Starting phenix.real_space_refine on Sun Aug 24 14:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eev_28060/08_2025/8eev_28060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eev_28060/08_2025/8eev_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/cci-nas-00/data/ceres_data/8eev_28060/08_2025/8eev_28060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eev_28060/08_2025/8eev_28060.map" model { file = "/net/cci-nas-00/data/ceres_data/8eev_28060/08_2025/8eev_28060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eev_28060/08_2025/8eev_28060.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.06, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 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: 1.28 Conformation dependent library (CDL) restraints added in 693.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.63 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: 4.40 Time building geometry restraints manager: 1.64 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: 0.00 - 3.44: 28413 3.44 - 6.87: 336 6.87 - 10.31: 12 10.31 - 13.75: 1 13.75 - 17.19: 1 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 3.040 nonbonded pdb=" OG1 THR K 297 " pdb=" OG1 THR K 307 " model vdw 1.998 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" OG1 THR B 307 " model vdw 2.014 3.040 nonbonded pdb=" OG SER J 297 " pdb=" O SER J 321 " model vdw 2.040 3.040 nonbonded pdb=" OG SER F 297 " pdb=" O SER F 321 " model vdw 2.053 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.950 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- 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 21242 Z= 0.395 Angle : 0.952 17.187 28851 Z= 0.523 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 : 4.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.000 0.000 ARG S 38 TYR 0.028 0.003 TYR J 308 PHE 0.042 0.003 PHE J 87 TRP 0.026 0.003 TRP H 100F HIS 0.016 0.003 HIS F 331 Details of bonding type rmsd covalent geometry : bond 0.00927 (21198) covalent geometry : angle 0.94946 (28763) SS BOND : bond 0.00599 ( 44) SS BOND : angle 1.52362 ( 88) hydrogen bonds : bond 0.15685 ( 590) hydrogen bonds : angle 8.51244 ( 1590) *********************** 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 to be fit. rotamer outliers: 0 poor density : 787 time to evaluate : 0.519 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: 0.1165 time to fit residues: 143.5084 Evaluate side-chains 673 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 0.6980 overall best weight: 0.3510 ------------------------------------------------------------------------------- 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 235 GLN A 270 ASN B 71 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 360 ASN ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 390 HIS K 52 GLN K 71 HIS K 121 HIS K 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 ASN V 90 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108702 restraints weight = 32943.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111821 restraints weight = 15409.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113703 restraints weight = 8957.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114817 restraints weight = 6217.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115463 restraints weight = 4965.134| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21242 Z= 0.177 Angle : 0.748 15.100 28851 Z= 0.427 Chirality : 0.046 0.189 3220 Planarity : 0.006 0.048 3703 Dihedral : 6.525 39.420 2695 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 2.26 % Allowed : 9.56 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.14), residues: 2677 helix: -1.13 (0.89), residues: 27 sheet: -1.62 (0.15), residues: 1082 loop : -3.04 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG V 54 TYR 0.019 0.001 TYR G 44 PHE 0.044 0.002 PHE J 398 TRP 0.028 0.002 TRP S 103 HIS 0.014 0.001 HIS G 333 Details of bonding type rmsd covalent geometry : bond 0.00350 (21198) covalent geometry : angle 0.74315 (28763) SS BOND : bond 0.00459 ( 44) SS BOND : angle 1.70739 ( 88) hydrogen bonds : bond 0.03507 ( 590) hydrogen bonds : angle 6.21535 ( 1590) *********************** 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 751 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 699 time to evaluate : 0.664 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: 0.7993 (mtpt) cc_final: 0.7660 (mtpp) REVERT: A 36 ILE cc_start: 0.8114 (mt) cc_final: 0.7829 (tt) REVERT: A 75 ASP cc_start: 0.7893 (t0) cc_final: 0.7369 (t0) REVERT: A 99 GLU cc_start: 0.8266 (pm20) cc_final: 0.7859 (pm20) REVERT: A 105 LYS cc_start: 0.8362 (mttt) cc_final: 0.8061 (mtmt) REVERT: A 137 VAL cc_start: 0.8408 (t) cc_final: 0.8077 (p) REVERT: A 153 PRO cc_start: 0.8585 (Cg_endo) cc_final: 0.8322 (Cg_exo) REVERT: A 173 PHE cc_start: 0.7482 (m-80) cc_final: 0.7209 (m-80) REVERT: A 225 LYS cc_start: 0.7144 (ttpp) cc_final: 0.6760 (ttmm) REVERT: A 269 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6653 (mt-10) REVERT: A 311 ASP cc_start: 0.6606 (p0) cc_final: 0.6167 (p0) REVERT: A 312 PHE cc_start: 0.7788 (m-10) cc_final: 0.7358 (m-10) REVERT: A 368 GLN cc_start: 0.8041 (tt0) cc_final: 0.7822 (tt0) REVERT: A 385 ASP cc_start: 0.6554 (p0) cc_final: 0.6290 (p0) REVERT: B 37 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7857 (mmtp) REVERT: B 153 VAL cc_start: 0.8444 (m) cc_final: 0.8194 (t) REVERT: B 286 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7468 (mtpp) REVERT: B 293 THR cc_start: 0.8122 (m) cc_final: 0.7556 (p) REVERT: F 42 VAL cc_start: 0.8447 (t) cc_final: 0.8196 (p) REVERT: F 52 LYS cc_start: 0.8168 (tttt) cc_final: 0.7718 (ttpp) REVERT: F 76 GLU cc_start: 0.7102 (tp30) cc_final: 0.6738 (tp30) REVERT: F 105 LYS cc_start: 0.8492 (mttt) cc_final: 0.7853 (mtpt) REVERT: F 204 GLN cc_start: 0.7571 (mt0) cc_final: 0.7246 (mt0) REVERT: F 216 ASN cc_start: 0.7531 (t0) cc_final: 0.7325 (t0) REVERT: F 225 LYS cc_start: 0.7919 (tttt) cc_final: 0.7620 (ttpp) REVERT: F 245 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7427 (ptpt) REVERT: F 317 THR cc_start: 0.7596 (m) cc_final: 0.7367 (p) REVERT: F 338 THR cc_start: 0.7674 (m) cc_final: 0.7453 (p) REVERT: F 340 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7799 (ttmm) REVERT: F 360 ASN cc_start: 0.6968 (m-40) cc_final: 0.6244 (m-40) REVERT: F 399 THR cc_start: 0.6791 (m) cc_final: 0.6440 (t) REVERT: G 37 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7937 (mmtp) REVERT: G 86 THR cc_start: 0.7655 (p) cc_final: 0.7305 (m) REVERT: G 167 MET cc_start: 0.7209 (ptp) cc_final: 0.6865 (ptp) REVERT: G 242 LYS cc_start: 0.8163 (mttm) cc_final: 0.7918 (mttt) REVERT: G 255 LEU cc_start: 0.7872 (pp) cc_final: 0.7443 (pt) REVERT: G 273 GLU cc_start: 0.7109 (tp30) cc_final: 0.6874 (tp30) REVERT: G 277 THR cc_start: 0.8057 (m) cc_final: 0.7681 (p) REVERT: G 286 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7421 (mtpp) REVERT: H 11 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6759 (pp) REVERT: J 66 GLN cc_start: 0.7616 (mt0) cc_final: 0.7411 (mt0) REVERT: J 99 GLU cc_start: 0.8317 (pm20) cc_final: 0.7494 (pm20) REVERT: J 105 LYS cc_start: 0.8558 (mttt) cc_final: 0.7935 (mtmt) REVERT: J 160 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7406 (ttpp) REVERT: J 217 THR cc_start: 0.8402 (p) cc_final: 0.7939 (t) REVERT: J 218 ASN cc_start: 0.8180 (t0) cc_final: 0.7935 (t0) REVERT: J 340 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7377 (ttmm) REVERT: J 355 HIS cc_start: 0.6977 (m-70) cc_final: 0.6539 (m-70) REVERT: J 361 ILE cc_start: 0.8433 (mp) cc_final: 0.8054 (tp) REVERT: J 385 ASP cc_start: 0.6992 (p0) cc_final: 0.6691 (p0) REVERT: K 37 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7375 (tppt) REVERT: K 39 ASP cc_start: 0.7013 (m-30) cc_final: 0.6744 (m-30) REVERT: K 84 LEU cc_start: 0.7841 (pt) cc_final: 0.7475 (pp) REVERT: K 94 ASP cc_start: 0.7406 (t0) cc_final: 0.7084 (t0) REVERT: K 245 LYS cc_start: 0.7678 (ptmt) cc_final: 0.7398 (ptmt) REVERT: K 252 LYS cc_start: 0.7833 (mmtm) cc_final: 0.7497 (mmtm) REVERT: K 283 VAL cc_start: 0.8534 (t) cc_final: 0.8254 (p) REVERT: S 107 ILE cc_start: 0.8031 (mm) cc_final: 0.7737 (mm) REVERT: T 23 CYS cc_start: 0.4815 (t) cc_final: 0.2978 (t) REVERT: U 71 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7346 (ttpp) REVERT: V 90 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7548 (tm-30) outliers start: 52 outliers final: 27 residues processed: 718 average time/residue: 0.1158 time to fit residues: 130.5367 Evaluate side-chains 684 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 655 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 297 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain G residue 83 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 88 MET Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain V residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 77 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 235 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 368 GLN ** 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 F 102 GLN F 218 ASN F 270 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 GLN G 239 ASN J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN J 304 ASN J 362 HIS J 381 HIS J 386 HIS J 394 HIS K 96 HIS K 121 HIS L 34 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.098663 restraints weight = 32731.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101713 restraints weight = 15491.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103582 restraints weight = 9138.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104615 restraints weight = 6409.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105317 restraints weight = 5196.062| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 21242 Z= 0.331 Angle : 0.852 21.285 28851 Z= 0.478 Chirality : 0.050 0.184 3220 Planarity : 0.006 0.060 3703 Dihedral : 6.912 43.148 2695 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.90 % Favored : 89.91 % Rotamer: Outliers : 4.26 % Allowed : 12.12 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.15), residues: 2677 helix: 0.12 (1.05), residues: 27 sheet: -1.47 (0.15), residues: 1102 loop : -2.82 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG V 61 TYR 0.027 0.003 TYR B 15 PHE 0.031 0.003 PHE J 156 TRP 0.038 0.003 TRP S 103 HIS 0.015 0.002 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00726 (21198) covalent geometry : angle 0.84599 (28763) SS BOND : bond 0.00606 ( 44) SS BOND : angle 1.99483 ( 88) hydrogen bonds : bond 0.03902 ( 590) hydrogen bonds : angle 6.15471 ( 1590) *********************** 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 788 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 690 time to evaluate : 0.806 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: 0.8088 (mtpt) cc_final: 0.7650 (mtpt) REVERT: A 36 ILE cc_start: 0.8373 (mt) cc_final: 0.8039 (tt) REVERT: A 75 ASP cc_start: 0.8035 (t0) cc_final: 0.7789 (t70) REVERT: A 76 GLU cc_start: 0.7024 (tp30) cc_final: 0.6668 (tp30) REVERT: A 99 GLU cc_start: 0.8278 (pm20) cc_final: 0.7916 (pm20) REVERT: A 105 LYS cc_start: 0.8469 (mttt) cc_final: 0.7653 (ttmm) REVERT: A 137 VAL cc_start: 0.8547 (t) cc_final: 0.8279 (p) REVERT: A 153 PRO cc_start: 0.8641 (Cg_endo) cc_final: 0.8382 (Cg_exo) REVERT: A 183 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6154 (mt-10) REVERT: A 216 ASN cc_start: 0.7628 (t0) cc_final: 0.7332 (t0) REVERT: A 225 LYS cc_start: 0.7443 (ttpp) cc_final: 0.7103 (ttmm) REVERT: A 269 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6951 (mt-10) REVERT: A 357 SER cc_start: 0.8484 (t) cc_final: 0.8017 (p) REVERT: A 368 GLN cc_start: 0.8242 (tt0) cc_final: 0.7955 (tt0) REVERT: A 369 ILE cc_start: 0.8476 (mp) cc_final: 0.8175 (mm) REVERT: A 385 ASP cc_start: 0.6911 (p0) cc_final: 0.6634 (p0) REVERT: A 390 HIS cc_start: 0.7340 (p90) cc_final: 0.6835 (p90) REVERT: B 37 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7823 (mmtp) REVERT: B 74 ILE cc_start: 0.8495 (mm) cc_final: 0.8280 (mt) REVERT: B 144 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6247 (mm-30) REVERT: B 283 VAL cc_start: 0.8521 (t) cc_final: 0.8016 (m) REVERT: B 286 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7576 (mtpp) REVERT: B 293 THR cc_start: 0.8255 (m) cc_final: 0.7778 (p) REVERT: B 319 PHE cc_start: 0.8541 (m-80) cc_final: 0.8281 (m-80) REVERT: F 52 LYS cc_start: 0.8328 (tttt) cc_final: 0.7850 (ttpp) REVERT: F 76 GLU cc_start: 0.7299 (tp30) cc_final: 0.6947 (tp30) REVERT: F 99 GLU cc_start: 0.8328 (pm20) cc_final: 0.7766 (pm20) REVERT: F 105 LYS cc_start: 0.8400 (mttt) cc_final: 0.7845 (mtpt) REVERT: F 186 ASN cc_start: 0.8139 (m-40) cc_final: 0.7905 (m-40) REVERT: F 204 GLN cc_start: 0.7561 (mt0) cc_final: 0.7300 (mt0) REVERT: F 216 ASN cc_start: 0.7729 (t0) cc_final: 0.7248 (t0) REVERT: F 241 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6698 (mm-30) REVERT: F 270 ASN cc_start: 0.8161 (m-40) cc_final: 0.7875 (m-40) REVERT: F 312 PHE cc_start: 0.7694 (m-10) cc_final: 0.7300 (m-80) REVERT: F 317 THR cc_start: 0.7842 (m) cc_final: 0.7568 (p) REVERT: F 324 LYS cc_start: 0.7354 (tppt) cc_final: 0.7104 (tppt) REVERT: F 340 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8043 (ttmm) REVERT: F 360 ASN cc_start: 0.7362 (m-40) cc_final: 0.6771 (m-40) REVERT: G 37 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7942 (tppt) REVERT: G 66 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: G 252 LYS cc_start: 0.8093 (mppt) cc_final: 0.7417 (mmtm) REVERT: G 255 LEU cc_start: 0.8135 (pp) cc_final: 0.7688 (pt) REVERT: G 277 THR cc_start: 0.8054 (m) cc_final: 0.7657 (p) REVERT: H 11 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6885 (pp) REVERT: J 96 CYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5564 (m) REVERT: J 99 GLU cc_start: 0.8308 (pm20) cc_final: 0.7489 (pm20) REVERT: J 105 LYS cc_start: 0.8458 (mttt) cc_final: 0.7770 (mtmt) REVERT: J 216 ASN cc_start: 0.7851 (t0) cc_final: 0.7580 (t0) REVERT: J 217 THR cc_start: 0.8587 (p) cc_final: 0.8116 (t) REVERT: J 218 ASN cc_start: 0.8331 (t0) cc_final: 0.8086 (t0) REVERT: J 242 GLN cc_start: 0.8510 (tp40) cc_final: 0.8189 (tp40) REVERT: J 311 ASP cc_start: 0.7519 (t0) cc_final: 0.7010 (t0) REVERT: J 338 THR cc_start: 0.7908 (m) cc_final: 0.7580 (p) REVERT: J 340 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7600 (ttmm) REVERT: J 355 HIS cc_start: 0.7210 (m-70) cc_final: 0.6779 (m-70) REVERT: J 357 SER cc_start: 0.8392 (t) cc_final: 0.7980 (t) REVERT: J 365 PHE cc_start: 0.8258 (p90) cc_final: 0.7986 (p90) REVERT: K 37 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7314 (tppt) REVERT: K 50 SER cc_start: 0.7839 (p) cc_final: 0.7454 (p) REVERT: K 167 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6875 (ptp) REVERT: K 239 ASN cc_start: 0.7833 (t0) cc_final: 0.7630 (m110) REVERT: K 245 LYS cc_start: 0.7721 (ptmt) cc_final: 0.7440 (ptmt) REVERT: K 252 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7425 (mmtm) REVERT: K 254 LYS cc_start: 0.7480 (pttt) cc_final: 0.7252 (pptt) REVERT: K 283 VAL cc_start: 0.8694 (t) cc_final: 0.8330 (p) REVERT: T 4 MET cc_start: 0.6499 (ptm) cc_final: 0.6228 (ptm) REVERT: T 23 CYS cc_start: 0.4525 (t) cc_final: 0.3532 (t) REVERT: U 71 LYS cc_start: 0.7660 (ttpp) cc_final: 0.7380 (ttpp) outliers start: 98 outliers final: 61 residues processed: 736 average time/residue: 0.1143 time to fit residues: 133.8244 Evaluate side-chains 727 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 662 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 317 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 140 THR 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 297 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 266 ILE 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 386 HIS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 93 VAL 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 H residue 7 SER 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 71 LYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 144 THR 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 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR 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 U residue 20 LEU Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 270 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS B 81 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN F 102 GLN F 157 ASN F 392 GLN F 394 HIS G 52 GLN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN G 305 HIS J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS J 386 HIS L 90 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.102144 restraints weight = 32905.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.105214 restraints weight = 15538.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107067 restraints weight = 9137.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108192 restraints weight = 6398.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108743 restraints weight = 5122.653| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21242 Z= 0.181 Angle : 0.720 17.830 28851 Z= 0.412 Chirality : 0.045 0.191 3220 Planarity : 0.005 0.051 3703 Dihedral : 6.229 40.773 2695 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 4.13 % Allowed : 14.60 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.15), residues: 2677 helix: 0.82 (1.11), residues: 27 sheet: -1.07 (0.15), residues: 1114 loop : -2.57 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 46 TYR 0.018 0.001 TYR U 35 PHE 0.032 0.002 PHE A 365 TRP 0.024 0.002 TRP U 103 HIS 0.010 0.001 HIS U 96 Details of bonding type rmsd covalent geometry : bond 0.00366 (21198) covalent geometry : angle 0.71776 (28763) SS BOND : bond 0.00389 ( 44) SS BOND : angle 1.21269 ( 88) hydrogen bonds : bond 0.03093 ( 590) hydrogen bonds : angle 5.71245 ( 1590) *********************** 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 772 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 677 time to evaluate : 0.547 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: 0.8053 (mtpt) cc_final: 0.7762 (mtpp) REVERT: A 62 CYS cc_start: 0.5393 (OUTLIER) cc_final: 0.4790 (p) REVERT: A 75 ASP cc_start: 0.8016 (t0) cc_final: 0.7782 (t70) REVERT: A 76 GLU cc_start: 0.7067 (tp30) cc_final: 0.6780 (tp30) REVERT: A 99 GLU cc_start: 0.8159 (pm20) cc_final: 0.7655 (pm20) REVERT: A 105 LYS cc_start: 0.8458 (mttt) cc_final: 0.7638 (ttmm) REVERT: A 137 VAL cc_start: 0.8487 (t) cc_final: 0.8198 (p) REVERT: A 143 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 148 VAL cc_start: 0.7476 (m) cc_final: 0.7255 (p) REVERT: A 183 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6076 (mt-10) REVERT: A 208 VAL cc_start: 0.8946 (p) cc_final: 0.8730 (p) REVERT: A 216 ASN cc_start: 0.7685 (t0) cc_final: 0.7334 (t0) REVERT: A 225 LYS cc_start: 0.7488 (ttpp) cc_final: 0.7089 (ttmm) REVERT: A 357 SER cc_start: 0.8519 (t) cc_final: 0.8193 (p) REVERT: A 384 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6432 (mttm) REVERT: A 385 ASP cc_start: 0.6875 (p0) cc_final: 0.6591 (p0) REVERT: A 390 HIS cc_start: 0.7333 (p90) cc_final: 0.6879 (p90) REVERT: B 37 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7785 (mmtp) REVERT: B 74 ILE cc_start: 0.8481 (mm) cc_final: 0.8275 (mt) REVERT: B 144 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6446 (mm-30) REVERT: B 167 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6781 (ptp) REVERT: B 255 LEU cc_start: 0.7924 (pp) cc_final: 0.7679 (pt) REVERT: B 286 LYS cc_start: 0.7867 (mtpp) cc_final: 0.7641 (mtpp) REVERT: F 52 LYS cc_start: 0.8394 (tttt) cc_final: 0.7920 (ttpp) REVERT: F 76 GLU cc_start: 0.7141 (tp30) cc_final: 0.6690 (tp30) REVERT: F 79 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8195 (ttpp) REVERT: F 99 GLU cc_start: 0.8366 (pm20) cc_final: 0.7971 (pm20) REVERT: F 105 LYS cc_start: 0.8344 (mttt) cc_final: 0.7889 (mtpt) REVERT: F 216 ASN cc_start: 0.7662 (t0) cc_final: 0.7270 (t0) REVERT: F 312 PHE cc_start: 0.7696 (m-10) cc_final: 0.7381 (m-80) REVERT: F 317 THR cc_start: 0.7795 (m) cc_final: 0.7524 (p) REVERT: F 339 LEU cc_start: 0.8850 (mt) cc_final: 0.8593 (mp) REVERT: F 340 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7946 (ttmm) REVERT: F 360 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6360 (m-40) REVERT: F 399 THR cc_start: 0.7174 (m) cc_final: 0.6926 (t) REVERT: G 37 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7821 (tppt) REVERT: G 167 MET cc_start: 0.7248 (ptp) cc_final: 0.6976 (ptp) REVERT: G 239 ASN cc_start: 0.7827 (m110) cc_final: 0.7563 (m110) REVERT: G 252 LYS cc_start: 0.8067 (mppt) cc_final: 0.7361 (mmtm) REVERT: G 277 THR cc_start: 0.8103 (m) cc_final: 0.7618 (p) REVERT: H 11 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6843 (pp) REVERT: J 31 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7706 (pt) REVERT: J 99 GLU cc_start: 0.8323 (pm20) cc_final: 0.7608 (pm20) REVERT: J 105 LYS cc_start: 0.8407 (mttt) cc_final: 0.7739 (mtmt) REVERT: J 151 GLU cc_start: 0.7380 (pm20) cc_final: 0.7158 (pm20) REVERT: J 160 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7224 (ttpp) REVERT: J 216 ASN cc_start: 0.7778 (t0) cc_final: 0.7513 (t0) REVERT: J 217 THR cc_start: 0.8497 (p) cc_final: 0.8056 (t) REVERT: J 218 ASN cc_start: 0.8339 (t0) cc_final: 0.8094 (t0) REVERT: J 242 GLN cc_start: 0.8367 (tp40) cc_final: 0.7836 (tp-100) REVERT: J 311 ASP cc_start: 0.7511 (t0) cc_final: 0.6897 (t0) REVERT: J 338 THR cc_start: 0.7855 (m) cc_final: 0.7521 (p) REVERT: J 340 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7472 (ttmm) REVERT: J 355 HIS cc_start: 0.7023 (m-70) cc_final: 0.6533 (m-70) REVERT: J 357 SER cc_start: 0.8409 (t) cc_final: 0.7972 (t) REVERT: J 365 PHE cc_start: 0.8277 (p90) cc_final: 0.8072 (p90) REVERT: K 37 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7256 (tppt) REVERT: K 42 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6763 (t70) REVERT: K 50 SER cc_start: 0.7657 (p) cc_final: 0.7313 (p) REVERT: K 84 LEU cc_start: 0.8175 (pt) cc_final: 0.7943 (pp) REVERT: K 245 LYS cc_start: 0.7741 (ptmt) cc_final: 0.7445 (ptmt) REVERT: K 252 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7442 (mmtm) REVERT: K 283 VAL cc_start: 0.8509 (t) cc_final: 0.8138 (p) REVERT: L 90 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: T 23 CYS cc_start: 0.4892 (t) cc_final: 0.3786 (t) REVERT: U 71 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7275 (ttpp) REVERT: U 96 HIS cc_start: 0.6897 (t-170) cc_final: 0.6603 (t-170) REVERT: U 97 PHE cc_start: 0.8424 (t80) cc_final: 0.8156 (t80) outliers start: 95 outliers final: 56 residues processed: 712 average time/residue: 0.1113 time to fit residues: 126.3685 Evaluate side-chains 716 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 651 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 62 CYS 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 302 THR Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 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 307 THR 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 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 271 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 360 ASN Chi-restraints excluded: chain F residue 369 ILE 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 122 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 7 SER 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 31 ILE Chi-restraints excluded: chain J residue 47 VAL 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 144 THR Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 381 HIS Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain S residue 100 PHE 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 V residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 208 optimal weight: 0.0370 chunk 127 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 149 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN F 102 GLN F 218 ASN F 386 HIS G 81 GLN G 121 HIS J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS L 90 GLN T 27DHIS ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.101286 restraints weight = 32596.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104328 restraints weight = 15423.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106186 restraints weight = 9095.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107294 restraints weight = 6370.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107892 restraints weight = 5112.339| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21242 Z= 0.199 Angle : 0.722 19.123 28851 Z= 0.412 Chirality : 0.046 0.186 3220 Planarity : 0.005 0.050 3703 Dihedral : 6.082 39.443 2695 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 4.74 % Allowed : 15.68 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.15), residues: 2677 helix: 0.97 (1.12), residues: 27 sheet: -0.90 (0.15), residues: 1117 loop : -2.44 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 73 TYR 0.016 0.002 TYR U 35 PHE 0.039 0.002 PHE J 398 TRP 0.026 0.002 TRP U 103 HIS 0.014 0.001 HIS F 394 Details of bonding type rmsd covalent geometry : bond 0.00416 (21198) covalent geometry : angle 0.72018 (28763) SS BOND : bond 0.00426 ( 44) SS BOND : angle 1.24308 ( 88) hydrogen bonds : bond 0.03034 ( 590) hydrogen bonds : angle 5.60780 ( 1590) *********************** 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 775 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 666 time to evaluate : 0.604 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: 0.8099 (mtpt) cc_final: 0.7495 (mtpp) REVERT: A 52 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7632 (ttpt) REVERT: A 76 GLU cc_start: 0.7061 (tp30) cc_final: 0.6802 (tp30) REVERT: A 105 LYS cc_start: 0.8427 (mttt) cc_final: 0.7532 (ttmm) REVERT: A 137 VAL cc_start: 0.8581 (t) cc_final: 0.8276 (p) REVERT: A 143 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (m) REVERT: A 148 VAL cc_start: 0.7545 (m) cc_final: 0.7334 (p) REVERT: A 183 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6255 (mt-10) REVERT: A 202 ASP cc_start: 0.8061 (p0) cc_final: 0.7858 (p0) REVERT: A 208 VAL cc_start: 0.8943 (p) cc_final: 0.8717 (p) REVERT: A 216 ASN cc_start: 0.7702 (t0) cc_final: 0.7303 (t0) REVERT: A 225 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7276 (ttmm) REVERT: A 269 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6679 (mt-10) REVERT: A 357 SER cc_start: 0.8458 (t) cc_final: 0.8133 (p) REVERT: A 360 ASN cc_start: 0.7102 (m-40) cc_final: 0.6671 (m-40) REVERT: A 385 ASP cc_start: 0.6909 (p0) cc_final: 0.6664 (p0) REVERT: A 390 HIS cc_start: 0.7513 (p90) cc_final: 0.6974 (p90) REVERT: A 399 THR cc_start: 0.7415 (m) cc_final: 0.7034 (p) REVERT: B 37 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7768 (mmtp) REVERT: B 74 ILE cc_start: 0.8492 (mm) cc_final: 0.8232 (mt) REVERT: B 140 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8180 (m) REVERT: B 144 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6530 (mm-30) REVERT: B 286 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7613 (mtpp) REVERT: F 52 LYS cc_start: 0.8376 (tttt) cc_final: 0.7922 (ttpp) REVERT: F 76 GLU cc_start: 0.7104 (tp30) cc_final: 0.6724 (tp30) REVERT: F 79 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8202 (ttmm) REVERT: F 99 GLU cc_start: 0.8303 (pm20) cc_final: 0.7994 (pm20) REVERT: F 105 LYS cc_start: 0.8416 (mttt) cc_final: 0.7964 (mtpt) REVERT: F 133 LEU cc_start: 0.8114 (mm) cc_final: 0.7876 (mt) REVERT: F 204 GLN cc_start: 0.7613 (mt0) cc_final: 0.7377 (mt0) REVERT: F 216 ASN cc_start: 0.7687 (t0) cc_final: 0.7269 (t0) REVERT: F 312 PHE cc_start: 0.7829 (m-10) cc_final: 0.7534 (m-80) REVERT: F 317 THR cc_start: 0.7781 (m) cc_final: 0.7510 (p) REVERT: F 340 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7970 (ttmm) REVERT: F 360 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6383 (m-40) REVERT: G 37 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7939 (mmtp) REVERT: G 252 LYS cc_start: 0.8111 (mppt) cc_final: 0.7451 (mmtm) REVERT: G 277 THR cc_start: 0.8115 (m) cc_final: 0.7603 (p) REVERT: H 11 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6877 (pp) REVERT: J 42 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8199 (p) REVERT: J 99 GLU cc_start: 0.8326 (pm20) cc_final: 0.7622 (pm20) REVERT: J 105 LYS cc_start: 0.8409 (mttt) cc_final: 0.7755 (mtmt) REVERT: J 151 GLU cc_start: 0.7366 (pm20) cc_final: 0.7142 (pm20) REVERT: J 160 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7228 (ttpp) REVERT: J 216 ASN cc_start: 0.7776 (t0) cc_final: 0.7503 (t0) REVERT: J 217 THR cc_start: 0.8512 (p) cc_final: 0.8064 (t) REVERT: J 218 ASN cc_start: 0.8354 (t0) cc_final: 0.8099 (t0) REVERT: J 242 GLN cc_start: 0.8419 (tp40) cc_final: 0.7939 (tp-100) REVERT: J 311 ASP cc_start: 0.7523 (t0) cc_final: 0.6869 (t0) REVERT: J 312 PHE cc_start: 0.7951 (m-10) cc_final: 0.7246 (m-10) REVERT: J 338 THR cc_start: 0.7915 (m) cc_final: 0.7560 (p) REVERT: J 340 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7444 (ttmm) REVERT: J 357 SER cc_start: 0.8334 (t) cc_final: 0.7913 (t) REVERT: J 387 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7761 (mt) REVERT: K 37 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7287 (tppt) REVERT: K 50 SER cc_start: 0.7804 (p) cc_final: 0.7477 (p) REVERT: K 84 LEU cc_start: 0.8201 (pt) cc_final: 0.7986 (pp) REVERT: K 239 ASN cc_start: 0.7781 (t0) cc_final: 0.7575 (m110) REVERT: K 245 LYS cc_start: 0.7718 (ptmt) cc_final: 0.7435 (ptmt) REVERT: K 252 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7520 (mmtm) REVERT: K 283 VAL cc_start: 0.8511 (t) cc_final: 0.8234 (p) REVERT: L 90 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: T 11 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6768 (tt) REVERT: U 71 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7330 (ttpp) REVERT: U 96 HIS cc_start: 0.7092 (t-170) cc_final: 0.6664 (t-90) REVERT: U 97 PHE cc_start: 0.8451 (t80) cc_final: 0.7914 (t80) outliers start: 109 outliers final: 70 residues processed: 714 average time/residue: 0.1095 time to fit residues: 125.1722 Evaluate side-chains 732 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 653 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 191 GLU 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 112 MET Chi-restraints excluded: chain B residue 140 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 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 130 GLN 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 271 CYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 360 ASN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain F residue 370 CYS 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 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 11 LEU 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 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 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 130 GLN Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 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 237 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 90 GLN 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 U residue 20 LEU Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain U residue 100 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 32 optimal weight: 9.9990 chunk 210 optimal weight: 0.0870 chunk 248 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.1578 ------------------------------------------------------------------------------- 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 149 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN F 102 GLN G 81 GLN G 239 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS L 90 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105271 restraints weight = 33053.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108448 restraints weight = 15539.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110413 restraints weight = 9045.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111570 restraints weight = 6244.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112302 restraints weight = 4955.157| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21242 Z= 0.205 Angle : 0.719 17.993 28851 Z= 0.411 Chirality : 0.046 0.232 3220 Planarity : 0.005 0.048 3703 Dihedral : 6.059 40.268 2695 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.70 % Favored : 92.23 % Rotamer: Outliers : 4.87 % Allowed : 16.16 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.16), residues: 2677 helix: 1.07 (1.13), residues: 27 sheet: -0.68 (0.15), residues: 1096 loop : -2.38 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG K 13 TYR 0.016 0.002 TYR U 35 PHE 0.044 0.002 PHE J 398 TRP 0.026 0.002 TRP U 103 HIS 0.008 0.001 HIS S 96 Details of bonding type rmsd covalent geometry : bond 0.00431 (21198) covalent geometry : angle 0.71659 (28763) SS BOND : bond 0.00398 ( 44) SS BOND : angle 1.20699 ( 88) hydrogen bonds : bond 0.03035 ( 590) hydrogen bonds : angle 5.57340 ( 1590) *********************** 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 779 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 667 time to evaluate : 0.746 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: 0.8111 (mtpt) cc_final: 0.7503 (mtpp) REVERT: A 76 GLU cc_start: 0.7073 (tp30) cc_final: 0.6824 (tp30) REVERT: A 99 GLU cc_start: 0.8215 (pm20) cc_final: 0.7840 (pm20) REVERT: A 105 LYS cc_start: 0.8454 (mttt) cc_final: 0.7576 (ttmm) REVERT: A 137 VAL cc_start: 0.8566 (t) cc_final: 0.8261 (p) REVERT: A 143 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7755 (m) REVERT: A 183 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6431 (mt-10) REVERT: A 208 VAL cc_start: 0.8953 (p) cc_final: 0.8725 (p) REVERT: A 216 ASN cc_start: 0.7684 (t0) cc_final: 0.7176 (t0) REVERT: A 225 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7278 (ttmm) REVERT: A 269 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6627 (mt-10) REVERT: A 357 SER cc_start: 0.8458 (t) cc_final: 0.8119 (p) REVERT: A 360 ASN cc_start: 0.7192 (m-40) cc_final: 0.6854 (m-40) REVERT: A 385 ASP cc_start: 0.6969 (p0) cc_final: 0.6738 (p0) REVERT: A 390 HIS cc_start: 0.7690 (p90) cc_final: 0.7160 (p90) REVERT: B 37 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7751 (mmtp) REVERT: B 74 ILE cc_start: 0.8478 (mm) cc_final: 0.8233 (mt) REVERT: B 137 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6959 (mt-10) REVERT: B 144 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6561 (mm-30) REVERT: B 242 LYS cc_start: 0.8312 (mptt) cc_final: 0.8060 (mptt) REVERT: B 286 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7581 (mtpp) REVERT: F 52 LYS cc_start: 0.8373 (tttt) cc_final: 0.7850 (ttpp) REVERT: F 76 GLU cc_start: 0.7145 (tp30) cc_final: 0.6763 (tp30) REVERT: F 79 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8236 (ttmm) REVERT: F 99 GLU cc_start: 0.8461 (pm20) cc_final: 0.8032 (pm20) REVERT: F 105 LYS cc_start: 0.8392 (mttt) cc_final: 0.7931 (mtpt) REVERT: F 133 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7839 (mt) REVERT: F 151 GLU cc_start: 0.7005 (pm20) cc_final: 0.6698 (pm20) REVERT: F 216 ASN cc_start: 0.7697 (t0) cc_final: 0.7258 (t0) REVERT: F 312 PHE cc_start: 0.7913 (m-10) cc_final: 0.7639 (m-80) REVERT: F 317 THR cc_start: 0.7834 (m) cc_final: 0.7560 (p) REVERT: F 340 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7846 (ttmm) REVERT: G 37 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7852 (tppt) REVERT: G 277 THR cc_start: 0.8117 (m) cc_final: 0.7599 (p) REVERT: H 11 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6882 (pp) REVERT: J 42 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8186 (p) REVERT: J 99 GLU cc_start: 0.8351 (pm20) cc_final: 0.7645 (pm20) REVERT: J 105 LYS cc_start: 0.8398 (mttt) cc_final: 0.7752 (mtmt) REVERT: J 151 GLU cc_start: 0.7361 (pm20) cc_final: 0.7139 (pm20) REVERT: J 160 LYS cc_start: 0.7711 (ttpp) cc_final: 0.7408 (ttpp) REVERT: J 216 ASN cc_start: 0.7783 (t0) cc_final: 0.7509 (t0) REVERT: J 217 THR cc_start: 0.8528 (p) cc_final: 0.8077 (t) REVERT: J 218 ASN cc_start: 0.8377 (t0) cc_final: 0.8126 (t0) REVERT: J 242 GLN cc_start: 0.8426 (tp40) cc_final: 0.7973 (tp-100) REVERT: J 311 ASP cc_start: 0.7588 (t0) cc_final: 0.7047 (t0) REVERT: J 312 PHE cc_start: 0.7983 (m-10) cc_final: 0.7282 (m-10) REVERT: J 338 THR cc_start: 0.7936 (m) cc_final: 0.7545 (p) REVERT: J 340 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7403 (ttmm) REVERT: J 357 SER cc_start: 0.8341 (t) cc_final: 0.7915 (t) REVERT: K 37 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7352 (tppt) REVERT: K 50 SER cc_start: 0.7770 (p) cc_final: 0.7410 (p) REVERT: K 239 ASN cc_start: 0.7787 (t0) cc_final: 0.7533 (m110) REVERT: K 245 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7433 (ptmt) REVERT: K 252 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7521 (mmtm) REVERT: K 254 LYS cc_start: 0.7499 (pptt) cc_final: 0.7197 (ptmm) REVERT: K 283 VAL cc_start: 0.8526 (t) cc_final: 0.8224 (p) REVERT: L 90 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: T 11 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6786 (tt) REVERT: U 71 LYS cc_start: 0.7529 (ttpp) cc_final: 0.7328 (ttpp) outliers start: 112 outliers final: 85 residues processed: 714 average time/residue: 0.1117 time to fit residues: 127.2740 Evaluate side-chains 744 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 653 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain A residue 151 GLU 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 388 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 140 THR 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 87 PHE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 133 LEU 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 338 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 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU 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 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 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 THR 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 388 VAL Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 275 MET Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 90 GLN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 15 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 130 GLN A 149 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 81 GLN B 96 HIS B 121 HIS B 305 HIS F 16 ASN F 102 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN J 50 HIS J 360 ASN K 80 HIS ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.098399 restraints weight = 32626.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101357 restraints weight = 15645.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103158 restraints weight = 9316.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104223 restraints weight = 6584.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104814 restraints weight = 5320.537| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 21242 Z= 0.310 Angle : 0.798 13.635 28851 Z= 0.454 Chirality : 0.049 0.253 3220 Planarity : 0.005 0.057 3703 Dihedral : 6.515 41.298 2695 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.40 % Rotamer: Outliers : 5.43 % Allowed : 16.38 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 2677 helix: 0.71 (1.05), residues: 27 sheet: -0.77 (0.15), residues: 1078 loop : -2.46 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG K 103 TYR 0.026 0.002 TYR B 15 PHE 0.043 0.002 PHE J 398 TRP 0.035 0.003 TRP U 103 HIS 0.013 0.002 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00681 (21198) covalent geometry : angle 0.79468 (28763) SS BOND : bond 0.00614 ( 44) SS BOND : angle 1.53468 ( 88) hydrogen bonds : bond 0.03525 ( 590) hydrogen bonds : angle 5.89643 ( 1590) *********************** 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 797 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 672 time to evaluate : 0.730 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: 0.8157 (mtpt) cc_final: 0.7552 (mtpp) REVERT: A 76 GLU cc_start: 0.7036 (tp30) cc_final: 0.6781 (tp30) REVERT: A 99 GLU cc_start: 0.8316 (pm20) cc_final: 0.7957 (pm20) REVERT: A 105 LYS cc_start: 0.8451 (mttt) cc_final: 0.7684 (ttmm) REVERT: A 137 VAL cc_start: 0.8637 (t) cc_final: 0.8323 (p) REVERT: A 143 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7776 (m) REVERT: A 153 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8360 (Cg_exo) REVERT: A 183 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6461 (mt-10) REVERT: A 196 GLN cc_start: 0.7267 (mm-40) cc_final: 0.7058 (mm-40) REVERT: A 208 VAL cc_start: 0.8983 (p) cc_final: 0.8768 (p) REVERT: A 216 ASN cc_start: 0.7717 (t0) cc_final: 0.7339 (t0) REVERT: A 225 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7293 (ttmm) REVERT: A 269 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6728 (mt-10) REVERT: A 357 SER cc_start: 0.8495 (t) cc_final: 0.8036 (p) REVERT: A 360 ASN cc_start: 0.7307 (m-40) cc_final: 0.6914 (m-40) REVERT: A 390 HIS cc_start: 0.7948 (p90) cc_final: 0.7728 (p90) REVERT: B 37 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7810 (mmmm) REVERT: B 74 ILE cc_start: 0.8571 (mm) cc_final: 0.8308 (mt) REVERT: B 144 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6558 (mm-30) REVERT: B 160 ASN cc_start: 0.8173 (t0) cc_final: 0.7901 (t0) REVERT: B 283 VAL cc_start: 0.8416 (t) cc_final: 0.7935 (m) REVERT: B 286 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7580 (mtpp) REVERT: F 31 ILE cc_start: 0.7911 (mp) cc_final: 0.7559 (mm) REVERT: F 52 LYS cc_start: 0.8426 (tttt) cc_final: 0.7969 (ttpp) REVERT: F 76 GLU cc_start: 0.7084 (tp30) cc_final: 0.6748 (tp30) REVERT: F 99 GLU cc_start: 0.8456 (pm20) cc_final: 0.8080 (pm20) REVERT: F 105 LYS cc_start: 0.8392 (mttt) cc_final: 0.7962 (mtpt) REVERT: F 151 GLU cc_start: 0.7058 (pm20) cc_final: 0.6799 (pm20) REVERT: F 156 PHE cc_start: 0.6952 (p90) cc_final: 0.6446 (p90) REVERT: F 216 ASN cc_start: 0.7830 (t0) cc_final: 0.7564 (t0) REVERT: F 241 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6709 (mm-30) REVERT: F 317 THR cc_start: 0.7938 (m) cc_final: 0.7669 (p) REVERT: F 340 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7904 (ttmm) REVERT: F 360 ASN cc_start: 0.7093 (m-40) cc_final: 0.6842 (m110) REVERT: G 37 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7832 (tppt) REVERT: G 252 LYS cc_start: 0.8167 (mppt) cc_final: 0.7544 (mmtm) REVERT: G 277 THR cc_start: 0.8058 (m) cc_final: 0.7559 (p) REVERT: G 323 GLU cc_start: 0.7040 (pp20) cc_final: 0.6432 (pp20) REVERT: H 11 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6914 (pp) REVERT: J 35 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7524 (mtpp) REVERT: J 42 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8207 (p) REVERT: J 99 GLU cc_start: 0.8394 (pm20) cc_final: 0.7712 (pm20) REVERT: J 105 LYS cc_start: 0.8331 (mttt) cc_final: 0.7747 (mtmt) REVERT: J 160 LYS cc_start: 0.7699 (ttpp) cc_final: 0.7412 (ttpp) REVERT: J 216 ASN cc_start: 0.7827 (t0) cc_final: 0.7618 (t0) REVERT: J 218 ASN cc_start: 0.8415 (t0) cc_final: 0.8135 (t0) REVERT: J 242 GLN cc_start: 0.8506 (tp40) cc_final: 0.8226 (tp40) REVERT: J 244 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7838 (ttmm) REVERT: J 245 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7960 (ptpp) REVERT: J 269 GLU cc_start: 0.7297 (tt0) cc_final: 0.6964 (mt-10) REVERT: J 311 ASP cc_start: 0.7650 (t0) cc_final: 0.7016 (t0) REVERT: J 338 THR cc_start: 0.7992 (m) cc_final: 0.7634 (p) REVERT: J 340 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7483 (ttmm) REVERT: J 357 SER cc_start: 0.8405 (t) cc_final: 0.7962 (t) REVERT: J 387 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.7942 (mt) REVERT: K 37 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7404 (tppt) REVERT: K 50 SER cc_start: 0.7866 (p) cc_final: 0.7502 (p) REVERT: K 239 ASN cc_start: 0.7824 (t0) cc_final: 0.7555 (m110) REVERT: K 245 LYS cc_start: 0.7687 (ptmt) cc_final: 0.7343 (ptmt) REVERT: K 252 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7536 (mmtm) REVERT: K 254 LYS cc_start: 0.7452 (pptt) cc_final: 0.7240 (ptmm) REVERT: K 283 VAL cc_start: 0.8528 (t) cc_final: 0.8229 (p) REVERT: T 11 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6947 (tt) REVERT: U 71 LYS cc_start: 0.7611 (ttpp) cc_final: 0.7325 (ttpp) REVERT: U 96 HIS cc_start: 0.7691 (t-90) cc_final: 0.7382 (t70) outliers start: 125 outliers final: 101 residues processed: 725 average time/residue: 0.1124 time to fit residues: 129.7076 Evaluate side-chains 762 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 656 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 129 VAL 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 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 A residue 388 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 166 GLU 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 307 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 98 THR Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 261 ILE 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 338 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 F residue 387 ILE Chi-restraints excluded: chain F residue 394 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 260 LEU Chi-restraints excluded: chain G residue 307 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 11 LEU 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 96 HIS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 42 VAL 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 96 CYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 241 GLU 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 J residue 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 275 MET Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain K residue 307 THR 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 152 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 159 GLN G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN J 16 ASN J 43 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 GLN L 27DHIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN ** V 90 GLN ** 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 = 0.3497 r_free = 0.3497 target = 0.126126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103892 restraints weight = 33073.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107014 restraints weight = 15818.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108965 restraints weight = 9262.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110098 restraints weight = 6405.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110803 restraints weight = 5106.075| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21242 Z= 0.240 Angle : 0.748 16.461 28851 Z= 0.428 Chirality : 0.047 0.206 3220 Planarity : 0.005 0.055 3703 Dihedral : 6.321 40.684 2695 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.26 % Favored : 91.63 % Rotamer: Outliers : 5.47 % Allowed : 17.20 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.16), residues: 2677 helix: 0.82 (1.06), residues: 27 sheet: -0.73 (0.15), residues: 1102 loop : -2.37 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 206 TYR 0.019 0.002 TYR U 35 PHE 0.047 0.002 PHE J 398 TRP 0.027 0.002 TRP U 103 HIS 0.010 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00515 (21198) covalent geometry : angle 0.74545 (28763) SS BOND : bond 0.00501 ( 44) SS BOND : angle 1.26445 ( 88) hydrogen bonds : bond 0.03214 ( 590) hydrogen bonds : angle 5.77090 ( 1590) *********************** 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 789 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 663 time to evaluate : 0.779 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: 0.8133 (mtpt) cc_final: 0.7474 (mtpp) REVERT: A 76 GLU cc_start: 0.7047 (tp30) cc_final: 0.6680 (tp30) REVERT: A 99 GLU cc_start: 0.8323 (pm20) cc_final: 0.7922 (pm20) REVERT: A 105 LYS cc_start: 0.8461 (mttt) cc_final: 0.7581 (ttmm) REVERT: A 137 VAL cc_start: 0.8583 (t) cc_final: 0.8273 (p) REVERT: A 143 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7775 (m) REVERT: A 183 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6452 (mt-10) REVERT: A 196 GLN cc_start: 0.7346 (mm-40) cc_final: 0.7044 (mm-40) REVERT: A 208 VAL cc_start: 0.8998 (p) cc_final: 0.8773 (p) REVERT: A 216 ASN cc_start: 0.7779 (t0) cc_final: 0.7081 (t0) REVERT: A 225 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7309 (ttmm) REVERT: A 269 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6702 (mt-10) REVERT: A 357 SER cc_start: 0.8601 (t) cc_final: 0.8134 (p) REVERT: A 360 ASN cc_start: 0.7277 (m-40) cc_final: 0.6958 (m-40) REVERT: A 390 HIS cc_start: 0.7920 (p-80) cc_final: 0.7657 (p90) REVERT: B 37 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7781 (mmmm) REVERT: B 137 GLU cc_start: 0.7226 (mt-10) cc_final: 0.7022 (mt-10) REVERT: B 144 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6652 (mm-30) REVERT: F 31 ILE cc_start: 0.7927 (mp) cc_final: 0.7633 (mm) REVERT: F 52 LYS cc_start: 0.8420 (tttt) cc_final: 0.7959 (ttpp) REVERT: F 76 GLU cc_start: 0.7111 (tp30) cc_final: 0.6709 (tp30) REVERT: F 99 GLU cc_start: 0.8426 (pm20) cc_final: 0.8212 (pm20) REVERT: F 105 LYS cc_start: 0.8363 (mttt) cc_final: 0.7900 (mtpt) REVERT: F 151 GLU cc_start: 0.7042 (pm20) cc_final: 0.6804 (pm20) REVERT: F 156 PHE cc_start: 0.6985 (p90) cc_final: 0.6538 (p90) REVERT: F 216 ASN cc_start: 0.7784 (t0) cc_final: 0.7542 (t0) REVERT: F 241 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6738 (mm-30) REVERT: F 317 THR cc_start: 0.7934 (m) cc_final: 0.7663 (p) REVERT: F 340 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7893 (ttmm) REVERT: G 37 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7834 (tppt) REVERT: G 66 MET cc_start: 0.8202 (ttt) cc_final: 0.7886 (ttt) REVERT: G 323 GLU cc_start: 0.7076 (pp20) cc_final: 0.6434 (pp20) REVERT: H 11 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6895 (pp) REVERT: J 35 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7639 (mtpp) REVERT: J 42 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8251 (p) REVERT: J 99 GLU cc_start: 0.8417 (pm20) cc_final: 0.7693 (pm20) REVERT: J 105 LYS cc_start: 0.8298 (mttt) cc_final: 0.7758 (mtmt) REVERT: J 160 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7405 (ttpp) REVERT: J 216 ASN cc_start: 0.7825 (t0) cc_final: 0.7581 (t0) REVERT: J 218 ASN cc_start: 0.8415 (t0) cc_final: 0.8120 (t0) REVERT: J 242 GLN cc_start: 0.8458 (tp40) cc_final: 0.8223 (tp40) REVERT: J 244 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7794 (ttmm) REVERT: J 269 GLU cc_start: 0.7320 (tt0) cc_final: 0.6925 (mt-10) REVERT: J 311 ASP cc_start: 0.7654 (t0) cc_final: 0.7054 (t0) REVERT: J 338 THR cc_start: 0.7978 (m) cc_final: 0.7594 (p) REVERT: J 340 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7434 (ttmm) REVERT: J 357 SER cc_start: 0.8380 (t) cc_final: 0.7943 (t) REVERT: J 387 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7822 (mt) REVERT: K 37 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7430 (tppt) REVERT: K 50 SER cc_start: 0.7835 (p) cc_final: 0.7472 (p) REVERT: K 81 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7805 (mm-40) REVERT: K 144 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6620 (mm-30) REVERT: K 239 ASN cc_start: 0.7773 (t0) cc_final: 0.7483 (m110) REVERT: K 252 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7535 (mmtm) REVERT: K 283 VAL cc_start: 0.8543 (t) cc_final: 0.8239 (p) REVERT: T 11 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6946 (tt) REVERT: U 71 LYS cc_start: 0.7596 (ttpp) cc_final: 0.7314 (ttpp) REVERT: U 96 HIS cc_start: 0.7674 (t-90) cc_final: 0.7372 (t70) outliers start: 126 outliers final: 103 residues processed: 721 average time/residue: 0.1149 time to fit residues: 131.1190 Evaluate side-chains 752 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 644 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU 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 A residue 388 VAL 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 166 GLU 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 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 327 GLU 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 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 148 VAL 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 338 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 F residue 394 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 167 MET 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 307 THR Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 339 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU 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 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 63 CYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 344 VAL 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 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 275 MET Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain L residue 26 SER 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 28 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 163 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 0.0070 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 130 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 381 HIS B 81 GLN B 121 HIS F 16 ASN F 100 ASN F 102 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 360 ASN ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 160 ASN G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106131 restraints weight = 33150.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109181 restraints weight = 15978.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111102 restraints weight = 9476.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112180 restraints weight = 6613.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112874 restraints weight = 5309.704| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21242 Z= 0.174 Angle : 0.702 14.836 28851 Z= 0.405 Chirality : 0.045 0.176 3220 Planarity : 0.005 0.051 3703 Dihedral : 5.918 39.858 2695 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 4.39 % Allowed : 18.68 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.16), residues: 2677 helix: 1.28 (1.14), residues: 27 sheet: -0.58 (0.15), residues: 1096 loop : -2.18 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 289 TYR 0.017 0.001 TYR U 35 PHE 0.045 0.002 PHE J 398 TRP 0.021 0.002 TRP J 170 HIS 0.010 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00349 (21198) covalent geometry : angle 0.70076 (28763) SS BOND : bond 0.00330 ( 44) SS BOND : angle 1.11934 ( 88) hydrogen bonds : bond 0.02897 ( 590) hydrogen bonds : angle 5.49390 ( 1590) *********************** 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 756 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 655 time to evaluate : 0.636 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: 0.8109 (mtpt) cc_final: 0.7732 (mtpp) REVERT: A 52 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7847 (mtpt) REVERT: A 105 LYS cc_start: 0.8426 (mttt) cc_final: 0.7570 (ttmm) REVERT: A 137 VAL cc_start: 0.8409 (t) cc_final: 0.8110 (p) REVERT: A 143 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7763 (m) REVERT: A 196 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7067 (mm-40) REVERT: A 208 VAL cc_start: 0.8945 (p) cc_final: 0.8710 (p) REVERT: A 216 ASN cc_start: 0.7728 (t0) cc_final: 0.7214 (t0) REVERT: A 225 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7178 (ttmm) REVERT: A 357 SER cc_start: 0.8577 (t) cc_final: 0.8180 (p) REVERT: A 390 HIS cc_start: 0.7901 (p-80) cc_final: 0.7612 (p90) REVERT: B 37 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7754 (mmtp) REVERT: F 31 ILE cc_start: 0.7897 (mp) cc_final: 0.7616 (mm) REVERT: F 52 LYS cc_start: 0.8249 (tttt) cc_final: 0.7813 (ttpp) REVERT: F 76 GLU cc_start: 0.7108 (tp30) cc_final: 0.6633 (tp30) REVERT: F 79 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8217 (ttmm) REVERT: F 105 LYS cc_start: 0.8372 (mttt) cc_final: 0.7913 (mtpt) REVERT: F 216 ASN cc_start: 0.7750 (t0) cc_final: 0.7482 (t0) REVERT: F 241 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6691 (mm-30) REVERT: F 317 THR cc_start: 0.7844 (m) cc_final: 0.7600 (p) REVERT: F 340 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7791 (ttmm) REVERT: G 37 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7868 (tppt) REVERT: G 323 GLU cc_start: 0.7110 (pp20) cc_final: 0.6338 (pp20) REVERT: H 11 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6864 (pp) REVERT: J 35 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7516 (mtpp) REVERT: J 37 LYS cc_start: 0.8668 (mttt) cc_final: 0.8349 (mttp) REVERT: J 42 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8223 (p) REVERT: J 52 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7921 (ptpt) REVERT: J 99 GLU cc_start: 0.8317 (pm20) cc_final: 0.7710 (pm20) REVERT: J 105 LYS cc_start: 0.8223 (mttt) cc_final: 0.7676 (mtmt) REVERT: J 160 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7396 (ttpp) REVERT: J 216 ASN cc_start: 0.7793 (t0) cc_final: 0.7552 (t0) REVERT: J 218 ASN cc_start: 0.8414 (t0) cc_final: 0.8092 (t0) REVERT: J 242 GLN cc_start: 0.8383 (tp40) cc_final: 0.7948 (tp-100) REVERT: J 244 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7760 (ttmm) REVERT: J 245 LYS cc_start: 0.8124 (ptpp) cc_final: 0.7839 (ptpp) REVERT: J 269 GLU cc_start: 0.7331 (tt0) cc_final: 0.6886 (mt-10) REVERT: J 311 ASP cc_start: 0.7671 (t0) cc_final: 0.7131 (t0) REVERT: J 338 THR cc_start: 0.7924 (m) cc_final: 0.7539 (p) REVERT: J 340 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7365 (ttmm) REVERT: J 357 SER cc_start: 0.8324 (t) cc_final: 0.7896 (t) REVERT: J 387 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7693 (mt) REVERT: K 37 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7388 (tppt) REVERT: K 50 SER cc_start: 0.7835 (p) cc_final: 0.7529 (p) REVERT: K 81 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7735 (mm-40) REVERT: K 115 LYS cc_start: 0.8269 (mttt) cc_final: 0.7959 (mmmt) REVERT: K 144 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6637 (mm-30) REVERT: K 245 LYS cc_start: 0.7703 (ptmt) cc_final: 0.7364 (ptmt) REVERT: K 252 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7493 (mmtm) REVERT: K 283 VAL cc_start: 0.8529 (t) cc_final: 0.8219 (p) REVERT: U 96 HIS cc_start: 0.7623 (t-90) cc_final: 0.7329 (t70) outliers start: 101 outliers final: 80 residues processed: 700 average time/residue: 0.1106 time to fit residues: 122.8045 Evaluate side-chains 729 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 644 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 151 GLU 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 140 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 307 THR 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 55 MET Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 130 GLN 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 338 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 112 MET Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 148 GLU 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 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 339 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU 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 96 HIS Chi-restraints excluded: chain J residue 42 VAL 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 129 VAL Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 275 MET Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 52 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 56 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 0.0030 chunk 159 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS F 16 ASN F 102 GLN F 360 ASN ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 160 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN J 20 ASN J 270 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 360 ASN K 159 GLN K 305 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107667 restraints weight = 32899.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110813 restraints weight = 15556.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112674 restraints weight = 9092.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113858 restraints weight = 6326.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114466 restraints weight = 5029.166| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21242 Z= 0.171 Angle : 0.703 13.284 28851 Z= 0.403 Chirality : 0.045 0.217 3220 Planarity : 0.005 0.080 3703 Dihedral : 5.734 39.445 2695 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.99 % Favored : 92.94 % Rotamer: Outliers : 4.04 % Allowed : 19.20 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.16), residues: 2677 helix: 2.20 (1.14), residues: 24 sheet: -0.44 (0.16), residues: 1101 loop : -2.05 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 73 TYR 0.016 0.001 TYR U 35 PHE 0.053 0.002 PHE J 398 TRP 0.020 0.001 TRP A 89 HIS 0.009 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00343 (21198) covalent geometry : angle 0.70106 (28763) SS BOND : bond 0.00399 ( 44) SS BOND : angle 1.18745 ( 88) hydrogen bonds : bond 0.02769 ( 590) hydrogen bonds : angle 5.45832 ( 1590) ********************** 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 734 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 641 time to evaluate : 0.566 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: 0.8085 (mtpt) cc_final: 0.7508 (mtpp) REVERT: A 52 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7810 (mtpt) REVERT: A 77 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7057 (mt0) REVERT: A 105 LYS cc_start: 0.8430 (mttt) cc_final: 0.7737 (ttmm) REVERT: A 137 VAL cc_start: 0.8328 (t) cc_final: 0.8004 (p) REVERT: A 143 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7735 (m) REVERT: A 196 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7071 (mm-40) REVERT: A 203 ILE cc_start: 0.8176 (mm) cc_final: 0.7927 (tp) REVERT: A 208 VAL cc_start: 0.8921 (p) cc_final: 0.8671 (p) REVERT: A 216 ASN cc_start: 0.7735 (t0) cc_final: 0.7101 (t0) REVERT: A 225 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7167 (ttmm) REVERT: A 269 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6654 (mt-10) REVERT: A 357 SER cc_start: 0.8479 (t) cc_final: 0.8125 (p) REVERT: B 37 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7774 (mmtp) REVERT: F 52 LYS cc_start: 0.8197 (tttt) cc_final: 0.7821 (ttpp) REVERT: F 76 GLU cc_start: 0.7098 (tp30) cc_final: 0.6554 (tp30) REVERT: F 79 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8238 (ttpp) REVERT: F 105 LYS cc_start: 0.8399 (mttt) cc_final: 0.7961 (mtpt) REVERT: F 216 ASN cc_start: 0.7787 (t0) cc_final: 0.7492 (t0) REVERT: F 317 THR cc_start: 0.7806 (m) cc_final: 0.7561 (p) REVERT: F 340 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7795 (ttmm) REVERT: G 37 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7842 (tppt) REVERT: G 323 GLU cc_start: 0.7115 (pp20) cc_final: 0.6254 (pp20) REVERT: H 11 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6836 (pp) REVERT: H 39 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6798 (tp40) REVERT: J 37 LYS cc_start: 0.8737 (mttt) cc_final: 0.8514 (mttp) REVERT: J 42 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8251 (p) REVERT: J 52 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7974 (ptmt) REVERT: J 99 GLU cc_start: 0.8312 (pm20) cc_final: 0.7693 (pm20) REVERT: J 105 LYS cc_start: 0.8181 (mttt) cc_final: 0.7663 (mtmt) REVERT: J 160 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7391 (ttpp) REVERT: J 216 ASN cc_start: 0.7790 (t0) cc_final: 0.7566 (t0) REVERT: J 217 THR cc_start: 0.8507 (p) cc_final: 0.8071 (t) REVERT: J 218 ASN cc_start: 0.8403 (t0) cc_final: 0.8151 (t0) REVERT: J 242 GLN cc_start: 0.8316 (tp40) cc_final: 0.7888 (tp-100) REVERT: J 244 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7736 (ttmm) REVERT: J 245 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7913 (ptpp) REVERT: J 311 ASP cc_start: 0.7666 (t0) cc_final: 0.7141 (t0) REVERT: J 340 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7290 (ttmm) REVERT: J 368 GLN cc_start: 0.8089 (tt0) cc_final: 0.7834 (tt0) REVERT: K 37 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7393 (tppt) REVERT: K 50 SER cc_start: 0.7879 (p) cc_final: 0.7576 (p) REVERT: K 115 LYS cc_start: 0.8184 (mttt) cc_final: 0.7910 (mmmt) REVERT: K 144 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6662 (mm-30) REVERT: K 235 LYS cc_start: 0.8222 (mmtp) cc_final: 0.8005 (mmtp) REVERT: K 239 ASN cc_start: 0.7728 (t0) cc_final: 0.7492 (m110) REVERT: K 245 LYS cc_start: 0.7720 (ptmt) cc_final: 0.7395 (ptmt) REVERT: K 252 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7490 (mmtm) REVERT: K 283 VAL cc_start: 0.8527 (t) cc_final: 0.8216 (p) REVERT: S 39 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7042 (tp40) REVERT: U 71 LYS cc_start: 0.7535 (ttpp) cc_final: 0.7254 (ttpp) REVERT: U 96 HIS cc_start: 0.7637 (t-90) cc_final: 0.7340 (t70) outliers start: 93 outliers final: 80 residues processed: 685 average time/residue: 0.1183 time to fit residues: 127.4039 Evaluate side-chains 704 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 620 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU 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 167 MET Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 307 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 42 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 130 GLN 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 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 112 MET Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 339 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU 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 J residue 10 GLN Chi-restraints excluded: chain J residue 42 VAL 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 96 CYS Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 275 MET Chi-restraints excluded: chain K residue 296 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 4 MET Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 28 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 37 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 362 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS F 16 ASN F 102 GLN F 222 GLN F 360 ASN F 381 HIS G 81 GLN G 160 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN J 270 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106332 restraints weight = 33153.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109482 restraints weight = 15845.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111277 restraints weight = 9319.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112562 restraints weight = 6553.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113162 restraints weight = 5157.852| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21242 Z= 0.182 Angle : 0.711 12.897 28851 Z= 0.406 Chirality : 0.045 0.186 3220 Planarity : 0.005 0.076 3703 Dihedral : 5.733 39.781 2695 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.17 % Favored : 92.75 % Rotamer: Outliers : 4.04 % Allowed : 19.20 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2677 helix: 2.25 (1.13), residues: 24 sheet: -0.39 (0.16), residues: 1104 loop : -2.00 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 206 TYR 0.017 0.001 TYR H 35 PHE 0.056 0.002 PHE J 398 TRP 0.022 0.002 TRP U 103 HIS 0.009 0.001 HIS S 96 Details of bonding type rmsd covalent geometry : bond 0.00375 (21198) covalent geometry : angle 0.70870 (28763) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.21246 ( 88) hydrogen bonds : bond 0.02815 ( 590) hydrogen bonds : angle 5.42935 ( 1590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.10 seconds wall clock time: 59 minutes 43.47 seconds (3583.47 seconds total)