 0.7689 (m-40) cc_final: 0.7182 (m110) REVERT: B 326 LYS cc_start: 0.7482 (mtpt) cc_final: 0.6835 (mtmt) REVERT: B 349 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7198 (mt-10) REVERT: B 399 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7421 (mttm) REVERT: B 472 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 495 ASP cc_start: 0.7328 (m-30) cc_final: 0.6765 (m-30) REVERT: B 530 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7729 (mt) REVERT: B 533 ASP cc_start: 0.8034 (t0) cc_final: 0.7422 (t0) REVERT: C 66 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: C 67 PHE cc_start: 0.5973 (m-10) cc_final: 0.5495 (t80) REVERT: C 252 HIS cc_start: 0.8041 (t-170) cc_final: 0.7709 (t-170) REVERT: C 282 ASN cc_start: 0.7820 (m-40) cc_final: 0.7538 (t0) REVERT: C 349 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7298 (mt-10) REVERT: C 399 LYS cc_start: 0.7374 (mmmt) cc_final: 0.7022 (mttt) REVERT: C 412 GLU cc_start: 0.7619 (pm20) cc_final: 0.7154 (tm-30) REVERT: C 475 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7068 (mm-30) REVERT: C 530 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7599 (mt) REVERT: C 533 ASP cc_start: 0.8032 (t0) cc_final: 0.7226 (t0) REVERT: D 66 PHE cc_start: 0.5769 (m-80) cc_final: 0.5481 (m-80) REVERT: D 67 PHE cc_start: 0.5841 (m-80) cc_final: 0.5238 (m-10) REVERT: D 76 ARG cc_start: 0.7399 (mtp85) cc_final: 0.7148 (mtp180) REVERT: D 133 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7271 (mp0) REVERT: D 262 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: D 266 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.6355 (m-70) REVERT: D 282 ASN cc_start: 0.7741 (m-40) cc_final: 0.7284 (m110) REVERT: D 311 ASN cc_start: 0.6751 (p0) cc_final: 0.6260 (m-40) REVERT: D 326 LYS cc_start: 0.8347 (mttp) cc_final: 0.7372 (ptmt) REVERT: D 338 TRP cc_start: 0.7411 (t-100) cc_final: 0.7128 (t-100) REVERT: D 349 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7249 (mt-10) REVERT: D 397 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7592 (tmtt) REVERT: D 399 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7191 (mttm) REVERT: D 495 ASP cc_start: 0.7406 (m-30) cc_final: 0.6978 (m-30) REVERT: D 528 TYR cc_start: 0.7393 (m-80) cc_final: 0.7182 (m-80) REVERT: D 530 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7646 (mt) REVERT: D 533 ASP cc_start: 0.8208 (t0) cc_final: 0.7710 (t0) REVERT: E 67 PHE cc_start: 0.5762 (m-10) cc_final: 0.4937 (m-10) REVERT: E 69 MET cc_start: 0.7376 (mmt) cc_final: 0.7145 (mtp) REVERT: E 326 LYS cc_start: 0.7459 (mtpt) cc_final: 0.7231 (ttpt) REVERT: E 349 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7243 (mt-10) REVERT: E 399 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7466 (mttm) REVERT: E 472 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6853 (mm-30) REVERT: E 495 ASP cc_start: 0.7269 (m-30) cc_final: 0.6783 (m-30) REVERT: E 530 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7716 (mt) REVERT: E 533 ASP cc_start: 0.8029 (t0) cc_final: 0.7418 (t0) REVERT: F 67 PHE cc_start: 0.5954 (m-10) cc_final: 0.5268 (t80) REVERT: F 252 HIS cc_start: 0.8075 (t-170) cc_final: 0.7755 (t-170) REVERT: F 282 ASN cc_start: 0.7828 (m-40) cc_final: 0.7553 (t0) REVERT: F 326 LYS cc_start: 0.7305 (ptmt) cc_final: 0.6659 (mtmt) REVERT: F 347 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8602 (tm-30) REVERT: F 349 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7351 (mp0) REVERT: F 387 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6823 (mm110) REVERT: F 399 LYS cc_start: 0.7388 (mmmt) cc_final: 0.6856 (mttm) REVERT: F 530 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7616 (mt) REVERT: F 533 ASP cc_start: 0.8098 (t0) cc_final: 0.7306 (t0) outliers start: 93 outliers final: 73 residues processed: 374 average time/residue: 0.3266 time to fit residues: 194.8560 Evaluate side-chains 387 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 302 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Chi-restraints excluded: chain F residue 530 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 9.9990 chunk 279 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 chunk 269 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN C 262 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN E 262 GLN F 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23231 Z= 0.187 Angle : 0.512 10.396 31413 Z= 0.263 Chirality : 0.043 0.222 3432 Planarity : 0.004 0.036 4121 Dihedral : 3.965 18.947 3228 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.99 % Allowed : 16.13 % Favored : 79.88 % 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: 1.42 (0.15), residues: 2952 helix: 2.37 (0.13), residues: 1560 sheet: -0.15 (0.26), residues: 378 loop : -0.93 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 129 HIS 0.004 0.001 HIS A 252 PHE 0.021 0.001 PHE C 417 TYR 0.009 0.001 TYR C 170 ARG 0.007 0.000 ARG F 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 301 time to evaluate : 2.636 Fit side-chains REVERT: A 67 PHE cc_start: 0.5903 (m-80) cc_final: 0.5318 (m-10) REVERT: A 133 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7265 (mp0) REVERT: A 262 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: A 266 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6451 (m-70) REVERT: A 281 GLU cc_start: 0.6718 (tp30) cc_final: 0.6431 (tp30) REVERT: A 282 ASN cc_start: 0.7851 (m-40) cc_final: 0.7218 (m110) REVERT: A 326 LYS cc_start: 0.8392 (mttp) cc_final: 0.7545 (ptmt) REVERT: A 338 TRP cc_start: 0.7351 (t-100) cc_final: 0.7122 (t-100) REVERT: A 399 LYS cc_start: 0.7456 (mmmt) cc_final: 0.7004 (mttm) REVERT: A 495 ASP cc_start: 0.7444 (m-30) cc_final: 0.6993 (m-30) REVERT: A 530 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7710 (mt) REVERT: B 67 PHE cc_start: 0.5744 (m-10) cc_final: 0.4921 (m-10) REVERT: B 99 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6343 (mmm-85) REVERT: B 282 ASN cc_start: 0.7674 (m-40) cc_final: 0.7185 (m110) REVERT: B 326 LYS cc_start: 0.7508 (mtpt) cc_final: 0.6827 (mtmt) REVERT: B 349 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7199 (mt-10) REVERT: B 399 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7369 (mttm) REVERT: B 472 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 495 ASP cc_start: 0.7336 (m-30) cc_final: 0.6780 (m-30) REVERT: B 530 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 533 ASP cc_start: 0.8036 (t0) cc_final: 0.7415 (t0) REVERT: C 66 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: C 67 PHE cc_start: 0.5980 (m-10) cc_final: 0.5493 (t80) REVERT: C 252 HIS cc_start: 0.8087 (t-170) cc_final: 0.7750 (t-170) REVERT: C 282 ASN cc_start: 0.7816 (m-40) cc_final: 0.7540 (t0) REVERT: C 349 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7307 (mt-10) REVERT: C 361 PHE cc_start: 0.7138 (t80) cc_final: 0.6902 (t80) REVERT: C 399 LYS cc_start: 0.7409 (mmmt) cc_final: 0.7069 (mttt) REVERT: C 412 GLU cc_start: 0.7599 (pm20) cc_final: 0.7132 (tm-30) REVERT: C 530 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7604 (mt) REVERT: C 533 ASP cc_start: 0.8033 (t0) cc_final: 0.7221 (t0) REVERT: D 66 PHE cc_start: 0.5804 (m-80) cc_final: 0.5514 (m-10) REVERT: D 67 PHE cc_start: 0.5858 (m-80) cc_final: 0.5258 (m-10) REVERT: D 76 ARG cc_start: 0.7414 (mtp85) cc_final: 0.7141 (mtp180) REVERT: D 133 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7255 (mp0) REVERT: D 262 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: D 266 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6370 (m-70) REVERT: D 282 ASN cc_start: 0.7661 (m-40) cc_final: 0.7175 (m110) REVERT: D 311 ASN cc_start: 0.6756 (p0) cc_final: 0.6273 (m-40) REVERT: D 326 LYS cc_start: 0.8359 (mttp) cc_final: 0.7391 (ptmt) REVERT: D 338 TRP cc_start: 0.7384 (t-100) cc_final: 0.7100 (t-100) REVERT: D 349 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7252 (mt-10) REVERT: D 397 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7596 (tmtt) REVERT: D 399 LYS cc_start: 0.7540 (mmmt) cc_final: 0.7185 (mttm) REVERT: D 495 ASP cc_start: 0.7420 (m-30) cc_final: 0.6989 (m-30) REVERT: D 530 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7648 (mt) REVERT: D 533 ASP cc_start: 0.8226 (t0) cc_final: 0.7748 (t0) REVERT: E 67 PHE cc_start: 0.5767 (m-10) cc_final: 0.4940 (m-10) REVERT: E 326 LYS cc_start: 0.7526 (mtpt) cc_final: 0.7167 (mtmt) REVERT: E 349 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7243 (mt-10) REVERT: E 399 LYS cc_start: 0.7685 (mmmt) cc_final: 0.7368 (mttm) REVERT: E 472 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6851 (mm-30) REVERT: E 495 ASP cc_start: 0.7285 (m-30) cc_final: 0.6798 (m-30) REVERT: E 530 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7714 (mt) REVERT: E 533 ASP cc_start: 0.8034 (t0) cc_final: 0.7416 (t0) REVERT: F 67 PHE cc_start: 0.6009 (m-10) cc_final: 0.5337 (t80) REVERT: F 116 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7819 (tp) REVERT: F 252 HIS cc_start: 0.8112 (t-170) cc_final: 0.7810 (t-170) REVERT: F 282 ASN cc_start: 0.7829 (m-40) cc_final: 0.7582 (t0) REVERT: F 326 LYS cc_start: 0.7324 (ptmt) cc_final: 0.6674 (mtmt) REVERT: F 347 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8620 (tm-30) REVERT: F 349 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7351 (mp0) REVERT: F 387 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6878 (mm110) REVERT: F 399 LYS cc_start: 0.7564 (mmmt) cc_final: 0.7032 (mttt) REVERT: F 412 GLU cc_start: 0.7854 (pm20) cc_final: 0.7248 (tm-30) REVERT: F 530 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7603 (mt) REVERT: F 533 ASP cc_start: 0.8121 (t0) cc_final: 0.7316 (t0) outliers start: 95 outliers final: 76 residues processed: 352 average time/residue: 0.3124 time to fit residues: 175.4253 Evaluate side-chains 385 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 296 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 SER Chi-restraints excluded: chain F residue 530 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.9990 chunk 248 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN C 262 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN E 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.180860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.141548 restraints weight = 29442.096| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.13 r_work: 0.3495 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.340 23231 Z= 0.459 Angle : 0.939 65.900 31413 Z= 0.596 Chirality : 0.048 0.873 3432 Planarity : 0.009 0.280 4121 Dihedral : 3.965 18.823 3228 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.82 % Allowed : 16.38 % Favored : 79.80 % Cbeta Deviations : 0.19 % 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: 1.42 (0.15), residues: 2952 helix: 2.37 (0.13), residues: 1560 sheet: -0.15 (0.26), residues: 378 loop : -0.92 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 129 HIS 0.003 0.001 HIS A 252 PHE 0.019 0.001 PHE C 417 TYR 0.009 0.001 TYR C 170 ARG 0.005 0.000 ARG F 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4998.64 seconds wall clock time: 91 minutes 3.98 seconds (5463.98 seconds total)