Starting phenix.real_space_refine on Sun Feb 18 03:48:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eev_28060/02_2024/8eev_28060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eev_28060/02_2024/8eev_28060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eev_28060/02_2024/8eev_28060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eev_28060/02_2024/8eev_28060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eev_28060/02_2024/8eev_28060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eev_28060/02_2024/8eev_28060.pdb" } resolution = 3.6 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= 0.003 sd= 0.034 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 123 5.16 5 C 13302 2.51 5 N 3373 2.21 5 O 3842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3019 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 372} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 8} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2092 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 21, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3019 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 371} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 8} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2092 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 21, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3019 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 371} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 8} Unresolved non-hydrogen planarities: 41 Chain: "K" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2092 Classifications: {'peptide': 268} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 21 Chain: "T" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 21 Chain: "V" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 11.05, per 1000 atoms: 0.54 Number of scatterers: 20640 At special positions: 0 Unit cell: (165.021, 160.095, 118.224, 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 123 16.00 O 3842 8.00 N 3373 7.00 C 13302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.02 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.02 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.02 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 123 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 27 " distance=2.02 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 100C" distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.02 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.02 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 123 " distance=2.04 Simple disulfide: pdb=" SG CYS K 90 " - pdb=" SG CYS K 104 " distance=2.02 Simple disulfide: pdb=" SG CYS K 151 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 98 " - pdb=" SG CYS S 100C" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS U 98 " - pdb=" SG CYS U 100C" distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.04 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: 7.66 Conformation dependent library (CDL) restraints added in 3.9 seconds 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5018 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 81 sheets defined 2.2% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.501A pdb=" N GLN A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 4.115A pdb=" N GLU A 292 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.692A pdb=" N GLN F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'J' and resid 238 through 247 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.829A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'S' and resid 100 through 100D removed outlier: 3.754A pdb=" N CYS S 100C" --> pdb=" O ASN S 100 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR S 100D" --> pdb=" O THR S 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 100 through 100D' Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.768A pdb=" N ASP T 82 " --> pdb=" O GLU T 79 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 79 through 83' Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.712A pdb=" N ASP V 82 " --> pdb=" O GLU V 79 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.785A pdb=" N HIS A 3 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 7.116A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 45 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 7.116A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 45 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 61 removed outlier: 4.082A pdb=" N LYS A 105 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 103 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 60 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 101 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 106 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 305 removed outlier: 7.082A pdb=" N ILE A 315 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.707A pdb=" N CYS A 376 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.684A pdb=" N TRP B 339 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.735A pdb=" N CYS B 19 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS B 27 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.590A pdb=" N ALA B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N SER B 50 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP B 69 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 73 " --> pdb=" O MET B 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.590A pdb=" N ALA B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 45 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR B 98 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N SER B 51 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS B 96 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N TYR B 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N ASP B 94 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AB8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AC1, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AC2, first strand: chain 'B' and resid 307 through 311 Processing sheet with id=AC3, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'F' and resid 15 through 19 removed outlier: 7.171A pdb=" N ILE F 29 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL F 137 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 31 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 135 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 133 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 131 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 37 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 129 " --> pdb=" O LYS F 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA F 127 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 142 through 147 removed outlier: 6.684A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA F 127 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 129 " --> pdb=" O LYS F 37 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 37 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 131 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 133 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 135 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 31 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL F 137 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE F 29 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 51 through 61 removed outlier: 4.332A pdb=" N LYS F 105 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL F 103 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE F 60 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 101 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 51 through 61 removed outlier: 4.332A pdb=" N LYS F 105 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL F 103 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE F 60 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 101 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC9, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'F' and resid 296 through 305 removed outlier: 4.582A pdb=" N ALA F 298 " --> pdb=" O SER F 321 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER F 321 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE F 315 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AD3, first strand: chain 'F' and resid 364 through 368 removed outlier: 3.650A pdb=" N PHE F 365 " --> pdb=" O CYS F 376 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS F 376 " --> pdb=" O PHE F 365 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 387 through 388 removed outlier: 3.502A pdb=" N TRP G 339 " --> pdb=" O VAL F 388 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 17 through 19 removed outlier: 3.819A pdb=" N CYS G 19 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS G 27 " --> pdb=" O CYS G 19 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 33 through 37 removed outlier: 6.851A pdb=" N GLN G 48 " --> pdb=" O GLU G 34 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL G 36 " --> pdb=" O ARG G 46 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG G 46 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR G 98 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N SER G 51 " --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS G 96 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR G 53 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N ASP G 94 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 65 through 66 Processing sheet with id=AD8, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.651A pdb=" N THR G 73 " --> pdb=" O MET G 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AE1, first strand: chain 'G' and resid 147 through 150 Processing sheet with id=AE2, first strand: chain 'G' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AE4, first strand: chain 'G' and resid 275 through 279 Processing sheet with id=AE5, first strand: chain 'G' and resid 307 through 311 Processing sheet with id=AE6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.755A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR H 35 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.755A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR H 35 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 8 Processing sheet with id=AF1, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.186A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN J 134 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS J 35 " --> pdb=" O PHE J 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 41 through 48 removed outlier: 7.069A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA J 119 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 51 through 55 Processing sheet with id=AF4, first strand: chain 'J' and resid 51 through 55 removed outlier: 3.539A pdb=" N SER J 104 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS J 79 " --> pdb=" O SER J 104 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AF6, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'J' and resid 260 through 262 Processing sheet with id=AF8, first strand: chain 'J' and resid 300 through 303 Processing sheet with id=AF9, first strand: chain 'J' and resid 306 through 307 removed outlier: 6.606A pdb=" N CYS J 306 " --> pdb=" O HIS J 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'J' and resid 327 through 329 Processing sheet with id=AG2, first strand: chain 'J' and resid 364 through 367 removed outlier: 3.644A pdb=" N CYS J 376 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.595A pdb=" N CYS K 19 " --> pdb=" O CYS K 27 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS K 27 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 33 through 37 removed outlier: 7.791A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N SER K 50 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP K 69 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 73 through 74 removed outlier: 4.769A pdb=" N ASP K 69 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N SER K 50 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR K 98 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N SER K 51 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS K 96 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR K 53 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ASP K 94 " --> pdb=" O TYR K 53 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 83 through 85 Processing sheet with id=AG7, first strand: chain 'K' and resid 147 through 150 Processing sheet with id=AG8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG9, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AH1, first strand: chain 'K' and resid 275 through 279 Processing sheet with id=AH2, first strand: chain 'K' and resid 307 through 311 Processing sheet with id=AH3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.081A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.650A pdb=" N SER S 7 " --> pdb=" O THR S 21 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 35 through 40 removed outlier: 3.937A pdb=" N GLY S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU S 45 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE S 58 " --> pdb=" O PHE S 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'S' and resid 88 through 90 Processing sheet with id=AH8, first strand: chain 'S' and resid 93 through 95 Processing sheet with id=AH9, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'T' and resid 27C through 27D removed outlier: 4.122A pdb=" N ASN T 30 " --> pdb=" O HIS T 27D" (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'T' and resid 53 through 54 removed outlier: 7.078A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.539A pdb=" N GLN U 5 " --> pdb=" O ALA U 23 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.539A pdb=" N GLN U 5 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP U 72 " --> pdb=" O GLN U 77 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 57 through 58 removed outlier: 5.874A pdb=" N LEU U 45 " --> pdb=" O SER U 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER U 40 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY U 49 " --> pdb=" O TRP U 36 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR U 35 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N CYS U 92 " --> pdb=" O TRP U 103 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP U 103 " --> pdb=" O CYS U 92 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG U 94 " --> pdb=" O ASP U 101 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 57 through 58 removed outlier: 5.874A pdb=" N LEU U 45 " --> pdb=" O SER U 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER U 40 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY U 49 " --> pdb=" O TRP U 36 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR U 35 " --> pdb=" O SER U 95 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AI8, first strand: chain 'V' and resid 10 through 12 removed outlier: 4.004A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'V' and resid 27C through 27D removed outlier: 3.753A pdb=" N ASN V 30 " --> pdb=" O HIS V 27D" (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.97 Time building geometry restraints manager: 8.34 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: 6549 1.34 - 1.47: 5626 1.47 - 1.59: 8867 1.59 - 1.71: 0 1.71 - 1.84: 156 Bond restraints: 21198 Sorted by residual: bond pdb=" CA GLN G 152 " pdb=" CB GLN G 152 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.53e-02 4.27e+03 7.51e+00 bond pdb=" CB PRO G 258 " pdb=" CG PRO G 258 " ideal model delta sigma weight residual 1.492 1.374 0.118 5.00e-02 4.00e+02 5.60e+00 bond pdb=" CA MET K 112 " pdb=" CB MET K 112 " ideal model delta sigma weight residual 1.533 1.493 0.040 1.72e-02 3.38e+03 5.42e+00 bond pdb=" CB TRP B 339 " pdb=" CG TRP B 339 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.95e+00 bond pdb=" CB PRO G 105 " pdb=" CG PRO G 105 " ideal model delta sigma weight residual 1.492 1.381 0.111 5.00e-02 4.00e+02 4.91e+00 ... (remaining 21193 not shown) Histogram of bond angle deviations from ideal: 92.62 - 101.16: 34 101.16 - 109.69: 4059 109.69 - 118.22: 12509 118.22 - 126.75: 11739 126.75 - 135.29: 422 Bond angle restraints: 28763 Sorted by residual: angle pdb=" N ASN J 264 " pdb=" CA ASN J 264 " pdb=" C ASN J 264 " ideal model delta sigma weight residual 109.81 92.62 17.19 2.21e+00 2.05e-01 6.05e+01 angle pdb=" N ILE F 369 " pdb=" CA ILE F 369 " pdb=" C ILE F 369 " ideal model delta sigma weight residual 109.34 99.57 9.77 2.08e+00 2.31e-01 2.21e+01 angle pdb=" C ASN J 264 " pdb=" CA ASN J 264 " pdb=" CB ASN J 264 " ideal model delta sigma weight residual 110.17 119.30 -9.13 1.97e+00 2.58e-01 2.15e+01 angle pdb=" C THR J 263 " pdb=" N ASN J 264 " pdb=" CA ASN J 264 " ideal model delta sigma weight residual 121.80 132.40 -10.60 2.44e+00 1.68e-01 1.89e+01 angle pdb=" CA ASN J 264 " pdb=" C ASN J 264 " pdb=" N PRO J 265 " ideal model delta sigma weight residual 118.44 125.00 -6.56 1.59e+00 3.96e-01 1.70e+01 ... (remaining 28758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 11909 15.01 - 30.03: 573 30.03 - 45.04: 118 45.04 - 60.06: 18 60.06 - 75.07: 4 Dihedral angle restraints: 12622 sinusoidal: 4909 harmonic: 7713 Sorted by residual: dihedral pdb=" CA VAL A 84 " pdb=" C VAL A 84 " pdb=" N TYR A 85 " pdb=" CA TYR A 85 " ideal model delta harmonic sigma weight residual 180.00 127.33 52.67 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA VAL J 148 " pdb=" C VAL J 148 " pdb=" N ASN J 149 " pdb=" CA ASN J 149 " ideal model delta harmonic sigma weight residual 180.00 140.09 39.91 0 5.00e+00 4.00e-02 6.37e+01 dihedral pdb=" CA ASP S 101 " pdb=" C ASP S 101 " pdb=" N VAL S 102 " pdb=" CA VAL S 102 " ideal model delta harmonic sigma weight residual -180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 12619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2079 0.046 - 0.092: 842 0.092 - 0.138: 256 0.138 - 0.184: 40 0.184 - 0.230: 3 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CG LEU T 46 " pdb=" CB LEU T 46 " pdb=" CD1 LEU T 46 " pdb=" CD2 LEU T 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU L 46 " pdb=" CB LEU L 46 " pdb=" CD1 LEU L 46 " pdb=" CD2 LEU L 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE A 369 " pdb=" N ILE A 369 " pdb=" C ILE A 369 " pdb=" CB ILE A 369 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 3217 not shown) Planarity restraints: 3703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 264 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C ASN J 264 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN J 264 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO J 265 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 29 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO B 30 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 88 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 89 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " -0.037 5.00e-02 4.00e+02 ... (remaining 3700 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 196 2.58 - 3.16: 17016 3.16 - 3.74: 28743 3.74 - 4.32: 41592 4.32 - 4.90: 71458 Nonbonded interactions: 159005 Sorted by model distance: nonbonded pdb=" OG1 THR G 297 " pdb=" OG1 THR G 307 " model vdw 1.996 2.440 nonbonded pdb=" OG1 THR K 297 " pdb=" OG1 THR K 307 " model vdw 1.998 2.440 nonbonded pdb=" OG1 THR B 297 " pdb=" OG1 THR B 307 " model vdw 2.014 2.440 nonbonded pdb=" OG SER J 297 " pdb=" O SER J 321 " model vdw 2.040 2.440 nonbonded pdb=" OG SER F 297 " pdb=" O SER F 321 " model vdw 2.053 2.440 ... (remaining 159000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'S' and resid 1 through 111) selection = (chain 'U' and resid 1 through 111) } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 4.350 Check model and map are aligned: 0.570 Set scattering table: 0.210 Process input model: 56.930 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.150 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 21198 Z= 0.621 Angle : 0.949 17.187 28763 Z= 0.522 Chirality : 0.054 0.230 3220 Planarity : 0.007 0.069 3703 Dihedral : 9.162 75.072 7472 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.62 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.36 % 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: -4.66 (0.13), residues: 2677 helix: -3.57 (0.54), residues: 27 sheet: -2.49 (0.14), residues: 1075 loop : -3.69 (0.12), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 100F HIS 0.016 0.003 HIS F 331 PHE 0.042 0.003 PHE J 87 TYR 0.028 0.003 TYR J 308 ARG 0.000 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 787 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7532 (mtpp) REVERT: A 41 THR cc_start: 0.8443 (m) cc_final: 0.8032 (p) REVERT: A 75 ASP cc_start: 0.7982 (t0) cc_final: 0.7486 (t0) REVERT: A 76 GLU cc_start: 0.6867 (tp30) cc_final: 0.6572 (tp30) REVERT: A 95 PHE cc_start: 0.7554 (t80) cc_final: 0.7309 (t80) REVERT: A 99 GLU cc_start: 0.7986 (pm20) cc_final: 0.7717 (pm20) REVERT: A 100 ASN cc_start: 0.8120 (m-40) cc_final: 0.7842 (m-40) REVERT: A 105 LYS cc_start: 0.8549 (mttt) cc_final: 0.8022 (mtpt) REVERT: A 137 VAL cc_start: 0.8610 (t) cc_final: 0.8288 (p) REVERT: A 153 PRO cc_start: 0.8631 (Cg_endo) cc_final: 0.8423 (Cg_exo) REVERT: A 183 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 230 HIS cc_start: 0.8051 (p90) cc_final: 0.7812 (p90) REVERT: A 269 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6733 (mt-10) REVERT: A 311 ASP cc_start: 0.6726 (p0) cc_final: 0.6206 (p0) REVERT: A 312 PHE cc_start: 0.7645 (m-10) cc_final: 0.7356 (m-10) REVERT: A 331 HIS cc_start: 0.7350 (t-90) cc_final: 0.7102 (t-90) REVERT: A 355 HIS cc_start: 0.6845 (m-70) cc_final: 0.6644 (m-70) REVERT: A 360 ASN cc_start: 0.6887 (m-40) cc_final: 0.6646 (m-40) REVERT: A 365 PHE cc_start: 0.8235 (p90) cc_final: 0.7961 (p90) REVERT: A 385 ASP cc_start: 0.6367 (p0) cc_final: 0.6021 (p0) REVERT: B 37 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7777 (mmmm) REVERT: B 74 ILE cc_start: 0.8352 (mm) cc_final: 0.8111 (mt) REVERT: B 94 ASP cc_start: 0.6987 (t0) cc_final: 0.6692 (t0) REVERT: B 130 LYS cc_start: 0.7376 (ptpp) cc_final: 0.7087 (ptpp) REVERT: B 137 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7222 (mt-10) REVERT: B 153 VAL cc_start: 0.8521 (m) cc_final: 0.8293 (t) REVERT: B 245 LYS cc_start: 0.7050 (ttpt) cc_final: 0.6833 (ttpt) REVERT: B 254 LYS cc_start: 0.7324 (pmtt) cc_final: 0.7098 (pmtt) REVERT: B 286 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7445 (mtpp) REVERT: B 293 THR cc_start: 0.8091 (m) cc_final: 0.7609 (p) REVERT: F 52 LYS cc_start: 0.8196 (tttt) cc_final: 0.7793 (ttpp) REVERT: F 76 GLU cc_start: 0.7171 (tp30) cc_final: 0.6828 (tp30) REVERT: F 105 LYS cc_start: 0.8563 (mttt) cc_final: 0.7933 (mtpt) REVERT: F 123 LYS cc_start: 0.8418 (mttt) cc_final: 0.8148 (mmtp) REVERT: F 225 LYS cc_start: 0.8251 (tttt) cc_final: 0.7918 (ttpp) REVERT: F 245 LYS cc_start: 0.7714 (ptpt) cc_final: 0.7419 (ptpt) REVERT: F 270 ASN cc_start: 0.8323 (m-40) cc_final: 0.7970 (m110) REVERT: F 302 THR cc_start: 0.7320 (p) cc_final: 0.7036 (p) REVERT: F 315 ILE cc_start: 0.8190 (mt) cc_final: 0.7647 (pt) REVERT: F 317 THR cc_start: 0.7625 (m) cc_final: 0.7122 (p) REVERT: F 338 THR cc_start: 0.7682 (m) cc_final: 0.7428 (p) REVERT: F 340 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7777 (ttmm) REVERT: G 37 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7813 (mmtp) REVERT: G 38 SER cc_start: 0.8630 (p) cc_final: 0.8255 (p) REVERT: G 75 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8063 (mmtt) REVERT: G 144 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6515 (mm-30) REVERT: G 167 MET cc_start: 0.7408 (ptp) cc_final: 0.6713 (ptp) REVERT: G 257 VAL cc_start: 0.7862 (t) cc_final: 0.7617 (p) REVERT: G 273 GLU cc_start: 0.7059 (tp30) cc_final: 0.6822 (tp30) REVERT: G 277 THR cc_start: 0.7932 (m) cc_final: 0.7524 (p) REVERT: G 286 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7432 (mtpp) REVERT: G 288 HIS cc_start: 0.7727 (m-70) cc_final: 0.7456 (m-70) REVERT: G 319 PHE cc_start: 0.8393 (m-80) cc_final: 0.8187 (m-80) REVERT: G 323 GLU cc_start: 0.6491 (pp20) cc_final: 0.6285 (pp20) REVERT: J 50 HIS cc_start: 0.7859 (m90) cc_final: 0.7569 (m170) REVERT: J 79 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8128 (mtpp) REVERT: J 99 GLU cc_start: 0.7912 (pm20) cc_final: 0.7232 (pm20) REVERT: J 105 LYS cc_start: 0.8511 (mttt) cc_final: 0.7915 (mtpt) REVERT: J 179 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7467 (tm-30) REVERT: J 196 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7291 (mm-40) REVERT: J 204 GLN cc_start: 0.7259 (mt0) cc_final: 0.7026 (mt0) REVERT: J 217 THR cc_start: 0.8296 (p) cc_final: 0.7988 (t) REVERT: J 218 ASN cc_start: 0.8056 (t0) cc_final: 0.7793 (t0) REVERT: J 219 LEU cc_start: 0.8613 (tp) cc_final: 0.8208 (tt) REVERT: J 312 PHE cc_start: 0.7703 (m-10) cc_final: 0.7219 (m-10) REVERT: J 333 PRO cc_start: 0.8650 (Cg_exo) cc_final: 0.8358 (Cg_endo) REVERT: J 340 LYS cc_start: 0.7579 (ttpt) cc_final: 0.7025 (ttpt) REVERT: J 354 ILE cc_start: 0.8011 (mt) cc_final: 0.7801 (mt) REVERT: J 355 HIS cc_start: 0.7157 (m-70) cc_final: 0.6424 (m170) REVERT: J 361 ILE cc_start: 0.8390 (mp) cc_final: 0.8036 (tp) REVERT: J 369 ILE cc_start: 0.7839 (mt) cc_final: 0.7634 (pt) REVERT: J 385 ASP cc_start: 0.7068 (p0) cc_final: 0.6618 (p0) REVERT: K 37 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7472 (mmmm) REVERT: K 94 ASP cc_start: 0.7486 (t0) cc_final: 0.7217 (t0) REVERT: K 167 MET cc_start: 0.7248 (ptp) cc_final: 0.6843 (ptp) REVERT: K 245 LYS cc_start: 0.7589 (ptmt) cc_final: 0.7347 (ptmt) REVERT: K 283 VAL cc_start: 0.8421 (t) cc_final: 0.8081 (p) REVERT: K 313 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6832 (mt-10) REVERT: S 107 ILE cc_start: 0.7973 (mm) cc_final: 0.7660 (mm) REVERT: T 23 CYS cc_start: 0.4813 (t) cc_final: 0.4442 (t) REVERT: T 45 GLN cc_start: 0.7338 (mt0) cc_final: 0.7125 (mt0) REVERT: U 71 LYS cc_start: 0.7670 (ttpp) cc_final: 0.7365 (ttpp) outliers start: 0 outliers final: 0 residues processed: 787 average time/residue: 0.3054 time to fit residues: 371.0128 Evaluate side-chains 673 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 673 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 209 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 242 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 222 GLN A 270 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 121 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN F 43 ASN F 218 ASN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 81 GLN G 121 HIS G 332 ASN J 43 ASN J 100 ASN ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN J 264 ASN ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN K 71 HIS K 96 HIS K 121 HIS K 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27DHIS ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21198 Z= 0.237 Angle : 0.736 15.112 28763 Z= 0.420 Chirality : 0.046 0.205 3220 Planarity : 0.005 0.049 3703 Dihedral : 6.492 40.203 2695 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.57 % Rotamer: Outliers : 2.52 % Allowed : 9.47 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % 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: -3.45 (0.14), residues: 2677 helix: -0.67 (0.95), residues: 27 sheet: -1.50 (0.15), residues: 1070 loop : -3.03 (0.13), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 103 HIS 0.007 0.001 HIS J 381 PHE 0.045 0.002 PHE J 398 TYR 0.019 0.002 TYR G 44 ARG 0.000 0.000 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 699 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7587 (mtpp) REVERT: A 75 ASP cc_start: 0.7921 (t0) cc_final: 0.7369 (t0) REVERT: A 76 GLU cc_start: 0.6866 (tp30) cc_final: 0.6486 (tp30) REVERT: A 99 GLU cc_start: 0.8176 (pm20) cc_final: 0.7641 (pm20) REVERT: A 100 ASN cc_start: 0.8103 (m-40) cc_final: 0.7820 (m-40) REVERT: A 105 LYS cc_start: 0.8355 (mttt) cc_final: 0.7893 (mtpt) REVERT: A 137 VAL cc_start: 0.8395 (t) cc_final: 0.8087 (p) REVERT: A 153 PRO cc_start: 0.8582 (Cg_endo) cc_final: 0.8307 (Cg_exo) REVERT: A 173 PHE cc_start: 0.7510 (m-80) cc_final: 0.7294 (m-80) REVERT: A 183 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6688 (mt-10) REVERT: A 225 LYS cc_start: 0.7204 (ttpp) cc_final: 0.6799 (ttmm) REVERT: A 311 ASP cc_start: 0.6560 (p0) cc_final: 0.6333 (p0) REVERT: A 331 HIS cc_start: 0.7336 (t-90) cc_final: 0.7095 (t-90) REVERT: A 357 SER cc_start: 0.8489 (t) cc_final: 0.8158 (p) REVERT: A 385 ASP cc_start: 0.6392 (p0) cc_final: 0.5900 (p0) REVERT: B 37 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7867 (mmtp) REVERT: B 74 ILE cc_start: 0.8533 (mm) cc_final: 0.8282 (mt) REVERT: B 286 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7519 (mtpp) REVERT: B 293 THR cc_start: 0.8160 (m) cc_final: 0.7583 (p) REVERT: B 319 PHE cc_start: 0.8538 (m-80) cc_final: 0.8315 (m-80) REVERT: B 332 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8136 (m-40) REVERT: F 37 LYS cc_start: 0.8273 (mttt) cc_final: 0.7984 (mttt) REVERT: F 42 VAL cc_start: 0.8491 (t) cc_final: 0.8267 (p) REVERT: F 52 LYS cc_start: 0.8176 (tttt) cc_final: 0.7705 (ttpp) REVERT: F 76 GLU cc_start: 0.7221 (tp30) cc_final: 0.6870 (tp30) REVERT: F 105 LYS cc_start: 0.8506 (mttt) cc_final: 0.7760 (mtpt) REVERT: F 123 LYS cc_start: 0.8394 (mttt) cc_final: 0.8131 (mmtp) REVERT: F 204 GLN cc_start: 0.7624 (mt0) cc_final: 0.7311 (mt0) REVERT: F 216 ASN cc_start: 0.7578 (t0) cc_final: 0.7354 (t0) REVERT: F 225 LYS cc_start: 0.7933 (tttt) cc_final: 0.7594 (ttpp) REVERT: F 312 PHE cc_start: 0.6846 (m-10) cc_final: 0.6212 (m-10) REVERT: F 324 LYS cc_start: 0.7423 (tppt) cc_final: 0.7153 (tppt) REVERT: F 338 THR cc_start: 0.7700 (m) cc_final: 0.7467 (p) REVERT: F 340 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7772 (ttmm) REVERT: F 360 ASN cc_start: 0.7004 (m110) cc_final: 0.6286 (m-40) REVERT: G 37 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7967 (mmtp) REVERT: G 86 THR cc_start: 0.7767 (p) cc_final: 0.7404 (m) REVERT: G 144 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6673 (mm-30) REVERT: G 167 MET cc_start: 0.7230 (ptp) cc_final: 0.6883 (ptp) REVERT: G 239 ASN cc_start: 0.7939 (m-40) cc_final: 0.7738 (m-40) REVERT: G 242 LYS cc_start: 0.8198 (mttm) cc_final: 0.7971 (mttt) REVERT: G 252 LYS cc_start: 0.7868 (mppt) cc_final: 0.7157 (mmtm) REVERT: G 255 LEU cc_start: 0.7911 (pp) cc_final: 0.7451 (pt) REVERT: G 273 GLU cc_start: 0.7031 (tp30) cc_final: 0.6794 (tp30) REVERT: G 277 THR cc_start: 0.8035 (m) cc_final: 0.7629 (p) REVERT: G 286 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7463 (mtpp) REVERT: G 323 GLU cc_start: 0.6753 (pp20) cc_final: 0.6316 (pp20) REVERT: H 11 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6825 (pp) REVERT: J 66 GLN cc_start: 0.7680 (mt0) cc_final: 0.7465 (mt0) REVERT: J 99 GLU cc_start: 0.8121 (pm20) cc_final: 0.7350 (pm20) REVERT: J 105 LYS cc_start: 0.8333 (mttt) cc_final: 0.7781 (mtmt) REVERT: J 160 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7181 (ttpp) REVERT: J 204 GLN cc_start: 0.7196 (mt0) cc_final: 0.6972 (mt0) REVERT: J 217 THR cc_start: 0.8348 (p) cc_final: 0.7985 (t) REVERT: J 218 ASN cc_start: 0.8194 (t0) cc_final: 0.7943 (t0) REVERT: J 219 LEU cc_start: 0.8499 (tp) cc_final: 0.8274 (tt) REVERT: J 312 PHE cc_start: 0.7658 (m-10) cc_final: 0.7173 (m-10) REVERT: J 339 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8200 (mm) REVERT: J 340 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7389 (ttmm) REVERT: J 355 HIS cc_start: 0.7049 (m-70) cc_final: 0.6582 (m-70) REVERT: J 361 ILE cc_start: 0.8372 (mp) cc_final: 0.7982 (tp) REVERT: J 365 PHE cc_start: 0.8330 (p90) cc_final: 0.8013 (p90) REVERT: J 385 ASP cc_start: 0.6957 (p0) cc_final: 0.6606 (p0) REVERT: K 37 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7372 (tppt) REVERT: K 39 ASP cc_start: 0.7040 (m-30) cc_final: 0.6806 (m-30) REVERT: K 84 LEU cc_start: 0.7954 (pt) cc_final: 0.7580 (pp) REVERT: K 94 ASP cc_start: 0.7449 (t0) cc_final: 0.7191 (t0) REVERT: K 245 LYS cc_start: 0.7719 (ptmt) cc_final: 0.7437 (ptmt) REVERT: K 252 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7514 (mmtm) REVERT: K 283 VAL cc_start: 0.8502 (t) cc_final: 0.8223 (p) REVERT: S 107 ILE cc_start: 0.7991 (mm) cc_final: 0.7688 (mm) REVERT: U 71 LYS cc_start: 0.7590 (ttpp) cc_final: 0.7320 (ttpp) outliers start: 58 outliers final: 33 residues processed: 720 average time/residue: 0.2982 time to fit residues: 335.2221 Evaluate side-chains 696 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 660 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 82 optimal weight: 0.0170 chunk 194 optimal weight: 2.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 222 GLN A 355 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN F 218 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 ASN F 386 HIS ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 381 HIS J 386 HIS J 394 HIS L 34 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 ASN ** U 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21198 Z= 0.349 Angle : 0.762 18.817 28763 Z= 0.433 Chirality : 0.047 0.194 3220 Planarity : 0.005 0.051 3703 Dihedral : 6.500 39.731 2695 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.85 % Favored : 90.96 % Rotamer: Outliers : 4.08 % Allowed : 12.42 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -3.02 (0.15), residues: 2677 helix: 0.19 (1.07), residues: 27 sheet: -1.21 (0.15), residues: 1081 loop : -2.75 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP S 103 HIS 0.016 0.002 HIS U 96 PHE 0.027 0.002 PHE A 365 TYR 0.020 0.002 TYR B 15 ARG 0.000 0.000 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 681 time to evaluate : 2.323 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: A 35 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7401 (mtpp) REVERT: A 75 ASP cc_start: 0.8013 (t0) cc_final: 0.7784 (t70) REVERT: A 76 GLU cc_start: 0.6908 (tp30) cc_final: 0.6562 (tp30) REVERT: A 99 GLU cc_start: 0.8256 (pm20) cc_final: 0.7793 (pm20) REVERT: A 105 LYS cc_start: 0.8328 (mttt) cc_final: 0.7891 (mtpt) REVERT: A 137 VAL cc_start: 0.8466 (t) cc_final: 0.8205 (p) REVERT: A 148 VAL cc_start: 0.7545 (m) cc_final: 0.7210 (p) REVERT: A 153 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8302 (Cg_exo) REVERT: A 183 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6631 (mt-10) REVERT: A 225 LYS cc_start: 0.7413 (ttpp) cc_final: 0.7046 (ttmm) REVERT: A 269 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 300 GLU cc_start: 0.6270 (tm-30) cc_final: 0.6061 (tm-30) REVERT: A 311 ASP cc_start: 0.6742 (p0) cc_final: 0.6517 (p0) REVERT: A 331 HIS cc_start: 0.7514 (t-90) cc_final: 0.7233 (t-90) REVERT: A 357 SER cc_start: 0.8482 (t) cc_final: 0.8165 (p) REVERT: A 358 THR cc_start: 0.8499 (t) cc_final: 0.8258 (t) REVERT: A 369 ILE cc_start: 0.8482 (mp) cc_final: 0.8206 (mm) REVERT: A 385 ASP cc_start: 0.6657 (p0) cc_final: 0.6033 (p0) REVERT: A 390 HIS cc_start: 0.7219 (p90) cc_final: 0.6869 (p90) REVERT: B 37 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7828 (mmtp) REVERT: B 245 LYS cc_start: 0.7293 (ttpt) cc_final: 0.7035 (ttpt) REVERT: B 286 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7567 (mtpp) REVERT: B 319 PHE cc_start: 0.8562 (m-80) cc_final: 0.8265 (m-80) REVERT: F 52 LYS cc_start: 0.8388 (tttt) cc_final: 0.7932 (ttpp) REVERT: F 76 GLU cc_start: 0.7327 (tp30) cc_final: 0.6946 (tp30) REVERT: F 99 GLU cc_start: 0.8373 (pm20) cc_final: 0.7927 (pm20) REVERT: F 105 LYS cc_start: 0.8395 (mttt) cc_final: 0.7836 (mtpt) REVERT: F 133 LEU cc_start: 0.8002 (mt) cc_final: 0.7719 (mm) REVERT: F 204 GLN cc_start: 0.7607 (mt0) cc_final: 0.7407 (mt0) REVERT: F 216 ASN cc_start: 0.7731 (t0) cc_final: 0.7354 (t0) REVERT: F 225 LYS cc_start: 0.7994 (tttt) cc_final: 0.7629 (tttp) REVERT: F 241 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6636 (mm-30) REVERT: F 270 ASN cc_start: 0.8141 (m-40) cc_final: 0.7827 (m-40) REVERT: F 317 THR cc_start: 0.7692 (m) cc_final: 0.7413 (p) REVERT: F 324 LYS cc_start: 0.7444 (tppt) cc_final: 0.7130 (tppt) REVERT: F 338 THR cc_start: 0.7926 (m) cc_final: 0.7693 (p) REVERT: F 340 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7807 (ttmm) REVERT: G 37 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8005 (tppt) REVERT: G 167 MET cc_start: 0.7277 (ptp) cc_final: 0.6890 (ptp) REVERT: G 252 LYS cc_start: 0.8046 (mppt) cc_final: 0.7326 (mmtm) REVERT: G 255 LEU cc_start: 0.8029 (pp) cc_final: 0.7621 (pt) REVERT: G 273 GLU cc_start: 0.7299 (tp30) cc_final: 0.7082 (tp30) REVERT: G 277 THR cc_start: 0.8078 (m) cc_final: 0.7580 (p) REVERT: G 323 GLU cc_start: 0.7131 (pp20) cc_final: 0.6802 (pp20) REVERT: J 99 GLU cc_start: 0.8275 (pm20) cc_final: 0.7425 (pm20) REVERT: J 105 LYS cc_start: 0.8367 (mttt) cc_final: 0.7803 (mtmt) REVERT: J 125 HIS cc_start: 0.7197 (p90) cc_final: 0.6965 (p-80) REVERT: J 204 GLN cc_start: 0.7359 (mt0) cc_final: 0.7073 (mt0) REVERT: J 217 THR cc_start: 0.8446 (p) cc_final: 0.8060 (t) REVERT: J 218 ASN cc_start: 0.8288 (t0) cc_final: 0.8052 (t0) REVERT: J 241 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6875 (mm-30) REVERT: J 242 GLN cc_start: 0.8358 (tp40) cc_final: 0.8148 (tp40) REVERT: J 311 ASP cc_start: 0.7539 (t0) cc_final: 0.7114 (t0) REVERT: J 338 THR cc_start: 0.7845 (m) cc_final: 0.7487 (p) REVERT: J 340 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7450 (ttmm) REVERT: J 355 HIS cc_start: 0.7113 (m-70) cc_final: 0.6589 (m-70) REVERT: J 357 SER cc_start: 0.8428 (t) cc_final: 0.7957 (t) REVERT: J 365 PHE cc_start: 0.8278 (p90) cc_final: 0.8017 (p90) REVERT: J 385 ASP cc_start: 0.7043 (p0) cc_final: 0.6630 (p0) REVERT: K 37 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7271 (tppt) REVERT: K 50 SER cc_start: 0.7603 (p) cc_final: 0.7243 (p) REVERT: K 84 LEU cc_start: 0.8114 (pt) cc_final: 0.7842 (pp) REVERT: K 137 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6930 (mt-10) REVERT: K 245 LYS cc_start: 0.7764 (ptmt) cc_final: 0.7474 (ptmt) REVERT: K 252 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7624 (mmtm) REVERT: K 254 LYS cc_start: 0.7457 (pttt) cc_final: 0.7220 (pptt) REVERT: K 283 VAL cc_start: 0.8524 (t) cc_final: 0.8175 (p) REVERT: K 319 PHE cc_start: 0.8477 (m-80) cc_final: 0.8256 (m-80) REVERT: U 71 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7291 (ttpp) outliers start: 94 outliers final: 57 residues processed: 719 average time/residue: 0.2982 time to fit residues: 334.4303 Evaluate side-chains 717 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 660 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 102 GLN A 130 GLN A 149 ASN A 222 GLN A 270 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS F 16 ASN F 102 GLN F 218 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 216 ASN J 362 HIS J 381 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21198 Z= 0.249 Angle : 0.704 16.938 28763 Z= 0.402 Chirality : 0.045 0.176 3220 Planarity : 0.004 0.046 3703 Dihedral : 6.017 40.462 2695 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 4.04 % Allowed : 14.51 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.15), residues: 2677 helix: 0.71 (1.08), residues: 27 sheet: -0.97 (0.15), residues: 1105 loop : -2.49 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP U 103 HIS 0.017 0.001 HIS U 96 PHE 0.032 0.002 PHE A 365 TYR 0.016 0.001 TYR U 35 ARG 0.000 0.000 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 671 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7695 (mtpp) REVERT: A 75 ASP cc_start: 0.8057 (t0) cc_final: 0.7792 (t70) REVERT: A 76 GLU cc_start: 0.6954 (tp30) cc_final: 0.6477 (tp30) REVERT: A 105 LYS cc_start: 0.8316 (mttt) cc_final: 0.7792 (mtpt) REVERT: A 137 VAL cc_start: 0.8417 (t) cc_final: 0.8167 (p) REVERT: A 143 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7753 (m) REVERT: A 148 VAL cc_start: 0.7381 (m) cc_final: 0.7146 (p) REVERT: A 183 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6566 (mt-10) REVERT: A 225 LYS cc_start: 0.7456 (ttpp) cc_final: 0.7072 (ttmm) REVERT: A 300 GLU cc_start: 0.6239 (tm-30) cc_final: 0.6033 (tm-30) REVERT: A 311 ASP cc_start: 0.6690 (p0) cc_final: 0.6322 (p0) REVERT: A 331 HIS cc_start: 0.7421 (t-90) cc_final: 0.7159 (t-90) REVERT: A 333 PRO cc_start: 0.8756 (Cg_exo) cc_final: 0.8443 (Cg_endo) REVERT: A 385 ASP cc_start: 0.6756 (p0) cc_final: 0.6476 (p0) REVERT: A 390 HIS cc_start: 0.7338 (p90) cc_final: 0.6896 (p90) REVERT: B 37 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7836 (mmtp) REVERT: B 144 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6491 (mm-30) REVERT: B 245 LYS cc_start: 0.7311 (ttpt) cc_final: 0.7067 (ttpt) REVERT: B 286 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7588 (mtpp) REVERT: B 303 GLU cc_start: 0.7706 (tp30) cc_final: 0.7433 (tp30) REVERT: B 313 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6906 (mp0) REVERT: B 319 PHE cc_start: 0.8584 (m-80) cc_final: 0.8356 (m-80) REVERT: B 336 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7829 (mmmm) REVERT: F 20 ASN cc_start: 0.7642 (p0) cc_final: 0.7295 (p0) REVERT: F 52 LYS cc_start: 0.8408 (tttt) cc_final: 0.7944 (ttpp) REVERT: F 76 GLU cc_start: 0.7299 (tp30) cc_final: 0.6910 (tp30) REVERT: F 87 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.5786 (t80) REVERT: F 99 GLU cc_start: 0.8348 (pm20) cc_final: 0.7957 (pm20) REVERT: F 105 LYS cc_start: 0.8383 (mttt) cc_final: 0.7806 (mtpt) REVERT: F 204 GLN cc_start: 0.7650 (mt0) cc_final: 0.7440 (mt0) REVERT: F 216 ASN cc_start: 0.7731 (t0) cc_final: 0.7438 (t0) REVERT: F 225 LYS cc_start: 0.8006 (tttt) cc_final: 0.7700 (tttp) REVERT: F 270 ASN cc_start: 0.7875 (m-40) cc_final: 0.7637 (m-40) REVERT: F 317 THR cc_start: 0.7693 (m) cc_final: 0.7422 (p) REVERT: F 324 LYS cc_start: 0.7462 (tppt) cc_final: 0.7118 (tppt) REVERT: F 338 THR cc_start: 0.7897 (m) cc_final: 0.7647 (p) REVERT: F 340 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7852 (ttmm) REVERT: F 360 ASN cc_start: 0.6807 (m-40) cc_final: 0.6579 (m-40) REVERT: F 392 GLN cc_start: 0.8237 (mt0) cc_final: 0.8004 (mt0) REVERT: G 28 HIS cc_start: 0.6448 (m170) cc_final: 0.6212 (m-70) REVERT: G 37 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7933 (tppt) REVERT: G 167 MET cc_start: 0.7187 (ptp) cc_final: 0.6857 (ptp) REVERT: G 252 LYS cc_start: 0.8103 (mppt) cc_final: 0.7426 (mmtm) REVERT: G 255 LEU cc_start: 0.7886 (pp) cc_final: 0.7418 (pt) REVERT: G 273 GLU cc_start: 0.7323 (tp30) cc_final: 0.7101 (tp30) REVERT: G 277 THR cc_start: 0.8129 (m) cc_final: 0.7539 (p) REVERT: G 323 GLU cc_start: 0.7349 (pp20) cc_final: 0.6484 (pp20) REVERT: J 105 LYS cc_start: 0.8329 (mttt) cc_final: 0.7761 (mtmt) REVERT: J 125 HIS cc_start: 0.7299 (p90) cc_final: 0.7020 (p-80) REVERT: J 160 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7243 (ttpp) REVERT: J 204 GLN cc_start: 0.7372 (mt0) cc_final: 0.7165 (mt0) REVERT: J 217 THR cc_start: 0.8473 (p) cc_final: 0.7962 (t) REVERT: J 218 ASN cc_start: 0.8306 (t0) cc_final: 0.8096 (t0) REVERT: J 241 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6739 (mm-30) REVERT: J 242 GLN cc_start: 0.8360 (tp40) cc_final: 0.7880 (tp-100) REVERT: J 269 GLU cc_start: 0.7229 (mt-10) cc_final: 0.7024 (tt0) REVERT: J 311 ASP cc_start: 0.7482 (t0) cc_final: 0.6925 (t0) REVERT: J 338 THR cc_start: 0.7823 (m) cc_final: 0.7454 (p) REVERT: J 340 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7441 (ttmm) REVERT: J 355 HIS cc_start: 0.7056 (m-70) cc_final: 0.6507 (m-70) REVERT: J 357 SER cc_start: 0.8390 (t) cc_final: 0.7946 (t) REVERT: J 365 PHE cc_start: 0.8291 (p90) cc_final: 0.8088 (p90) REVERT: J 385 ASP cc_start: 0.7117 (p0) cc_final: 0.6673 (p0) REVERT: K 37 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7295 (tppt) REVERT: K 42 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6703 (t70) REVERT: K 50 SER cc_start: 0.7548 (p) cc_final: 0.7238 (p) REVERT: K 84 LEU cc_start: 0.8103 (pt) cc_final: 0.7824 (pp) REVERT: K 239 ASN cc_start: 0.7809 (t0) cc_final: 0.7591 (m110) REVERT: K 245 LYS cc_start: 0.7754 (ptmt) cc_final: 0.7472 (ptmt) REVERT: K 252 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7630 (mmtm) REVERT: K 254 LYS cc_start: 0.7423 (pttt) cc_final: 0.7215 (pptt) REVERT: K 283 VAL cc_start: 0.8495 (t) cc_final: 0.8140 (p) REVERT: S 39 GLN cc_start: 0.7508 (tm-30) cc_final: 0.6621 (tm-30) REVERT: U 71 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7253 (ttpp) REVERT: U 97 PHE cc_start: 0.8377 (t80) cc_final: 0.8139 (t80) outliers start: 93 outliers final: 55 residues processed: 708 average time/residue: 0.3118 time to fit residues: 343.9390 Evaluate side-chains 711 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 653 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 381 HIS Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain K residue 342 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 204 GLN A 222 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS F 16 ASN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN F 218 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 222 GLN J 362 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21198 Z= 0.375 Angle : 0.752 14.788 28763 Z= 0.428 Chirality : 0.047 0.177 3220 Planarity : 0.005 0.068 3703 Dihedral : 6.273 39.719 2695 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.30 % Favored : 90.59 % Rotamer: Outliers : 4.91 % Allowed : 14.90 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.15), residues: 2677 helix: 0.69 (1.06), residues: 27 sheet: -0.88 (0.15), residues: 1114 loop : -2.47 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP U 103 HIS 0.021 0.002 HIS F 394 PHE 0.042 0.002 PHE J 398 TYR 0.021 0.002 TYR B 15 ARG 0.000 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 685 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7479 (mtpp) REVERT: A 75 ASP cc_start: 0.8037 (t0) cc_final: 0.7765 (t70) REVERT: A 99 GLU cc_start: 0.8288 (pm20) cc_final: 0.7901 (pm20) REVERT: A 137 VAL cc_start: 0.8483 (t) cc_final: 0.8217 (p) REVERT: A 143 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7768 (m) REVERT: A 148 VAL cc_start: 0.7670 (m) cc_final: 0.7398 (p) REVERT: A 183 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6570 (mt-10) REVERT: A 203 ILE cc_start: 0.8202 (mm) cc_final: 0.7934 (tp) REVERT: A 208 VAL cc_start: 0.8934 (p) cc_final: 0.8730 (p) REVERT: A 225 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7253 (ttmm) REVERT: A 269 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6812 (mt-10) REVERT: A 311 ASP cc_start: 0.6882 (p0) cc_final: 0.6565 (p0) REVERT: A 331 HIS cc_start: 0.7519 (t-90) cc_final: 0.7258 (t-90) REVERT: A 333 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8438 (Cg_endo) REVERT: A 357 SER cc_start: 0.8430 (t) cc_final: 0.8069 (p) REVERT: A 360 ASN cc_start: 0.7174 (m-40) cc_final: 0.6848 (m-40) REVERT: A 369 ILE cc_start: 0.8425 (mp) cc_final: 0.8138 (mm) REVERT: A 385 ASP cc_start: 0.6912 (p0) cc_final: 0.6645 (p0) REVERT: A 390 HIS cc_start: 0.7704 (p90) cc_final: 0.7194 (p90) REVERT: B 37 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7841 (mmtp) REVERT: B 144 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6563 (mm-30) REVERT: B 245 LYS cc_start: 0.7429 (ttpt) cc_final: 0.7181 (ttpt) REVERT: B 286 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7597 (mtpp) REVERT: B 303 GLU cc_start: 0.7708 (tp30) cc_final: 0.7456 (tp30) REVERT: B 313 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6988 (mp0) REVERT: F 20 ASN cc_start: 0.7666 (p0) cc_final: 0.7349 (p0) REVERT: F 52 LYS cc_start: 0.8392 (tttt) cc_final: 0.7943 (ttpp) REVERT: F 76 GLU cc_start: 0.7243 (tp30) cc_final: 0.6881 (tp30) REVERT: F 99 GLU cc_start: 0.8565 (pm20) cc_final: 0.8030 (pm20) REVERT: F 105 LYS cc_start: 0.8394 (mttt) cc_final: 0.7893 (mtpt) REVERT: F 204 GLN cc_start: 0.7652 (mt0) cc_final: 0.7425 (mt0) REVERT: F 216 ASN cc_start: 0.7826 (t0) cc_final: 0.7380 (t0) REVERT: F 225 LYS cc_start: 0.8029 (tttt) cc_final: 0.7738 (tttp) REVERT: F 241 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6694 (mm-30) REVERT: F 324 LYS cc_start: 0.7504 (tppt) cc_final: 0.7167 (tppt) REVERT: F 338 THR cc_start: 0.7918 (m) cc_final: 0.7680 (p) REVERT: F 340 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7790 (ttmm) REVERT: F 360 ASN cc_start: 0.7135 (m-40) cc_final: 0.6716 (m-40) REVERT: F 365 PHE cc_start: 0.8221 (p90) cc_final: 0.7979 (p90) REVERT: G 37 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7896 (mmtp) REVERT: G 111 THR cc_start: 0.8390 (m) cc_final: 0.7804 (p) REVERT: G 167 MET cc_start: 0.7147 (ptp) cc_final: 0.6871 (ptp) REVERT: G 252 LYS cc_start: 0.8095 (mppt) cc_final: 0.7376 (mmtm) REVERT: G 255 LEU cc_start: 0.7980 (pp) cc_final: 0.7337 (pt) REVERT: G 273 GLU cc_start: 0.7403 (tp30) cc_final: 0.7186 (tp30) REVERT: G 277 THR cc_start: 0.8106 (m) cc_final: 0.7497 (p) REVERT: G 323 GLU cc_start: 0.7424 (pp20) cc_final: 0.6760 (pp20) REVERT: J 42 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8187 (p) REVERT: J 99 GLU cc_start: 0.8405 (pm20) cc_final: 0.8126 (pm20) REVERT: J 105 LYS cc_start: 0.8253 (mttt) cc_final: 0.7765 (mtmt) REVERT: J 160 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7466 (ttpp) REVERT: J 204 GLN cc_start: 0.7432 (mt0) cc_final: 0.7186 (mt0) REVERT: J 218 ASN cc_start: 0.8357 (t0) cc_final: 0.8069 (t0) REVERT: J 242 GLN cc_start: 0.8460 (tp40) cc_final: 0.7963 (tp-100) REVERT: J 311 ASP cc_start: 0.7542 (t0) cc_final: 0.7009 (t0) REVERT: J 338 THR cc_start: 0.7861 (m) cc_final: 0.7483 (p) REVERT: J 340 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7415 (ttmm) REVERT: J 357 SER cc_start: 0.8406 (t) cc_final: 0.7937 (t) REVERT: J 385 ASP cc_start: 0.7161 (p0) cc_final: 0.6725 (p0) REVERT: J 387 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7813 (mt) REVERT: K 37 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7368 (tppt) REVERT: K 42 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6784 (t70) REVERT: K 50 SER cc_start: 0.7705 (p) cc_final: 0.7338 (p) REVERT: K 84 LEU cc_start: 0.8185 (pt) cc_final: 0.7941 (pp) REVERT: K 239 ASN cc_start: 0.7826 (t0) cc_final: 0.7549 (m110) REVERT: K 245 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7430 (ptmt) REVERT: K 252 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7518 (mmtm) REVERT: K 254 LYS cc_start: 0.7451 (pttt) cc_final: 0.7219 (pptt) REVERT: K 283 VAL cc_start: 0.8517 (t) cc_final: 0.8212 (p) REVERT: T 11 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6808 (tt) REVERT: U 71 LYS cc_start: 0.7612 (ttpp) cc_final: 0.7271 (ttpp) outliers start: 113 outliers final: 85 residues processed: 732 average time/residue: 0.3019 time to fit residues: 344.1824 Evaluate side-chains 762 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 672 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 381 HIS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 3.9990 chunk 232 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN F 218 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 GLN G 81 GLN H 76 ASN J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 381 HIS K 80 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21198 Z= 0.375 Angle : 0.762 21.355 28763 Z= 0.430 Chirality : 0.047 0.199 3220 Planarity : 0.005 0.055 3703 Dihedral : 6.365 41.014 2695 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.15 % Favored : 90.74 % Rotamer: Outliers : 5.43 % Allowed : 15.64 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.15), residues: 2677 helix: 0.62 (1.03), residues: 27 sheet: -0.81 (0.15), residues: 1082 loop : -2.41 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP U 103 HIS 0.014 0.002 HIS S 96 PHE 0.046 0.002 PHE J 398 TYR 0.021 0.002 TYR B 15 ARG 0.000 0.000 ARG F 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 680 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7732 (mtpp) REVERT: A 75 ASP cc_start: 0.7960 (t0) cc_final: 0.7640 (t70) REVERT: A 76 GLU cc_start: 0.7077 (tp30) cc_final: 0.6462 (tp30) REVERT: A 99 GLU cc_start: 0.8271 (pm20) cc_final: 0.7868 (pm20) REVERT: A 105 LYS cc_start: 0.8299 (mttt) cc_final: 0.7810 (mtpt) REVERT: A 137 VAL cc_start: 0.8485 (t) cc_final: 0.8220 (p) REVERT: A 143 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7750 (m) REVERT: A 148 VAL cc_start: 0.7685 (m) cc_final: 0.7429 (p) REVERT: A 153 PRO cc_start: 0.8591 (Cg_endo) cc_final: 0.8328 (Cg_exo) REVERT: A 183 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 203 ILE cc_start: 0.8196 (mm) cc_final: 0.7935 (tp) REVERT: A 225 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7223 (ttmm) REVERT: A 311 ASP cc_start: 0.6943 (p0) cc_final: 0.6582 (p0) REVERT: A 331 HIS cc_start: 0.7498 (t-90) cc_final: 0.7233 (t-90) REVERT: A 333 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8447 (Cg_endo) REVERT: A 357 SER cc_start: 0.8412 (t) cc_final: 0.8047 (p) REVERT: A 360 ASN cc_start: 0.7250 (m-40) cc_final: 0.6853 (m-40) REVERT: A 385 ASP cc_start: 0.7025 (p0) cc_final: 0.6590 (p0) REVERT: A 390 HIS cc_start: 0.7920 (p90) cc_final: 0.7537 (p90) REVERT: B 37 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7847 (mmtp) REVERT: B 144 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6587 (mm-30) REVERT: B 286 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7642 (mtpp) REVERT: B 303 GLU cc_start: 0.7631 (tp30) cc_final: 0.7413 (tp30) REVERT: B 313 GLU cc_start: 0.7215 (mt-10) cc_final: 0.7009 (mp0) REVERT: F 20 ASN cc_start: 0.7685 (p0) cc_final: 0.7371 (p0) REVERT: F 31 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7652 (mm) REVERT: F 52 LYS cc_start: 0.8390 (tttt) cc_final: 0.7915 (ttpp) REVERT: F 76 GLU cc_start: 0.7248 (tp30) cc_final: 0.6887 (tp30) REVERT: F 99 GLU cc_start: 0.8513 (pm20) cc_final: 0.7998 (pm20) REVERT: F 105 LYS cc_start: 0.8396 (mttt) cc_final: 0.7914 (mtpt) REVERT: F 204 GLN cc_start: 0.7647 (mt0) cc_final: 0.7414 (mt0) REVERT: F 216 ASN cc_start: 0.7809 (t0) cc_final: 0.7531 (t0) REVERT: F 241 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6723 (mm-30) REVERT: F 324 LYS cc_start: 0.7542 (tppt) cc_final: 0.7204 (tppt) REVERT: F 338 THR cc_start: 0.7899 (m) cc_final: 0.7659 (p) REVERT: F 340 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7729 (ttmm) REVERT: F 360 ASN cc_start: 0.7160 (m-40) cc_final: 0.6682 (m-40) REVERT: F 365 PHE cc_start: 0.8295 (p90) cc_final: 0.8020 (p90) REVERT: G 37 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7945 (mmtp) REVERT: G 111 THR cc_start: 0.8433 (m) cc_final: 0.7817 (p) REVERT: G 167 MET cc_start: 0.7033 (ptp) cc_final: 0.6829 (ptp) REVERT: G 252 LYS cc_start: 0.8150 (mppt) cc_final: 0.7410 (mmtm) REVERT: G 255 LEU cc_start: 0.7817 (pp) cc_final: 0.7146 (pt) REVERT: G 273 GLU cc_start: 0.7478 (tp30) cc_final: 0.7215 (tp30) REVERT: G 323 GLU cc_start: 0.7466 (pp20) cc_final: 0.6744 (pp20) REVERT: J 42 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8240 (p) REVERT: J 99 GLU cc_start: 0.8398 (pm20) cc_final: 0.8112 (pm20) REVERT: J 105 LYS cc_start: 0.8224 (mttt) cc_final: 0.7766 (mtmt) REVERT: J 160 LYS cc_start: 0.7766 (ttpp) cc_final: 0.7445 (ttpp) REVERT: J 204 GLN cc_start: 0.7474 (mt0) cc_final: 0.7255 (mt0) REVERT: J 218 ASN cc_start: 0.8369 (t0) cc_final: 0.8122 (t0) REVERT: J 242 GLN cc_start: 0.8462 (tp40) cc_final: 0.8060 (tp-100) REVERT: J 244 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7736 (ttmm) REVERT: J 245 LYS cc_start: 0.8189 (ptpp) cc_final: 0.7818 (ptpp) REVERT: J 311 ASP cc_start: 0.7604 (t0) cc_final: 0.7049 (t0) REVERT: J 338 THR cc_start: 0.7951 (m) cc_final: 0.7523 (p) REVERT: J 340 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7404 (ttmm) REVERT: J 357 SER cc_start: 0.8358 (t) cc_final: 0.7913 (t) REVERT: J 385 ASP cc_start: 0.7267 (p0) cc_final: 0.6835 (p0) REVERT: J 387 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7771 (mt) REVERT: K 37 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7404 (tppt) REVERT: K 42 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6755 (t70) REVERT: K 50 SER cc_start: 0.7706 (p) cc_final: 0.7330 (p) REVERT: K 84 LEU cc_start: 0.8189 (pt) cc_final: 0.7944 (pp) REVERT: K 130 LYS cc_start: 0.8286 (ptpp) cc_final: 0.7911 (mtmm) REVERT: K 144 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6654 (mm-30) REVERT: K 245 LYS cc_start: 0.7740 (ptmt) cc_final: 0.7409 (ptmt) REVERT: K 252 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7528 (mmtm) REVERT: K 283 VAL cc_start: 0.8535 (t) cc_final: 0.8248 (p) REVERT: T 11 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6898 (tt) REVERT: U 71 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7203 (ttpp) outliers start: 125 outliers final: 95 residues processed: 736 average time/residue: 0.3158 time to fit residues: 366.9935 Evaluate side-chains 753 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 652 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 381 HIS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 217 optimal weight: 0.0980 chunk 144 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 204 GLN A 222 GLN B 81 GLN B 121 HIS F 16 ASN F 50 HIS F 102 GLN F 222 GLN G 81 GLN G 239 ASN J 16 ASN J 50 HIS ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 381 HIS ** J 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21198 Z= 0.265 Angle : 0.710 20.494 28763 Z= 0.405 Chirality : 0.045 0.188 3220 Planarity : 0.005 0.055 3703 Dihedral : 6.060 40.188 2695 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.14 % Favored : 91.78 % Rotamer: Outliers : 4.78 % Allowed : 16.81 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2677 helix: 1.82 (1.08), residues: 24 sheet: -0.73 (0.15), residues: 1093 loop : -2.25 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 103 HIS 0.015 0.001 HIS S 96 PHE 0.044 0.002 PHE J 398 TYR 0.016 0.001 TYR U 35 ARG 0.000 0.000 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 659 time to evaluate : 2.488 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 35 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7425 (mtpp) REVERT: A 75 ASP cc_start: 0.8008 (t0) cc_final: 0.7696 (t70) REVERT: A 76 GLU cc_start: 0.7058 (tp30) cc_final: 0.6344 (tp30) REVERT: A 105 LYS cc_start: 0.8314 (mttt) cc_final: 0.7770 (mtpt) REVERT: A 137 VAL cc_start: 0.8461 (t) cc_final: 0.8182 (p) REVERT: A 143 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (m) REVERT: A 183 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6541 (mt-10) REVERT: A 203 ILE cc_start: 0.8204 (mm) cc_final: 0.7950 (tp) REVERT: A 225 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7148 (ttmm) REVERT: A 269 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6703 (mt-10) REVERT: A 311 ASP cc_start: 0.6926 (p0) cc_final: 0.6594 (p0) REVERT: A 331 HIS cc_start: 0.7436 (t-90) cc_final: 0.7189 (t-90) REVERT: A 333 PRO cc_start: 0.8733 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: A 357 SER cc_start: 0.8429 (t) cc_final: 0.8090 (p) REVERT: A 360 ASN cc_start: 0.7220 (m-40) cc_final: 0.6914 (m-40) REVERT: A 385 ASP cc_start: 0.7068 (p0) cc_final: 0.6841 (p0) REVERT: A 390 HIS cc_start: 0.7961 (p90) cc_final: 0.7620 (p90) REVERT: B 37 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7852 (mmtp) REVERT: B 144 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6690 (mm-30) REVERT: B 286 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7586 (mtpp) REVERT: B 313 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6986 (mp0) REVERT: B 336 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7857 (mmmm) REVERT: F 20 ASN cc_start: 0.7642 (p0) cc_final: 0.7294 (p0) REVERT: F 52 LYS cc_start: 0.8354 (tttt) cc_final: 0.7827 (ttpp) REVERT: F 76 GLU cc_start: 0.7222 (tp30) cc_final: 0.6844 (tp30) REVERT: F 79 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8219 (ttmm) REVERT: F 99 GLU cc_start: 0.8463 (pm20) cc_final: 0.8020 (pm20) REVERT: F 105 LYS cc_start: 0.8411 (mttt) cc_final: 0.8127 (mtpt) REVERT: F 204 GLN cc_start: 0.7659 (mt0) cc_final: 0.7454 (mt0) REVERT: F 216 ASN cc_start: 0.7858 (t0) cc_final: 0.7635 (t0) REVERT: F 324 LYS cc_start: 0.7538 (tppt) cc_final: 0.7334 (tppt) REVERT: F 338 THR cc_start: 0.7892 (m) cc_final: 0.7642 (p) REVERT: F 340 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7723 (ttmm) REVERT: F 360 ASN cc_start: 0.7139 (m-40) cc_final: 0.6684 (m-40) REVERT: F 365 PHE cc_start: 0.8288 (p90) cc_final: 0.7992 (p90) REVERT: G 37 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7878 (tppt) REVERT: G 111 THR cc_start: 0.8448 (m) cc_final: 0.7825 (p) REVERT: G 252 LYS cc_start: 0.8114 (mppt) cc_final: 0.7368 (mmtm) REVERT: G 273 GLU cc_start: 0.7449 (tp30) cc_final: 0.7206 (tp30) REVERT: G 305 HIS cc_start: 0.7475 (m-70) cc_final: 0.6995 (m-70) REVERT: G 323 GLU cc_start: 0.7458 (pp20) cc_final: 0.6716 (pp20) REVERT: J 42 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8258 (p) REVERT: J 45 GLU cc_start: 0.7167 (tp30) cc_final: 0.6787 (mp0) REVERT: J 52 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7509 (mtpt) REVERT: J 99 GLU cc_start: 0.8418 (pm20) cc_final: 0.7695 (pm20) REVERT: J 105 LYS cc_start: 0.8204 (mttt) cc_final: 0.7726 (mtmt) REVERT: J 160 LYS cc_start: 0.7752 (ttpp) cc_final: 0.7431 (ttpp) REVERT: J 218 ASN cc_start: 0.8372 (t0) cc_final: 0.8120 (t0) REVERT: J 241 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: J 242 GLN cc_start: 0.8427 (tp40) cc_final: 0.7983 (tp-100) REVERT: J 311 ASP cc_start: 0.7609 (t0) cc_final: 0.7038 (t0) REVERT: J 338 THR cc_start: 0.7917 (m) cc_final: 0.7465 (p) REVERT: J 340 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7390 (ttmm) REVERT: J 357 SER cc_start: 0.8311 (t) cc_final: 0.7869 (t) REVERT: J 385 ASP cc_start: 0.7262 (p0) cc_final: 0.6826 (p0) REVERT: J 387 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7647 (mt) REVERT: K 37 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7421 (tppt) REVERT: K 42 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6686 (t70) REVERT: K 50 SER cc_start: 0.7683 (p) cc_final: 0.7335 (p) REVERT: K 84 LEU cc_start: 0.8184 (pt) cc_final: 0.7942 (pp) REVERT: K 130 LYS cc_start: 0.8237 (ptpp) cc_final: 0.7984 (mtmm) REVERT: K 144 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6690 (mm-30) REVERT: K 245 LYS cc_start: 0.7758 (ptmt) cc_final: 0.7430 (ptmt) REVERT: K 252 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7537 (mmtm) REVERT: K 283 VAL cc_start: 0.8511 (t) cc_final: 0.8216 (p) REVERT: T 11 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6863 (tt) REVERT: U 71 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7217 (ttpp) REVERT: V 23 CYS cc_start: 0.4775 (t) cc_final: 0.3851 (t) outliers start: 110 outliers final: 83 residues processed: 702 average time/residue: 0.2965 time to fit residues: 327.0603 Evaluate side-chains 747 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 658 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 96 HIS Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 202 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 102 GLN A 149 ASN A 222 GLN A 360 ASN B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 381 HIS ** J 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21198 Z= 0.236 Angle : 0.693 16.722 28763 Z= 0.397 Chirality : 0.045 0.184 3220 Planarity : 0.005 0.052 3703 Dihedral : 5.835 39.751 2695 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.40 % Favored : 92.53 % Rotamer: Outliers : 5.08 % Allowed : 16.85 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2677 helix: 2.03 (1.09), residues: 24 sheet: -0.50 (0.16), residues: 1072 loop : -2.18 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP U 103 HIS 0.015 0.001 HIS S 96 PHE 0.053 0.002 PHE J 398 TYR 0.015 0.001 TYR U 35 ARG 0.000 0.000 ARG V 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 663 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7416 (mtpp) REVERT: A 52 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: A 105 LYS cc_start: 0.8321 (mttt) cc_final: 0.7578 (ttmm) REVERT: A 137 VAL cc_start: 0.8349 (t) cc_final: 0.8094 (p) REVERT: A 143 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7713 (m) REVERT: A 203 ILE cc_start: 0.8205 (mm) cc_final: 0.7937 (tp) REVERT: A 225 LYS cc_start: 0.7634 (ttpp) cc_final: 0.7166 (ttmm) REVERT: A 269 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 311 ASP cc_start: 0.6896 (p0) cc_final: 0.6588 (p0) REVERT: A 331 HIS cc_start: 0.7438 (t-90) cc_final: 0.7209 (t-90) REVERT: A 333 PRO cc_start: 0.8713 (Cg_exo) cc_final: 0.8420 (Cg_endo) REVERT: A 357 SER cc_start: 0.8434 (t) cc_final: 0.8091 (p) REVERT: A 385 ASP cc_start: 0.7084 (p0) cc_final: 0.6854 (p0) REVERT: A 390 HIS cc_start: 0.7981 (p90) cc_final: 0.7696 (p90) REVERT: B 37 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7845 (mmtp) REVERT: B 144 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6718 (mm-30) REVERT: B 245 LYS cc_start: 0.7486 (ttpt) cc_final: 0.7211 (ttpt) REVERT: B 286 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7595 (mtpp) REVERT: B 313 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7005 (mp0) REVERT: F 20 ASN cc_start: 0.7647 (p0) cc_final: 0.7395 (p0) REVERT: F 31 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7545 (mm) REVERT: F 52 LYS cc_start: 0.8346 (tttt) cc_final: 0.7893 (ttpp) REVERT: F 76 GLU cc_start: 0.7217 (tp30) cc_final: 0.6683 (tp30) REVERT: F 98 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7374 (m) REVERT: F 99 GLU cc_start: 0.8348 (pm20) cc_final: 0.8010 (pm20) REVERT: F 105 LYS cc_start: 0.8504 (mttt) cc_final: 0.8111 (mtpt) REVERT: F 204 GLN cc_start: 0.7673 (mt0) cc_final: 0.7456 (mt0) REVERT: F 216 ASN cc_start: 0.7883 (t0) cc_final: 0.7541 (t0) REVERT: F 217 THR cc_start: 0.8564 (p) cc_final: 0.8216 (t) REVERT: F 338 THR cc_start: 0.7834 (m) cc_final: 0.7593 (p) REVERT: F 340 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7693 (ttmm) REVERT: F 360 ASN cc_start: 0.7096 (m-40) cc_final: 0.6667 (m-40) REVERT: F 365 PHE cc_start: 0.8285 (p90) cc_final: 0.7997 (p90) REVERT: G 28 HIS cc_start: 0.6284 (m170) cc_final: 0.6017 (m-70) REVERT: G 37 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7915 (tppt) REVERT: G 252 LYS cc_start: 0.8026 (mppt) cc_final: 0.7339 (mmtm) REVERT: G 273 GLU cc_start: 0.7444 (tp30) cc_final: 0.7243 (tp30) REVERT: G 305 HIS cc_start: 0.7448 (m-70) cc_final: 0.7049 (m-70) REVERT: G 323 GLU cc_start: 0.7471 (pp20) cc_final: 0.6724 (pp20) REVERT: G 336 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7732 (tttm) REVERT: J 42 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8258 (p) REVERT: J 45 GLU cc_start: 0.7164 (tp30) cc_final: 0.6786 (mp0) REVERT: J 52 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7755 (mtpt) REVERT: J 99 GLU cc_start: 0.8427 (pm20) cc_final: 0.7693 (pm20) REVERT: J 105 LYS cc_start: 0.8213 (mttt) cc_final: 0.7723 (mtmt) REVERT: J 160 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7505 (ttpp) REVERT: J 218 ASN cc_start: 0.8361 (t0) cc_final: 0.8107 (t0) REVERT: J 241 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: J 242 GLN cc_start: 0.8414 (tp40) cc_final: 0.7899 (tp-100) REVERT: J 311 ASP cc_start: 0.7613 (t0) cc_final: 0.7063 (t0) REVERT: J 338 THR cc_start: 0.7906 (m) cc_final: 0.7444 (p) REVERT: J 340 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7356 (ttmm) REVERT: J 357 SER cc_start: 0.8346 (t) cc_final: 0.7864 (t) REVERT: J 385 ASP cc_start: 0.7275 (p0) cc_final: 0.6842 (p0) REVERT: K 37 LYS cc_start: 0.7711 (mmmt) cc_final: 0.7354 (tppt) REVERT: K 42 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6603 (t70) REVERT: K 50 SER cc_start: 0.7707 (p) cc_final: 0.7368 (p) REVERT: K 84 LEU cc_start: 0.8165 (pt) cc_final: 0.7902 (pp) REVERT: K 130 LYS cc_start: 0.8274 (ptpp) cc_final: 0.7992 (mtmm) REVERT: K 144 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6658 (mm-30) REVERT: K 245 LYS cc_start: 0.7735 (ptmt) cc_final: 0.7433 (ptmt) REVERT: K 252 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7532 (mmtm) REVERT: K 283 VAL cc_start: 0.8511 (t) cc_final: 0.8219 (p) outliers start: 117 outliers final: 90 residues processed: 712 average time/residue: 0.3060 time to fit residues: 340.0371 Evaluate side-chains 754 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 656 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 336 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 96 HIS Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 0.0060 chunk 188 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 270 ASN A 360 ASN B 121 HIS F 16 ASN F 102 GLN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN J 66 GLN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 381 HIS ** J 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21198 Z= 0.308 Angle : 0.731 18.595 28763 Z= 0.414 Chirality : 0.046 0.222 3220 Planarity : 0.005 0.063 3703 Dihedral : 5.999 40.227 2695 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.85 % Rotamer: Outliers : 4.91 % Allowed : 17.33 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2677 helix: 2.00 (1.08), residues: 24 sheet: -0.48 (0.16), residues: 1060 loop : -2.16 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP U 103 HIS 0.015 0.001 HIS S 96 PHE 0.049 0.002 PHE J 398 TYR 0.017 0.002 TYR B 15 ARG 0.000 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 665 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7466 (mtpp) REVERT: A 137 VAL cc_start: 0.8315 (t) cc_final: 0.8051 (p) REVERT: A 143 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7735 (m) REVERT: A 183 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6610 (mt-10) REVERT: A 203 ILE cc_start: 0.8222 (mm) cc_final: 0.7958 (tp) REVERT: A 225 LYS cc_start: 0.7752 (ttpp) cc_final: 0.7268 (ttmm) REVERT: A 269 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6731 (mt-10) REVERT: A 311 ASP cc_start: 0.6987 (p0) cc_final: 0.6644 (p0) REVERT: A 331 HIS cc_start: 0.7506 (t-90) cc_final: 0.7267 (t-90) REVERT: A 333 PRO cc_start: 0.8712 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: A 357 SER cc_start: 0.8419 (t) cc_final: 0.8057 (p) REVERT: A 385 ASP cc_start: 0.7138 (p0) cc_final: 0.6908 (p0) REVERT: B 37 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7855 (mmtp) REVERT: B 144 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6683 (mm-30) REVERT: B 245 LYS cc_start: 0.7505 (ttpt) cc_final: 0.7217 (ttpt) REVERT: B 286 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7603 (mtpp) REVERT: B 313 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7029 (mp0) REVERT: F 20 ASN cc_start: 0.7675 (p0) cc_final: 0.7443 (p0) REVERT: F 52 LYS cc_start: 0.8365 (tttt) cc_final: 0.7928 (ttpp) REVERT: F 76 GLU cc_start: 0.7210 (tp30) cc_final: 0.6776 (tp30) REVERT: F 99 GLU cc_start: 0.8413 (pm20) cc_final: 0.8054 (pm20) REVERT: F 105 LYS cc_start: 0.8582 (mttt) cc_final: 0.8090 (mtpt) REVERT: F 204 GLN cc_start: 0.7674 (mt0) cc_final: 0.7443 (mt0) REVERT: F 216 ASN cc_start: 0.7884 (t0) cc_final: 0.7586 (t0) REVERT: F 217 THR cc_start: 0.8683 (p) cc_final: 0.8277 (t) REVERT: F 241 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6557 (mm-30) REVERT: F 338 THR cc_start: 0.7851 (m) cc_final: 0.7596 (p) REVERT: F 340 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7673 (ttmm) REVERT: F 360 ASN cc_start: 0.7204 (m-40) cc_final: 0.6761 (m-40) REVERT: F 365 PHE cc_start: 0.8288 (p90) cc_final: 0.7995 (p90) REVERT: G 37 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7854 (tppt) REVERT: G 252 LYS cc_start: 0.8065 (mppt) cc_final: 0.7387 (mmtm) REVERT: G 254 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7324 (tttm) REVERT: G 273 GLU cc_start: 0.7465 (tp30) cc_final: 0.7257 (tp30) REVERT: G 323 GLU cc_start: 0.7472 (pp20) cc_final: 0.6711 (pp20) REVERT: G 336 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7720 (tttm) REVERT: J 42 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (p) REVERT: J 45 GLU cc_start: 0.7185 (tp30) cc_final: 0.6771 (mp0) REVERT: J 52 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7504 (mtpt) REVERT: J 99 GLU cc_start: 0.8439 (pm20) cc_final: 0.7778 (pm20) REVERT: J 105 LYS cc_start: 0.8194 (mttt) cc_final: 0.7737 (mtmt) REVERT: J 160 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7516 (ttpp) REVERT: J 218 ASN cc_start: 0.8372 (t0) cc_final: 0.8105 (t0) REVERT: J 241 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6607 (tm-30) REVERT: J 242 GLN cc_start: 0.8453 (tp40) cc_final: 0.8128 (tp40) REVERT: J 311 ASP cc_start: 0.7614 (t0) cc_final: 0.7042 (t0) REVERT: J 338 THR cc_start: 0.7969 (m) cc_final: 0.7505 (p) REVERT: J 340 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7329 (ttmm) REVERT: J 357 SER cc_start: 0.8333 (t) cc_final: 0.7874 (t) REVERT: J 385 ASP cc_start: 0.7312 (p0) cc_final: 0.6891 (p0) REVERT: J 387 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7686 (mt) REVERT: K 37 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7398 (tppt) REVERT: K 42 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6705 (t70) REVERT: K 50 SER cc_start: 0.7774 (p) cc_final: 0.7409 (p) REVERT: K 81 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7776 (mm-40) REVERT: K 84 LEU cc_start: 0.8134 (pt) cc_final: 0.7914 (pp) REVERT: K 130 LYS cc_start: 0.8272 (ptpp) cc_final: 0.7971 (mtmm) REVERT: K 144 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6675 (mm-30) REVERT: K 245 LYS cc_start: 0.7743 (ptmt) cc_final: 0.7405 (ptmt) REVERT: K 252 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7552 (mmtm) REVERT: K 283 VAL cc_start: 0.8496 (t) cc_final: 0.8218 (p) REVERT: T 4 MET cc_start: 0.6616 (ptp) cc_final: 0.6109 (ttp) outliers start: 113 outliers final: 99 residues processed: 711 average time/residue: 0.3014 time to fit residues: 333.2034 Evaluate side-chains 770 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 665 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 336 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 381 HIS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain V residue 4 MET Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 270 ASN A 360 ASN B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS ** J 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21198 Z= 0.320 Angle : 0.737 20.114 28763 Z= 0.417 Chirality : 0.046 0.214 3220 Planarity : 0.005 0.056 3703 Dihedral : 6.061 40.507 2695 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.70 % Favored : 91.22 % Rotamer: Outliers : 4.82 % Allowed : 17.38 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2677 helix: 2.05 (1.08), residues: 24 sheet: -0.50 (0.16), residues: 1066 loop : -2.15 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP U 103 HIS 0.015 0.001 HIS S 96 PHE 0.056 0.002 PHE J 398 TYR 0.017 0.002 TYR B 15 ARG 0.000 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 678 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7499 (mtpp) REVERT: A 137 VAL cc_start: 0.8290 (t) cc_final: 0.8028 (p) REVERT: A 143 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7736 (m) REVERT: A 183 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 203 ILE cc_start: 0.8206 (mm) cc_final: 0.7956 (tp) REVERT: A 225 LYS cc_start: 0.7766 (ttpp) cc_final: 0.7273 (ttmm) REVERT: A 269 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6757 (mt-10) REVERT: A 311 ASP cc_start: 0.6881 (p0) cc_final: 0.6604 (p0) REVERT: A 331 HIS cc_start: 0.7509 (t-90) cc_final: 0.7269 (t-90) REVERT: A 333 PRO cc_start: 0.8716 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: A 357 SER cc_start: 0.8409 (t) cc_final: 0.8041 (p) REVERT: B 37 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7856 (mmtp) REVERT: B 144 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 286 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7599 (mtpp) REVERT: B 313 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7006 (mp0) REVERT: F 20 ASN cc_start: 0.7665 (p0) cc_final: 0.7437 (p0) REVERT: F 31 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7480 (mm) REVERT: F 52 LYS cc_start: 0.8358 (tttt) cc_final: 0.7932 (ttpp) REVERT: F 76 GLU cc_start: 0.7212 (tp30) cc_final: 0.6763 (tp30) REVERT: F 99 GLU cc_start: 0.8406 (pm20) cc_final: 0.8032 (pm20) REVERT: F 105 LYS cc_start: 0.8578 (mttt) cc_final: 0.8082 (mtpt) REVERT: F 156 PHE cc_start: 0.7078 (p90) cc_final: 0.6593 (p90) REVERT: F 204 GLN cc_start: 0.7664 (mt0) cc_final: 0.7446 (mt0) REVERT: F 216 ASN cc_start: 0.7888 (t0) cc_final: 0.7594 (t0) REVERT: F 217 THR cc_start: 0.8678 (p) cc_final: 0.8312 (t) REVERT: F 241 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6535 (mm-30) REVERT: F 327 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7522 (ttmm) REVERT: F 338 THR cc_start: 0.7849 (m) cc_final: 0.7583 (p) REVERT: F 340 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7586 (ttmm) REVERT: F 360 ASN cc_start: 0.7157 (m-40) cc_final: 0.6702 (m-40) REVERT: F 365 PHE cc_start: 0.8291 (p90) cc_final: 0.7998 (p90) REVERT: G 37 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7859 (tppt) REVERT: G 252 LYS cc_start: 0.8077 (mppt) cc_final: 0.7394 (mmtm) REVERT: G 273 GLU cc_start: 0.7382 (tp30) cc_final: 0.7150 (tp30) REVERT: G 323 GLU cc_start: 0.7466 (pp20) cc_final: 0.6703 (pp20) REVERT: G 336 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7718 (tttm) REVERT: J 42 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8271 (p) REVERT: J 45 GLU cc_start: 0.7192 (tp30) cc_final: 0.6779 (mp0) REVERT: J 52 LYS cc_start: 0.7795 (ttpt) cc_final: 0.7507 (mtpt) REVERT: J 99 GLU cc_start: 0.8447 (pm20) cc_final: 0.7826 (pm20) REVERT: J 105 LYS cc_start: 0.8163 (mttt) cc_final: 0.7744 (mtmt) REVERT: J 160 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7521 (ttpp) REVERT: J 218 ASN cc_start: 0.8392 (t0) cc_final: 0.8075 (t0) REVERT: J 241 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: J 244 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7756 (ttmm) REVERT: J 269 GLU cc_start: 0.7397 (tt0) cc_final: 0.6936 (tt0) REVERT: J 311 ASP cc_start: 0.7598 (t0) cc_final: 0.7052 (t0) REVERT: J 338 THR cc_start: 0.7979 (m) cc_final: 0.7514 (p) REVERT: J 340 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7352 (ttmm) REVERT: J 357 SER cc_start: 0.8337 (t) cc_final: 0.7887 (t) REVERT: J 385 ASP cc_start: 0.7313 (p0) cc_final: 0.6939 (p0) REVERT: J 387 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8072 (mm) REVERT: K 37 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7412 (tppt) REVERT: K 42 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6723 (t70) REVERT: K 50 SER cc_start: 0.7780 (p) cc_final: 0.7425 (p) REVERT: K 81 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7755 (mm-40) REVERT: K 84 LEU cc_start: 0.8135 (pt) cc_final: 0.7916 (pp) REVERT: K 130 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7968 (mtmm) REVERT: K 144 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6688 (mm-30) REVERT: K 245 LYS cc_start: 0.7751 (ptmt) cc_final: 0.7412 (ptmt) REVERT: K 252 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7543 (mmtm) REVERT: K 283 VAL cc_start: 0.8524 (t) cc_final: 0.8230 (p) REVERT: T 4 MET cc_start: 0.6687 (ptp) cc_final: 0.6213 (ttp) REVERT: U 71 LYS cc_start: 0.7564 (ttpp) cc_final: 0.7202 (ttpp) outliers start: 111 outliers final: 100 residues processed: 724 average time/residue: 0.3072 time to fit residues: 345.2165 Evaluate side-chains 776 residues out of total 2302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 669 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 267 ARG Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 336 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 202 ASP Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain V residue 4 MET Chi-restraints excluded: chain V residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.5980 chunk 225 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 212 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 270 ASN A 360 ASN B 81 GLN B 121 HIS F 16 ASN F 102 GLN F 222 GLN ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN J 20 ASN J 66 GLN J 270 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS ** J 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105412 restraints weight = 33287.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108568 restraints weight = 15660.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110512 restraints weight = 9130.369| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21198 Z= 0.274 Angle : 0.717 17.108 28763 Z= 0.409 Chirality : 0.045 0.188 3220 Planarity : 0.005 0.050 3703 Dihedral : 5.947 40.237 2695 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 4.91 % Allowed : 17.94 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.99 (0.16), residues: 2677 helix: 2.04 (1.08), residues: 24 sheet: -0.46 (0.16), residues: 1066 loop : -2.09 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 103 HIS 0.015 0.001 HIS S 96 PHE 0.055 0.002 PHE J 398 TYR 0.015 0.001 TYR H 35 ARG 0.000 0.000 ARG V 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5737.50 seconds wall clock time: 103 minutes 51.71 seconds (6231.71 seconds total)