Starting phenix.real_space_refine on Wed Jun 18 00:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eev_28060/06_2025/8eev_28060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eev_28060/06_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_28060/06_2025/8eev_28060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eev_28060/06_2025/8eev_28060.map" model { file = "/net/cci-nas-00/data/ceres_data/8eev_28060/06_2025/8eev_28060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eev_28060/06_2025/8eev_28060.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 13302 2.51 5 N 3373 2.21 5 O 3842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3019 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 372} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 8} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2092 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 21, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3019 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 371} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 8} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2092 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 21, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3019 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 371} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 8} Unresolved non-hydrogen planarities: 41 Chain: "K" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2092 Classifications: {'peptide': 268} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 21 Chain: "T" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 21 Chain: "V" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 11.47, per 1000 atoms: 0.56 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: 4.70 Conformation dependent library (CDL) restraints added in 2.6 seconds 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5018 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 81 sheets defined 2.2% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.501A pdb=" N GLN A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 4.115A pdb=" N GLU A 292 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.692A pdb=" N GLN F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'J' and resid 238 through 247 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.829A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'S' and resid 100 through 100D removed outlier: 3.754A pdb=" N CYS S 100C" --> pdb=" O ASN S 100 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR S 100D" --> pdb=" O THR S 100A" (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 100 through 100D' Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.768A pdb=" N ASP T 82 " --> pdb=" O GLU T 79 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 79 through 83' Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.712A pdb=" N ASP V 82 " --> pdb=" O GLU V 79 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.785A pdb=" N HIS A 3 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 7.116A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 45 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 7.116A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 45 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 61 removed outlier: 4.082A pdb=" N LYS A 105 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 103 " --> pdb=" O PRO A 58 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 60 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 101 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 106 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 305 removed outlier: 7.082A pdb=" N ILE A 315 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.707A pdb=" N CYS A 376 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.684A pdb=" N TRP B 339 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.735A pdb=" N CYS B 19 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS B 27 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.590A pdb=" N ALA B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N SER B 50 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP B 69 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 73 " --> pdb=" O MET B 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.590A pdb=" N ALA B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 45 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR B 98 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N SER B 51 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS B 96 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N TYR B 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N ASP B 94 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AB8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AC1, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AC2, first strand: chain 'B' and resid 307 through 311 Processing sheet with id=AC3, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'F' and resid 15 through 19 removed outlier: 7.171A pdb=" N ILE F 29 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL F 137 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 31 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 135 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 133 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 131 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 37 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 129 " --> pdb=" O LYS F 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA F 127 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 142 through 147 removed outlier: 6.684A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA F 127 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 129 " --> pdb=" O LYS F 37 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 37 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 131 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 133 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 135 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 31 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL F 137 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE F 29 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 51 through 61 removed outlier: 4.332A pdb=" N LYS F 105 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL F 103 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE F 60 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 101 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 51 through 61 removed outlier: 4.332A pdb=" N LYS F 105 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL F 103 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE F 60 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 101 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC9, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'F' and resid 296 through 305 removed outlier: 4.582A pdb=" N ALA F 298 " --> pdb=" O SER F 321 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER F 321 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE F 315 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AD3, first strand: chain 'F' and resid 364 through 368 removed outlier: 3.650A pdb=" N PHE F 365 " --> pdb=" O CYS F 376 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS F 376 " --> pdb=" O PHE F 365 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 387 through 388 removed outlier: 3.502A pdb=" N TRP G 339 " --> pdb=" O VAL F 388 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 17 through 19 removed outlier: 3.819A pdb=" N CYS G 19 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS G 27 " --> pdb=" O CYS G 19 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 33 through 37 removed outlier: 6.851A pdb=" N GLN G 48 " --> pdb=" O GLU G 34 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL G 36 " --> pdb=" O ARG G 46 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG G 46 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR G 98 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N SER G 51 " --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS G 96 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR G 53 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N ASP G 94 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 65 through 66 Processing sheet with id=AD8, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.651A pdb=" N THR G 73 " --> pdb=" O MET G 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AE1, first strand: chain 'G' and resid 147 through 150 Processing sheet with id=AE2, first strand: chain 'G' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AE4, first strand: chain 'G' and resid 275 through 279 Processing sheet with id=AE5, first strand: chain 'G' and resid 307 through 311 Processing sheet with id=AE6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.755A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR H 35 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.755A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR H 35 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 8 Processing sheet with id=AF1, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.186A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN J 134 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS J 35 " --> pdb=" O PHE J 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 41 through 48 removed outlier: 7.069A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA J 119 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 51 through 55 Processing sheet with id=AF4, first strand: chain 'J' and resid 51 through 55 removed outlier: 3.539A pdb=" N SER J 104 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS J 79 " --> pdb=" O SER J 104 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AF6, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'J' and resid 260 through 262 Processing sheet with id=AF8, first strand: chain 'J' and resid 300 through 303 Processing sheet with id=AF9, first strand: chain 'J' and resid 306 through 307 removed outlier: 6.606A pdb=" N CYS J 306 " --> pdb=" O HIS J 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'J' and resid 327 through 329 Processing sheet with id=AG2, first strand: chain 'J' and resid 364 through 367 removed outlier: 3.644A pdb=" N CYS J 376 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.595A pdb=" N CYS K 19 " --> pdb=" O CYS K 27 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS K 27 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 33 through 37 removed outlier: 7.791A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N SER K 50 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP K 69 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 73 through 74 removed outlier: 4.769A pdb=" N ASP K 69 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N SER K 50 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR K 98 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N SER K 51 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS K 96 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR K 53 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N ASP K 94 " --> pdb=" O TYR K 53 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 83 through 85 Processing sheet with id=AG7, first strand: chain 'K' and resid 147 through 150 Processing sheet with id=AG8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG9, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AH1, first strand: chain 'K' and resid 275 through 279 Processing sheet with id=AH2, first strand: chain 'K' and resid 307 through 311 Processing sheet with id=AH3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.081A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.650A pdb=" N SER S 7 " --> pdb=" O THR S 21 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 35 through 40 removed outlier: 3.937A pdb=" N GLY S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU S 45 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE S 58 " --> pdb=" O PHE S 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'S' and resid 88 through 90 Processing sheet with id=AH8, first strand: chain 'S' and resid 93 through 95 Processing sheet with id=AH9, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'T' and resid 27C through 27D removed outlier: 4.122A pdb=" N ASN T 30 " --> pdb=" O HIS T 27D" (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'T' and resid 53 through 54 removed outlier: 7.078A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.539A pdb=" N GLN U 5 " --> pdb=" O ALA U 23 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.539A pdb=" N GLN U 5 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP U 72 " --> pdb=" O GLN U 77 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 57 through 58 removed outlier: 5.874A pdb=" N LEU U 45 " --> pdb=" O SER U 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER U 40 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY U 49 " --> pdb=" O TRP U 36 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR U 35 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N CYS U 92 " --> pdb=" O TRP U 103 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP U 103 " --> pdb=" O CYS U 92 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG U 94 " --> pdb=" O ASP U 101 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 57 through 58 removed outlier: 5.874A pdb=" N LEU U 45 " --> pdb=" O SER U 40 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER U 40 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY U 49 " --> pdb=" O TRP U 36 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR U 35 " --> pdb=" O SER U 95 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AI8, first strand: chain 'V' and resid 10 through 12 removed outlier: 4.004A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'V' and resid 27C through 27D removed outlier: 3.753A pdb=" N ASN V 30 " --> pdb=" O HIS V 27D" (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 5.69 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.090 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.060 ------------------------------------------------------------------------------- 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 : 4.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.62 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.13), residues: 2677 helix: -3.57 (0.54), residues: 27 sheet: -2.49 (0.14), residues: 1075 loop : -3.69 (0.12), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 100F HIS 0.016 0.003 HIS F 331 PHE 0.042 0.003 PHE J 87 TYR 0.028 0.003 TYR J 308 ARG 0.000 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.15685 ( 590) hydrogen bonds : angle 8.51244 ( 1590) SS BOND : bond 0.00599 ( 44) SS BOND : angle 1.52362 ( 88) covalent geometry : bond 0.00927 (21198) covalent geometry : angle 0.94946 (28763) *********************** 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 : 2.225 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: 0.3124 time to fit residues: 382.6239 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 : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 155 optimal weight: 0.0670 chunk 242 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 50 HIS F 218 ASN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** K 52 GLN K 71 HIS K 121 HIS K 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27DHIS ** U 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106966 restraints weight = 32591.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110076 restraints weight = 15272.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111936 restraints weight = 8880.198| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21242 Z= 0.189 Angle : 0.761 15.478 28851 Z= 0.435 Chirality : 0.047 0.215 3220 Planarity : 0.006 0.051 3703 Dihedral : 6.582 39.822 2695 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.32 % Favored : 92.53 % Rotamer: Outliers : 2.48 % Allowed : 9.47 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.14), residues: 2677 helix: -1.10 (0.88), residues: 27 sheet: -1.62 (0.15), residues: 1082 loop : -3.06 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 103 HIS 0.014 0.001 HIS G 333 PHE 0.046 0.002 PHE J 398 TYR 0.020 0.002 TYR G 44 ARG 0.000 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 590) hydrogen bonds : angle 6.20282 ( 1590) SS BOND : bond 0.00420 ( 44) SS BOND : angle 1.77261 ( 88) covalent geometry : bond 0.00383 (21198) covalent geometry : angle 0.75628 (28763) *********************** 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 758 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 701 time to evaluate : 2.307 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: 0.8041 (mtpt) cc_final: 0.7612 (mtpp) REVERT: A 75 ASP cc_start: 0.7919 (t0) cc_final: 0.7390 (t0) REVERT: A 99 GLU cc_start: 0.8265 (pm20) cc_final: 0.7877 (pm20) REVERT: A 137 VAL cc_start: 0.8422 (t) cc_final: 0.8089 (p) REVERT: A 153 PRO cc_start: 0.8591 (Cg_endo) cc_final: 0.8329 (Cg_exo) REVERT: A 173 PHE cc_start: 0.7516 (m-80) cc_final: 0.7307 (m-80) REVERT: A 225 LYS cc_start: 0.7162 (ttpp) cc_final: 0.6772 (ttmm) REVERT: A 269 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 312 PHE cc_start: 0.7828 (m-10) cc_final: 0.7576 (m-10) REVERT: A 357 SER cc_start: 0.8521 (t) cc_final: 0.8188 (p) REVERT: A 385 ASP cc_start: 0.6648 (p0) cc_final: 0.6292 (p0) REVERT: B 37 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7853 (mmtp) REVERT: B 137 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 153 VAL cc_start: 0.8472 (m) cc_final: 0.8218 (t) REVERT: B 286 LYS cc_start: 0.7746 (mtpp) cc_final: 0.7522 (mtpp) REVERT: B 293 THR cc_start: 0.8149 (m) cc_final: 0.7628 (p) REVERT: B 319 PHE cc_start: 0.8582 (m-80) cc_final: 0.8362 (m-80) REVERT: F 42 VAL cc_start: 0.8476 (t) cc_final: 0.8226 (p) REVERT: F 52 LYS cc_start: 0.8201 (tttt) cc_final: 0.7736 (ttpp) REVERT: F 76 GLU cc_start: 0.7144 (tp30) cc_final: 0.6781 (tp30) REVERT: F 105 LYS cc_start: 0.8504 (mttt) cc_final: 0.7861 (mtpt) REVERT: F 123 LYS cc_start: 0.8397 (mttt) cc_final: 0.8125 (mmtp) REVERT: F 216 ASN cc_start: 0.7587 (t0) cc_final: 0.7385 (t0) REVERT: F 225 LYS cc_start: 0.7932 (tttt) cc_final: 0.7623 (ttpp) REVERT: F 245 LYS cc_start: 0.7828 (ptpt) cc_final: 0.7625 (ptpt) REVERT: F 312 PHE cc_start: 0.6828 (m-10) cc_final: 0.6238 (m-10) REVERT: F 317 THR cc_start: 0.7658 (m) cc_final: 0.7427 (p) REVERT: F 324 LYS cc_start: 0.7355 (tppt) cc_final: 0.7093 (tppt) REVERT: F 340 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7872 (ttmm) REVERT: F 360 ASN cc_start: 0.7057 (m110) cc_final: 0.6298 (m-40) REVERT: F 399 THR cc_start: 0.6788 (m) cc_final: 0.6421 (t) REVERT: G 37 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7871 (mmtp) REVERT: G 86 THR cc_start: 0.7708 (p) cc_final: 0.7370 (m) REVERT: G 144 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6628 (mm-30) REVERT: G 167 MET cc_start: 0.7248 (ptp) cc_final: 0.6917 (ptp) REVERT: G 242 LYS cc_start: 0.8177 (mttm) cc_final: 0.7912 (mttt) REVERT: G 255 LEU cc_start: 0.7995 (pp) cc_final: 0.7558 (pt) REVERT: G 273 GLU cc_start: 0.7142 (tp30) cc_final: 0.6911 (tp30) REVERT: G 277 THR cc_start: 0.8055 (m) cc_final: 0.7688 (p) REVERT: G 286 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7473 (mtpp) REVERT: J 99 GLU cc_start: 0.8322 (pm20) cc_final: 0.7510 (pm20) REVERT: J 105 LYS cc_start: 0.8593 (mttt) cc_final: 0.7932 (mtmt) REVERT: J 160 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7206 (ttpp) REVERT: J 217 THR cc_start: 0.8427 (p) cc_final: 0.7953 (t) REVERT: J 218 ASN cc_start: 0.8218 (t0) cc_final: 0.7989 (t0) REVERT: J 338 THR cc_start: 0.7651 (m) cc_final: 0.7344 (p) REVERT: J 339 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8204 (mm) REVERT: J 340 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7425 (ttmm) REVERT: J 355 HIS cc_start: 0.7002 (m-70) cc_final: 0.6567 (m-70) REVERT: J 361 ILE cc_start: 0.8457 (mp) cc_final: 0.8077 (tp) REVERT: J 362 HIS cc_start: 0.7358 (m170) cc_final: 0.7035 (m-70) REVERT: J 365 PHE cc_start: 0.8311 (p90) cc_final: 0.7984 (p90) REVERT: J 385 ASP cc_start: 0.7032 (p0) cc_final: 0.6756 (p0) REVERT: K 37 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7391 (tppt) REVERT: K 39 ASP cc_start: 0.7104 (m-30) cc_final: 0.6836 (m-30) REVERT: K 84 LEU cc_start: 0.7991 (pt) cc_final: 0.7667 (pp) REVERT: K 94 ASP cc_start: 0.7437 (t0) cc_final: 0.7108 (t0) REVERT: K 245 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7437 (ptmt) REVERT: K 252 LYS cc_start: 0.7854 (mmtm) cc_final: 0.7458 (mmtm) REVERT: K 283 VAL cc_start: 0.8545 (t) cc_final: 0.8264 (p) REVERT: S 107 ILE cc_start: 0.8046 (mm) cc_final: 0.7748 (mm) REVERT: T 23 CYS cc_start: 0.4884 (t) cc_final: 0.3066 (t) REVERT: U 71 LYS cc_start: 0.7522 (ttpp) cc_final: 0.7271 (ttpp) outliers start: 57 outliers final: 33 residues processed: 721 average time/residue: 0.3083 time to fit residues: 347.1697 Evaluate side-chains 684 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 650 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 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 F residue 353 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain U residue 100 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 218 optimal weight: 20.0000 chunk 65 optimal weight: 0.0770 chunk 204 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 222 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 218 ASN F 270 ASN ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** 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 270 ASN J 304 ASN ** J 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097590 restraints weight = 32565.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.100693 restraints weight = 15307.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102597 restraints weight = 9007.567| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 21242 Z= 0.383 Angle : 0.898 22.377 28851 Z= 0.499 Chirality : 0.052 0.195 3220 Planarity : 0.006 0.062 3703 Dihedral : 7.139 46.096 2695 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.27 % Favored : 89.54 % Rotamer: Outliers : 4.34 % Allowed : 12.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.15), residues: 2677 helix: -0.05 (1.05), residues: 27 sheet: -1.56 (0.15), residues: 1102 loop : -2.91 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP U 103 HIS 0.019 0.002 HIS F 381 PHE 0.032 0.003 PHE J 156 TYR 0.031 0.003 TYR B 15 ARG 0.000 0.000 ARG V 61 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 590) hydrogen bonds : angle 6.31348 ( 1590) SS BOND : bond 0.00777 ( 44) SS BOND : angle 2.25208 ( 88) covalent geometry : bond 0.00845 (21198) covalent geometry : angle 0.89027 (28763) *********************** 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 797 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 697 time to evaluate : 2.209 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: 0.8111 (mtpt) cc_final: 0.7710 (mtpt) REVERT: A 75 ASP cc_start: 0.8011 (t0) cc_final: 0.7759 (t70) REVERT: A 76 GLU cc_start: 0.7056 (tp30) cc_final: 0.6700 (tp30) REVERT: A 99 GLU cc_start: 0.8279 (pm20) cc_final: 0.7973 (pm20) REVERT: A 105 LYS cc_start: 0.8429 (mttt) cc_final: 0.7629 (ttmm) REVERT: A 137 VAL cc_start: 0.8542 (t) cc_final: 0.8279 (p) REVERT: A 153 PRO cc_start: 0.8667 (Cg_endo) cc_final: 0.8447 (Cg_exo) REVERT: A 183 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6124 (mt-10) REVERT: A 216 ASN cc_start: 0.7626 (t0) cc_final: 0.7358 (t0) REVERT: A 225 LYS cc_start: 0.7482 (ttpp) cc_final: 0.7135 (ttmm) REVERT: A 269 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 300 GLU cc_start: 0.6342 (tm-30) cc_final: 0.6111 (tm-30) REVERT: A 357 SER cc_start: 0.8509 (t) cc_final: 0.7974 (p) REVERT: A 385 ASP cc_start: 0.6974 (p0) cc_final: 0.6714 (p0) REVERT: A 390 HIS cc_start: 0.7425 (p90) cc_final: 0.6905 (p90) REVERT: B 37 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7886 (mmtp) REVERT: B 144 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6283 (mm-30) REVERT: B 160 ASN cc_start: 0.8231 (t0) cc_final: 0.7926 (t0) REVERT: B 245 LYS cc_start: 0.7350 (ttpt) cc_final: 0.7117 (ttpt) REVERT: B 255 LEU cc_start: 0.7883 (mp) cc_final: 0.7604 (mt) REVERT: B 283 VAL cc_start: 0.8646 (t) cc_final: 0.8215 (p) REVERT: B 286 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7588 (mtpp) REVERT: F 52 LYS cc_start: 0.8340 (tttt) cc_final: 0.7824 (ttpp) REVERT: F 76 GLU cc_start: 0.7228 (tp30) cc_final: 0.6860 (tp30) REVERT: F 99 GLU cc_start: 0.8430 (pm20) cc_final: 0.7938 (pm20) REVERT: F 105 LYS cc_start: 0.8413 (mttt) cc_final: 0.7876 (mtpt) REVERT: F 112 ASP cc_start: 0.7452 (m-30) cc_final: 0.7247 (m-30) REVERT: F 133 LEU cc_start: 0.8076 (mt) cc_final: 0.7870 (mm) REVERT: F 216 ASN cc_start: 0.7780 (t0) cc_final: 0.7521 (t0) REVERT: F 225 LYS cc_start: 0.8028 (tttt) cc_final: 0.7804 (tttp) REVERT: F 241 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6789 (mm-30) REVERT: F 242 GLN cc_start: 0.8363 (tp40) cc_final: 0.8044 (tp40) REVERT: F 270 ASN cc_start: 0.8175 (m-40) cc_final: 0.7898 (m-40) REVERT: F 312 PHE cc_start: 0.7777 (m-10) cc_final: 0.7388 (m-80) REVERT: F 317 THR cc_start: 0.7906 (m) cc_final: 0.7591 (p) REVERT: F 324 LYS cc_start: 0.7446 (tppt) cc_final: 0.7133 (tppt) REVERT: F 340 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7910 (ttmm) REVERT: F 360 ASN cc_start: 0.7352 (m110) cc_final: 0.6703 (m-40) REVERT: F 392 GLN cc_start: 0.8242 (mt0) cc_final: 0.8040 (mt0) REVERT: G 37 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7938 (tppt) REVERT: G 66 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7778 (ttt) REVERT: G 167 MET cc_start: 0.7180 (ptp) cc_final: 0.6953 (ptp) REVERT: G 252 LYS cc_start: 0.8106 (mppt) cc_final: 0.7385 (mmtm) REVERT: G 255 LEU cc_start: 0.8129 (pp) cc_final: 0.7655 (pt) REVERT: G 273 GLU cc_start: 0.7330 (tp30) cc_final: 0.7122 (tp30) REVERT: G 277 THR cc_start: 0.8063 (m) cc_final: 0.7652 (p) REVERT: G 290 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8456 (mmmm) REVERT: J 99 GLU cc_start: 0.8299 (pm20) cc_final: 0.7495 (pm20) REVERT: J 105 LYS cc_start: 0.8465 (mttt) cc_final: 0.7811 (mtmt) REVERT: J 117 ASP cc_start: 0.7534 (t0) cc_final: 0.7316 (t0) REVERT: J 157 ASN cc_start: 0.7158 (t0) cc_final: 0.6886 (m-40) REVERT: J 216 ASN cc_start: 0.7887 (t0) cc_final: 0.7663 (t0) REVERT: J 217 THR cc_start: 0.8599 (p) cc_final: 0.8152 (t) REVERT: J 218 ASN cc_start: 0.8363 (t0) cc_final: 0.8141 (t0) REVERT: J 242 GLN cc_start: 0.8549 (tp40) cc_final: 0.8263 (tp40) REVERT: J 311 ASP cc_start: 0.7514 (t0) cc_final: 0.7041 (t0) REVERT: J 338 THR cc_start: 0.7935 (m) cc_final: 0.7599 (p) REVERT: J 340 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7631 (ttmm) REVERT: J 355 HIS cc_start: 0.7292 (m-70) cc_final: 0.6843 (m-70) REVERT: J 357 SER cc_start: 0.8419 (t) cc_final: 0.8006 (t) REVERT: J 365 PHE cc_start: 0.8250 (p90) cc_final: 0.7972 (p90) REVERT: K 37 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7280 (tppt) REVERT: K 239 ASN cc_start: 0.7863 (m-40) cc_final: 0.7618 (m110) REVERT: K 245 LYS cc_start: 0.7736 (ptmt) cc_final: 0.7442 (ptmt) REVERT: K 252 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7628 (mmtm) REVERT: K 283 VAL cc_start: 0.8710 (t) cc_final: 0.8349 (p) REVERT: T 4 MET cc_start: 0.6735 (ptm) cc_final: 0.6489 (ptm) REVERT: T 23 CYS cc_start: 0.4454 (t) cc_final: 0.3405 (t) REVERT: U 71 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7330 (ttpp) REVERT: U 96 HIS cc_start: 0.7045 (t-170) cc_final: 0.6509 (t-90) REVERT: U 97 PHE cc_start: 0.8425 (t80) cc_final: 0.8167 (t80) REVERT: V 63 SER cc_start: 0.6604 (p) cc_final: 0.6214 (p) outliers start: 100 outliers final: 66 residues processed: 744 average time/residue: 0.3610 time to fit residues: 427.8493 Evaluate side-chains 739 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 671 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 302 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 41 HIS 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 290 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 307 THR 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 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 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 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 G residue 240 SER Chi-restraints excluded: chain G residue 290 LYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 38 LEU 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 129 VAL 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 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 141 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 102 GLN A 149 ASN A 222 GLN A 270 ASN A 355 HIS A 368 GLN B 81 GLN B 121 HIS F 16 ASN F 218 ASN F 360 ASN G 239 ASN ** G 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105006 restraints weight = 33448.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107941 restraints weight = 16102.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109841 restraints weight = 9639.133| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21242 Z= 0.212 Angle : 0.749 20.131 28851 Z= 0.426 Chirality : 0.046 0.202 3220 Planarity : 0.005 0.057 3703 Dihedral : 6.497 43.203 2695 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.55 % Favored : 92.27 % Rotamer: Outliers : 4.34 % Allowed : 14.90 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.15), residues: 2677 helix: 0.44 (1.09), residues: 27 sheet: -1.24 (0.15), residues: 1102 loop : -2.64 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP U 103 HIS 0.009 0.001 HIS U 96 PHE 0.031 0.002 PHE A 365 TYR 0.018 0.002 TYR U 35 ARG 0.000 0.000 ARG V 61 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 590) hydrogen bonds : angle 5.85453 ( 1590) SS BOND : bond 0.00457 ( 44) SS BOND : angle 1.30404 ( 88) covalent geometry : bond 0.00443 (21198) covalent geometry : angle 0.74622 (28763) *********************** 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 787 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 687 time to evaluate : 2.866 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: 0.8093 (mtpt) cc_final: 0.7783 (mtpp) REVERT: A 75 ASP cc_start: 0.8018 (t0) cc_final: 0.7745 (t70) REVERT: A 76 GLU cc_start: 0.7101 (tp30) cc_final: 0.6822 (tp30) REVERT: A 99 GLU cc_start: 0.8332 (pm20) cc_final: 0.7846 (pm20) REVERT: A 105 LYS cc_start: 0.8477 (mttt) cc_final: 0.7621 (ttmm) REVERT: A 137 VAL cc_start: 0.8488 (t) cc_final: 0.8209 (p) REVERT: A 143 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7758 (m) REVERT: A 148 VAL cc_start: 0.7643 (m) cc_final: 0.7369 (p) REVERT: A 183 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6115 (mt-10) REVERT: A 225 LYS cc_start: 0.7646 (ttpp) cc_final: 0.7246 (ttmm) REVERT: A 300 GLU cc_start: 0.6341 (tm-30) cc_final: 0.6118 (tm-30) REVERT: A 357 SER cc_start: 0.8472 (t) cc_final: 0.8110 (p) REVERT: A 368 GLN cc_start: 0.8170 (tt0) cc_final: 0.7913 (tt0) REVERT: A 385 ASP cc_start: 0.7005 (p0) cc_final: 0.6751 (p0) REVERT: A 390 HIS cc_start: 0.7517 (p90) cc_final: 0.6988 (p90) REVERT: B 37 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7837 (mmtp) REVERT: B 144 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6565 (mm-30) REVERT: B 241 ASP cc_start: 0.7932 (p0) cc_final: 0.7722 (p0) REVERT: B 245 LYS cc_start: 0.7417 (ttpt) cc_final: 0.7170 (ttpt) REVERT: B 255 LEU cc_start: 0.7821 (mp) cc_final: 0.7542 (mt) REVERT: B 286 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7633 (mtpp) REVERT: F 37 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8250 (mtmt) REVERT: F 52 LYS cc_start: 0.8365 (tttt) cc_final: 0.7874 (ttpp) REVERT: F 76 GLU cc_start: 0.7220 (tp30) cc_final: 0.6814 (tp30) REVERT: F 79 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8274 (mtpp) REVERT: F 99 GLU cc_start: 0.8413 (pm20) cc_final: 0.7894 (pm20) REVERT: F 105 LYS cc_start: 0.8419 (mttt) cc_final: 0.7854 (mtpt) REVERT: F 133 LEU cc_start: 0.7972 (mt) cc_final: 0.7753 (mm) REVERT: F 216 ASN cc_start: 0.7729 (t0) cc_final: 0.7445 (t0) REVERT: F 225 LYS cc_start: 0.8054 (tttt) cc_final: 0.7761 (tttp) REVERT: F 241 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6617 (mm-30) REVERT: F 270 ASN cc_start: 0.7951 (m-40) cc_final: 0.7737 (m-40) REVERT: F 312 PHE cc_start: 0.7794 (m-10) cc_final: 0.7495 (m-80) REVERT: F 317 THR cc_start: 0.7849 (m) cc_final: 0.7570 (p) REVERT: F 340 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7860 (ttmm) REVERT: F 360 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.6854 (m-40) REVERT: G 37 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7905 (tppt) REVERT: G 66 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7774 (ttt) REVERT: G 167 MET cc_start: 0.7169 (ptp) cc_final: 0.6890 (ptp) REVERT: G 252 LYS cc_start: 0.8094 (mppt) cc_final: 0.7349 (mmtm) REVERT: G 255 LEU cc_start: 0.7858 (pp) cc_final: 0.7297 (pt) REVERT: G 273 GLU cc_start: 0.7339 (tp30) cc_final: 0.7087 (tp30) REVERT: G 277 THR cc_start: 0.8131 (m) cc_final: 0.7651 (p) REVERT: J 31 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7724 (pt) REVERT: J 42 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8244 (m) REVERT: J 99 GLU cc_start: 0.8355 (pm20) cc_final: 0.7934 (pm20) REVERT: J 105 LYS cc_start: 0.8428 (mttt) cc_final: 0.7721 (mtmt) REVERT: J 117 ASP cc_start: 0.7434 (t0) cc_final: 0.7161 (t0) REVERT: J 151 GLU cc_start: 0.7419 (pm20) cc_final: 0.7217 (pm20) REVERT: J 157 ASN cc_start: 0.7273 (t0) cc_final: 0.6448 (t0) REVERT: J 160 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7248 (ttpp) REVERT: J 216 ASN cc_start: 0.7818 (t0) cc_final: 0.7516 (t0) REVERT: J 217 THR cc_start: 0.8535 (p) cc_final: 0.8035 (t) REVERT: J 218 ASN cc_start: 0.8353 (t0) cc_final: 0.8098 (t0) REVERT: J 242 GLN cc_start: 0.8376 (tp40) cc_final: 0.7890 (tp-100) REVERT: J 311 ASP cc_start: 0.7598 (t0) cc_final: 0.7076 (t0) REVERT: J 338 THR cc_start: 0.7881 (m) cc_final: 0.7509 (p) REVERT: J 340 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7590 (ttmm) REVERT: J 355 HIS cc_start: 0.7260 (m-70) cc_final: 0.6757 (m-70) REVERT: J 357 SER cc_start: 0.8422 (t) cc_final: 0.7979 (t) REVERT: J 385 ASP cc_start: 0.7314 (p0) cc_final: 0.7039 (p0) REVERT: K 37 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7308 (tppt) REVERT: K 42 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6819 (t70) REVERT: K 137 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6995 (tt0) REVERT: K 239 ASN cc_start: 0.7805 (t0) cc_final: 0.7541 (m110) REVERT: K 245 LYS cc_start: 0.7759 (ptmt) cc_final: 0.7443 (ptmt) REVERT: K 252 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7601 (mmtm) REVERT: K 254 LYS cc_start: 0.7507 (pptt) cc_final: 0.7216 (ptmm) REVERT: K 283 VAL cc_start: 0.8574 (t) cc_final: 0.8182 (p) REVERT: T 23 CYS cc_start: 0.4911 (t) cc_final: 0.3675 (t) REVERT: U 71 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7231 (ttpp) REVERT: U 97 PHE cc_start: 0.8342 (t80) cc_final: 0.8014 (t80) REVERT: V 63 SER cc_start: 0.6645 (p) cc_final: 0.6264 (p) outliers start: 100 outliers final: 62 residues processed: 730 average time/residue: 0.3229 time to fit residues: 372.3663 Evaluate side-chains 738 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 670 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain 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 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 339 TRP 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 293 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 341 GLU 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 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 83 SER Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 31 ILE 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 302 THR Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 369 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 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 290 LYS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 26 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 204 GLN A 222 GLN B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 392 GLN F 394 HIS G 81 GLN G 305 HIS J 16 ASN J 50 HIS J 381 HIS ** L 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 = 0.3526 r_free = 0.3526 target = 0.131287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108568 restraints weight = 32762.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111656 restraints weight = 15644.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113514 restraints weight = 9305.249| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21242 Z= 0.242 Angle : 0.766 21.980 28851 Z= 0.432 Chirality : 0.047 0.224 3220 Planarity : 0.005 0.057 3703 Dihedral : 6.435 42.081 2695 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.04 % Favored : 90.81 % Rotamer: Outliers : 5.08 % Allowed : 15.81 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 2677 helix: 0.66 (1.10), residues: 27 sheet: -1.00 (0.15), residues: 1081 loop : -2.58 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 103 HIS 0.013 0.001 HIS J 381 PHE 0.029 0.002 PHE J 156 TYR 0.018 0.002 TYR U 35 ARG 0.000 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 590) hydrogen bonds : angle 5.82930 ( 1590) SS BOND : bond 0.00487 ( 44) SS BOND : angle 1.42019 ( 88) covalent geometry : bond 0.00521 (21198) covalent geometry : angle 0.76333 (28763) *********************** 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 806 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 689 time to evaluate : 2.385 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: 0.8142 (mtpt) cc_final: 0.7821 (mtpp) REVERT: A 75 ASP cc_start: 0.7984 (t0) cc_final: 0.7698 (t70) REVERT: A 76 GLU cc_start: 0.7079 (tp30) cc_final: 0.6815 (tp30) REVERT: A 99 GLU cc_start: 0.8306 (pm20) cc_final: 0.7860 (pm20) REVERT: A 105 LYS cc_start: 0.8449 (mttt) cc_final: 0.7590 (ttmm) REVERT: A 137 VAL cc_start: 0.8521 (t) cc_final: 0.8223 (p) REVERT: A 143 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7784 (m) REVERT: A 148 VAL cc_start: 0.7724 (m) cc_final: 0.7425 (p) REVERT: A 183 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6329 (mt-10) REVERT: A 203 ILE cc_start: 0.8282 (mm) cc_final: 0.7966 (tp) REVERT: A 208 VAL cc_start: 0.8988 (p) cc_final: 0.8763 (p) REVERT: A 217 THR cc_start: 0.8630 (p) cc_final: 0.8157 (t) REVERT: A 225 LYS cc_start: 0.7552 (ttpp) cc_final: 0.7133 (ttmm) REVERT: A 357 SER cc_start: 0.8469 (t) cc_final: 0.8086 (p) REVERT: A 360 ASN cc_start: 0.7231 (m-40) cc_final: 0.6836 (m-40) REVERT: A 385 ASP cc_start: 0.7055 (p0) cc_final: 0.6846 (p0) REVERT: A 390 HIS cc_start: 0.7680 (p90) cc_final: 0.7243 (p90) REVERT: B 37 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7800 (mmtp) REVERT: B 144 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6582 (mm-30) REVERT: B 255 LEU cc_start: 0.7892 (mp) cc_final: 0.7632 (mt) REVERT: B 286 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7617 (mtpp) REVERT: F 37 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8259 (mtmt) REVERT: F 52 LYS cc_start: 0.8405 (tttt) cc_final: 0.7921 (ttpp) REVERT: F 76 GLU cc_start: 0.7115 (tp30) cc_final: 0.6708 (tp30) REVERT: F 99 GLU cc_start: 0.8482 (pm20) cc_final: 0.7963 (pm20) REVERT: F 105 LYS cc_start: 0.8438 (mttt) cc_final: 0.7981 (mtpt) REVERT: F 133 LEU cc_start: 0.7982 (mt) cc_final: 0.7750 (mm) REVERT: F 151 GLU cc_start: 0.7063 (pm20) cc_final: 0.6821 (pm20) REVERT: F 225 LYS cc_start: 0.8028 (tttt) cc_final: 0.7766 (tttp) REVERT: F 241 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6686 (mm-30) REVERT: F 270 ASN cc_start: 0.7781 (m-40) cc_final: 0.7526 (m-40) REVERT: F 312 PHE cc_start: 0.7926 (m-10) cc_final: 0.7634 (m-80) REVERT: F 317 THR cc_start: 0.7871 (m) cc_final: 0.7599 (p) REVERT: F 324 LYS cc_start: 0.7402 (tppt) cc_final: 0.7095 (tppt) REVERT: F 340 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7885 (ttmm) REVERT: F 360 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6498 (m-40) REVERT: G 37 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7907 (tppt) REVERT: G 252 LYS cc_start: 0.8132 (mppt) cc_final: 0.7376 (mmtm) REVERT: G 255 LEU cc_start: 0.7766 (pp) cc_final: 0.7186 (pt) REVERT: G 273 GLU cc_start: 0.7319 (tp30) cc_final: 0.7099 (tp30) REVERT: G 277 THR cc_start: 0.8140 (m) cc_final: 0.7665 (p) REVERT: J 31 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7807 (pt) REVERT: J 42 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8183 (p) REVERT: J 99 GLU cc_start: 0.8404 (pm20) cc_final: 0.8005 (pm20) REVERT: J 105 LYS cc_start: 0.8390 (mttt) cc_final: 0.7794 (mtmt) REVERT: J 117 ASP cc_start: 0.7429 (t0) cc_final: 0.7222 (t0) REVERT: J 157 ASN cc_start: 0.7242 (t0) cc_final: 0.6410 (t0) REVERT: J 160 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7243 (ttpp) REVERT: J 216 ASN cc_start: 0.7819 (t0) cc_final: 0.7572 (t0) REVERT: J 217 THR cc_start: 0.8549 (p) cc_final: 0.8064 (t) REVERT: J 218 ASN cc_start: 0.8380 (t0) cc_final: 0.8119 (t0) REVERT: J 241 GLU cc_start: 0.7107 (tp30) cc_final: 0.6897 (tp30) REVERT: J 242 GLN cc_start: 0.8477 (tp40) cc_final: 0.8151 (tp40) REVERT: J 311 ASP cc_start: 0.7626 (t0) cc_final: 0.7099 (t0) REVERT: J 338 THR cc_start: 0.7913 (m) cc_final: 0.7537 (p) REVERT: J 340 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7631 (ttmm) REVERT: J 355 HIS cc_start: 0.7083 (m-70) cc_final: 0.6588 (m-70) REVERT: J 357 SER cc_start: 0.8369 (t) cc_final: 0.7949 (t) REVERT: J 387 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7867 (mt) REVERT: K 37 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7460 (tppt) REVERT: K 42 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6809 (t70) REVERT: K 239 ASN cc_start: 0.7847 (t0) cc_final: 0.7570 (m110) REVERT: K 245 LYS cc_start: 0.7744 (ptmt) cc_final: 0.7415 (ptmt) REVERT: K 252 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7492 (mmtm) REVERT: K 254 LYS cc_start: 0.7432 (pptt) cc_final: 0.7185 (ptmm) REVERT: K 283 VAL cc_start: 0.8589 (t) cc_final: 0.8226 (p) REVERT: T 11 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6845 (tt) REVERT: U 71 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7216 (ttpp) REVERT: U 96 HIS cc_start: 0.7413 (t-90) cc_final: 0.7145 (t70) REVERT: U 97 PHE cc_start: 0.8322 (t80) cc_final: 0.7995 (t80) REVERT: V 63 SER cc_start: 0.6609 (p) cc_final: 0.6222 (p) outliers start: 117 outliers final: 85 residues processed: 741 average time/residue: 0.4048 time to fit residues: 478.1218 Evaluate side-chains 753 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 661 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 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 261 LEU 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 55 MET 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 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 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 140 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 260 GLU 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 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 167 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 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 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 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 99 SER 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 11 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 163 optimal weight: 0.0470 chunk 139 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 ASN F 381 HIS ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 159 GLN H 76 ASN J 16 ASN J 381 HIS K 80 HIS ** L 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 = 0.3502 r_free = 0.3502 target = 0.126315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104049 restraints weight = 33095.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107078 restraints weight = 15849.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108840 restraints weight = 9427.340| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21242 Z= 0.218 Angle : 0.741 19.689 28851 Z= 0.421 Chirality : 0.046 0.215 3220 Planarity : 0.005 0.054 3703 Dihedral : 6.289 40.520 2695 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.99 % Favored : 91.89 % Rotamer: Outliers : 5.17 % Allowed : 16.68 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.15), residues: 2677 helix: 0.75 (1.08), residues: 27 sheet: -0.82 (0.15), residues: 1102 loop : -2.49 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP U 103 HIS 0.009 0.001 HIS S 96 PHE 0.045 0.002 PHE J 398 TYR 0.017 0.002 TYR U 35 ARG 0.000 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 590) hydrogen bonds : angle 5.72152 ( 1590) SS BOND : bond 0.00439 ( 44) SS BOND : angle 1.20256 ( 88) covalent geometry : bond 0.00462 (21198) covalent geometry : angle 0.73886 (28763) *********************** 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 804 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 685 time to evaluate : 2.973 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: 0.8140 (mtpt) cc_final: 0.7526 (mtpp) REVERT: A 76 GLU cc_start: 0.7058 (tp30) cc_final: 0.6815 (tp30) REVERT: A 99 GLU cc_start: 0.8296 (pm20) cc_final: 0.7851 (pm20) REVERT: A 105 LYS cc_start: 0.8458 (mttt) cc_final: 0.7604 (ttmm) REVERT: A 137 VAL cc_start: 0.8599 (t) cc_final: 0.8293 (p) REVERT: A 143 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7786 (m) REVERT: A 148 VAL cc_start: 0.7587 (m) cc_final: 0.7382 (p) REVERT: A 183 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6505 (mt-10) REVERT: A 203 ILE cc_start: 0.8333 (mm) cc_final: 0.8000 (tp) REVERT: A 208 VAL cc_start: 0.8974 (p) cc_final: 0.8734 (p) REVERT: A 217 THR cc_start: 0.8613 (p) cc_final: 0.8176 (t) REVERT: A 225 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7207 (ttmm) REVERT: A 269 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6659 (mt-10) REVERT: A 357 SER cc_start: 0.8497 (t) cc_final: 0.8097 (p) REVERT: A 360 ASN cc_start: 0.7269 (m-40) cc_final: 0.6903 (m-40) REVERT: A 385 ASP cc_start: 0.7090 (p0) cc_final: 0.6887 (p0) REVERT: A 390 HIS cc_start: 0.7810 (p90) cc_final: 0.7471 (p90) REVERT: B 37 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7874 (mmmm) REVERT: B 137 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7022 (mt-10) REVERT: B 144 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6628 (mm-30) REVERT: B 255 LEU cc_start: 0.7816 (mp) cc_final: 0.7540 (mt) REVERT: B 286 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7617 (mtpp) REVERT: F 42 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8091 (p) REVERT: F 52 LYS cc_start: 0.8314 (tttt) cc_final: 0.7833 (ttpp) REVERT: F 76 GLU cc_start: 0.7087 (tp30) cc_final: 0.6682 (tp30) REVERT: F 99 GLU cc_start: 0.8447 (pm20) cc_final: 0.8009 (pm20) REVERT: F 105 LYS cc_start: 0.8418 (mttt) cc_final: 0.7969 (mtpt) REVERT: F 133 LEU cc_start: 0.7982 (mt) cc_final: 0.7753 (mm) REVERT: F 151 GLU cc_start: 0.7078 (pm20) cc_final: 0.6757 (pm20) REVERT: F 225 LYS cc_start: 0.8004 (tttt) cc_final: 0.7717 (tttp) REVERT: F 241 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6667 (mm-30) REVERT: F 270 ASN cc_start: 0.7711 (m-40) cc_final: 0.7397 (m-40) REVERT: F 312 PHE cc_start: 0.7936 (m-10) cc_final: 0.7682 (m-80) REVERT: F 317 THR cc_start: 0.7911 (m) cc_final: 0.7636 (p) REVERT: F 340 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7856 (ttmm) REVERT: F 399 THR cc_start: 0.7068 (t) cc_final: 0.6757 (p) REVERT: G 252 LYS cc_start: 0.8180 (mppt) cc_final: 0.7611 (mmtm) REVERT: G 273 GLU cc_start: 0.7341 (tp30) cc_final: 0.7113 (tp30) REVERT: G 277 THR cc_start: 0.8107 (m) cc_final: 0.7646 (p) REVERT: J 31 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7814 (pt) REVERT: J 37 LYS cc_start: 0.8668 (mttt) cc_final: 0.8400 (mttp) REVERT: J 42 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8170 (p) REVERT: J 99 GLU cc_start: 0.8389 (pm20) cc_final: 0.7989 (pm20) REVERT: J 105 LYS cc_start: 0.8372 (mttt) cc_final: 0.7781 (mtmt) REVERT: J 117 ASP cc_start: 0.7439 (t0) cc_final: 0.7189 (t0) REVERT: J 160 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7428 (ttpp) REVERT: J 216 ASN cc_start: 0.7805 (t0) cc_final: 0.7560 (t0) REVERT: J 217 THR cc_start: 0.8556 (p) cc_final: 0.8063 (t) REVERT: J 218 ASN cc_start: 0.8394 (t0) cc_final: 0.8145 (t0) REVERT: J 241 GLU cc_start: 0.7077 (tp30) cc_final: 0.6807 (tp30) REVERT: J 242 GLN cc_start: 0.8465 (tp40) cc_final: 0.8098 (tp-100) REVERT: J 244 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7843 (ttmm) REVERT: J 311 ASP cc_start: 0.7655 (t0) cc_final: 0.7111 (t0) REVERT: J 338 THR cc_start: 0.7914 (m) cc_final: 0.7563 (p) REVERT: J 340 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7511 (ttmm) REVERT: J 357 SER cc_start: 0.8389 (t) cc_final: 0.7953 (t) REVERT: K 37 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7446 (tppt) REVERT: K 42 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6781 (t70) REVERT: K 49 THR cc_start: 0.8467 (p) cc_final: 0.8012 (t) REVERT: K 239 ASN cc_start: 0.7821 (t0) cc_final: 0.7555 (m110) REVERT: K 245 LYS cc_start: 0.7728 (ptmt) cc_final: 0.7409 (ptmt) REVERT: K 252 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7518 (mmtm) REVERT: K 254 LYS cc_start: 0.7422 (pttt) cc_final: 0.7184 (ptmm) REVERT: K 283 VAL cc_start: 0.8546 (t) cc_final: 0.8184 (p) REVERT: T 11 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6834 (tt) REVERT: U 71 LYS cc_start: 0.7551 (ttpp) cc_final: 0.7243 (ttpp) REVERT: U 96 HIS cc_start: 0.7574 (t-90) cc_final: 0.7340 (t70) REVERT: U 97 PHE cc_start: 0.8330 (t80) cc_final: 0.8043 (t80) REVERT: V 63 SER cc_start: 0.6583 (p) cc_final: 0.6208 (p) outliers start: 119 outliers final: 91 residues processed: 734 average time/residue: 0.3888 time to fit residues: 451.5438 Evaluate side-chains 772 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 675 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 41 HIS 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 261 LEU 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 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 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 140 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 328 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 130 GLN 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 353 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 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 84 LEU 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 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 67 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 149 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN F 102 GLN F 204 GLN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 HIS F 386 HIS F 394 HIS G 81 GLN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN J 16 ASN J 43 ASN K 305 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105295 restraints weight = 33064.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108435 restraints weight = 15735.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110372 restraints weight = 9213.745| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21242 Z= 0.186 Angle : 0.716 16.027 28851 Z= 0.409 Chirality : 0.045 0.190 3220 Planarity : 0.005 0.052 3703 Dihedral : 6.057 40.282 2695 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 4.65 % Allowed : 17.85 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2677 helix: 0.86 (1.08), residues: 27 sheet: -0.68 (0.15), residues: 1102 loop : -2.36 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 103 HIS 0.011 0.001 HIS J 381 PHE 0.046 0.002 PHE J 398 TYR 0.016 0.001 TYR U 35 ARG 0.000 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 590) hydrogen bonds : angle 5.56002 ( 1590) SS BOND : bond 0.00370 ( 44) SS BOND : angle 1.09330 ( 88) covalent geometry : bond 0.00381 (21198) covalent geometry : angle 0.71429 (28763) *********************** 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 791 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 684 time to evaluate : 3.309 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: 0.8140 (mtpt) cc_final: 0.7813 (mtpp) REVERT: A 52 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7928 (ttpt) REVERT: A 76 GLU cc_start: 0.7098 (tp30) cc_final: 0.6819 (tp30) REVERT: A 99 GLU cc_start: 0.8289 (pm20) cc_final: 0.7828 (pm20) REVERT: A 137 VAL cc_start: 0.8556 (t) cc_final: 0.8221 (p) REVERT: A 143 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7764 (m) REVERT: A 183 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6483 (mt-10) REVERT: A 203 ILE cc_start: 0.8285 (mm) cc_final: 0.7994 (tp) REVERT: A 208 VAL cc_start: 0.8986 (p) cc_final: 0.8741 (p) REVERT: A 225 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7199 (ttmm) REVERT: A 357 SER cc_start: 0.8480 (t) cc_final: 0.8088 (p) REVERT: A 390 HIS cc_start: 0.7892 (p90) cc_final: 0.7632 (p90) REVERT: B 37 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7857 (mmtp) REVERT: B 130 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7767 (mtmm) REVERT: B 144 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6701 (mm-30) REVERT: B 149 GLN cc_start: 0.8336 (mt0) cc_final: 0.8054 (tt0) REVERT: B 255 LEU cc_start: 0.7786 (mp) cc_final: 0.7489 (mt) REVERT: B 286 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7616 (mtpp) REVERT: F 42 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8103 (p) REVERT: F 52 LYS cc_start: 0.8300 (tttt) cc_final: 0.7774 (ttpp) REVERT: F 76 GLU cc_start: 0.7145 (tp30) cc_final: 0.6702 (tp30) REVERT: F 98 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7357 (m) REVERT: F 99 GLU cc_start: 0.8401 (pm20) cc_final: 0.8008 (pm20) REVERT: F 105 LYS cc_start: 0.8434 (mttt) cc_final: 0.7929 (mtpt) REVERT: F 133 LEU cc_start: 0.7952 (mt) cc_final: 0.7670 (mm) REVERT: F 151 GLU cc_start: 0.6968 (pm20) cc_final: 0.6738 (pm20) REVERT: F 217 THR cc_start: 0.8729 (p) cc_final: 0.8329 (t) REVERT: F 225 LYS cc_start: 0.7963 (tttt) cc_final: 0.7637 (tttp) REVERT: F 241 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6659 (mm-30) REVERT: F 269 GLU cc_start: 0.7512 (tt0) cc_final: 0.7309 (tt0) REVERT: F 312 PHE cc_start: 0.7915 (m-10) cc_final: 0.7681 (m-80) REVERT: F 317 THR cc_start: 0.7861 (m) cc_final: 0.7580 (p) REVERT: F 340 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7776 (ttmm) REVERT: G 66 MET cc_start: 0.8217 (ttt) cc_final: 0.7723 (ttt) REVERT: G 77 ILE cc_start: 0.8256 (mt) cc_final: 0.8040 (pt) REVERT: G 252 LYS cc_start: 0.8190 (mppt) cc_final: 0.7630 (mmtm) REVERT: G 265 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7854 (mmmm) REVERT: G 277 THR cc_start: 0.8115 (m) cc_final: 0.7620 (p) REVERT: J 31 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7755 (pt) REVERT: J 42 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8270 (p) REVERT: J 99 GLU cc_start: 0.8405 (pm20) cc_final: 0.8027 (pm20) REVERT: J 105 LYS cc_start: 0.8359 (mttt) cc_final: 0.7748 (mtmt) REVERT: J 117 ASP cc_start: 0.7387 (t0) cc_final: 0.7139 (t0) REVERT: J 160 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7423 (ttpp) REVERT: J 216 ASN cc_start: 0.7822 (t0) cc_final: 0.7555 (t0) REVERT: J 217 THR cc_start: 0.8552 (p) cc_final: 0.8042 (t) REVERT: J 218 ASN cc_start: 0.8390 (t0) cc_final: 0.8129 (t0) REVERT: J 241 GLU cc_start: 0.7090 (tp30) cc_final: 0.6338 (tp30) REVERT: J 242 GLN cc_start: 0.8419 (tp40) cc_final: 0.8082 (tp40) REVERT: J 244 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7798 (ttmm) REVERT: J 245 LYS cc_start: 0.8164 (ptpp) cc_final: 0.7568 (ptpp) REVERT: J 311 ASP cc_start: 0.7658 (t0) cc_final: 0.7098 (t0) REVERT: J 338 THR cc_start: 0.7928 (m) cc_final: 0.7502 (p) REVERT: J 340 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7592 (ttpp) REVERT: J 357 SER cc_start: 0.8360 (t) cc_final: 0.7910 (t) REVERT: J 387 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7734 (mt) REVERT: K 37 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7456 (tppt) REVERT: K 42 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6686 (t70) REVERT: K 49 THR cc_start: 0.8463 (p) cc_final: 0.8010 (t) REVERT: K 144 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6656 (mm-30) REVERT: K 239 ASN cc_start: 0.7781 (t0) cc_final: 0.7505 (m110) REVERT: K 245 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7421 (ptmt) REVERT: K 252 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7537 (mmtm) REVERT: K 254 LYS cc_start: 0.7408 (pttt) cc_final: 0.7123 (ptmm) REVERT: K 283 VAL cc_start: 0.8534 (t) cc_final: 0.8235 (p) REVERT: T 11 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6837 (tt) REVERT: U 96 HIS cc_start: 0.7539 (t-90) cc_final: 0.7268 (t70) REVERT: U 97 PHE cc_start: 0.8324 (t80) cc_final: 0.8029 (t80) REVERT: V 63 SER cc_start: 0.6570 (p) cc_final: 0.6209 (p) outliers start: 107 outliers final: 78 residues processed: 729 average time/residue: 0.4560 time to fit residues: 525.4597 Evaluate side-chains 748 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 662 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET 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 B residue 41 HIS 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 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 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 87 PHE Chi-restraints excluded: chain F residue 98 THR 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 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 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 H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 130 GLN Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 183 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 381 HIS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 42 ASP 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 307 THR Chi-restraints excluded: chain K residue 327 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain T residue 11 LEU 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 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 120 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 130 optimal weight: 0.0770 chunk 205 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** 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 F 381 HIS ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN J 381 HIS K 81 GLN K 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103134 restraints weight = 33226.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106291 restraints weight = 15567.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108256 restraints weight = 9059.735| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21242 Z= 0.258 Angle : 0.764 20.822 28851 Z= 0.432 Chirality : 0.047 0.202 3220 Planarity : 0.005 0.054 3703 Dihedral : 6.295 40.714 2695 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.19 % Favored : 90.70 % Rotamer: Outliers : 5.26 % Allowed : 17.29 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2677 helix: 0.71 (1.04), residues: 27 sheet: -0.68 (0.15), residues: 1099 loop : -2.37 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 103 HIS 0.019 0.002 HIS F 394 PHE 0.050 0.002 PHE J 398 TYR 0.020 0.002 TYR B 15 ARG 0.000 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 590) hydrogen bonds : angle 5.73924 ( 1590) SS BOND : bond 0.00527 ( 44) SS BOND : angle 1.28285 ( 88) covalent geometry : bond 0.00560 (21198) covalent geometry : angle 0.76188 (28763) *********************** 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 794 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 673 time to evaluate : 2.293 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: 0.8163 (mtpt) cc_final: 0.7857 (mtpp) REVERT: A 76 GLU cc_start: 0.7018 (tp30) cc_final: 0.6798 (tp30) REVERT: A 99 GLU cc_start: 0.8330 (pm20) cc_final: 0.7881 (pm20) REVERT: A 105 LYS cc_start: 0.8417 (mttt) cc_final: 0.7592 (ttmm) REVERT: A 137 VAL cc_start: 0.8464 (t) cc_final: 0.8183 (p) REVERT: A 143 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7808 (m) REVERT: A 183 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6501 (mt-10) REVERT: A 196 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7123 (mm-40) REVERT: A 203 ILE cc_start: 0.8304 (mm) cc_final: 0.8006 (tp) REVERT: A 208 VAL cc_start: 0.9006 (p) cc_final: 0.8769 (p) REVERT: A 225 LYS cc_start: 0.7803 (ttpp) cc_final: 0.7314 (ttmm) REVERT: A 357 SER cc_start: 0.8616 (t) cc_final: 0.8073 (p) REVERT: A 360 ASN cc_start: 0.7300 (m-40) cc_final: 0.6794 (m-40) REVERT: A 390 HIS cc_start: 0.7937 (p-80) cc_final: 0.7672 (p90) REVERT: A 399 THR cc_start: 0.7507 (m) cc_final: 0.7023 (p) REVERT: B 37 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7816 (mmtp) REVERT: B 137 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 144 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6672 (mm-30) REVERT: B 245 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7109 (ttpp) REVERT: B 255 LEU cc_start: 0.7862 (mp) cc_final: 0.7550 (mt) REVERT: B 285 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7992 (mp) REVERT: B 286 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7642 (mtpp) REVERT: F 20 ASN cc_start: 0.7683 (p0) cc_final: 0.7377 (p0) REVERT: F 52 LYS cc_start: 0.8262 (tttt) cc_final: 0.7995 (ttpt) REVERT: F 76 GLU cc_start: 0.7162 (tp30) cc_final: 0.6760 (tp30) REVERT: F 99 GLU cc_start: 0.8484 (pm20) cc_final: 0.8090 (pm20) REVERT: F 105 LYS cc_start: 0.8453 (mttt) cc_final: 0.7944 (mtpt) REVERT: F 125 HIS cc_start: 0.7328 (p90) cc_final: 0.7095 (p90) REVERT: F 133 LEU cc_start: 0.8008 (mt) cc_final: 0.7753 (mm) REVERT: F 151 GLU cc_start: 0.7045 (pm20) cc_final: 0.6815 (pm20) REVERT: F 217 THR cc_start: 0.8733 (p) cc_final: 0.8340 (t) REVERT: F 241 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6674 (mm-30) REVERT: F 317 THR cc_start: 0.7908 (m) cc_final: 0.7621 (p) REVERT: F 340 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7854 (ttmm) REVERT: G 66 MET cc_start: 0.8186 (ttt) cc_final: 0.7720 (ttt) REVERT: G 252 LYS cc_start: 0.8147 (mppt) cc_final: 0.7449 (mmtm) REVERT: G 254 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7257 (tttm) REVERT: G 265 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7771 (mmmt) REVERT: G 277 THR cc_start: 0.8145 (m) cc_final: 0.7627 (p) REVERT: G 323 GLU cc_start: 0.7082 (pp20) cc_final: 0.6430 (pp20) REVERT: J 31 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7815 (pt) REVERT: J 42 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8241 (p) REVERT: J 99 GLU cc_start: 0.8407 (pm20) cc_final: 0.8014 (pm20) REVERT: J 105 LYS cc_start: 0.8339 (mttt) cc_final: 0.7813 (mtmt) REVERT: J 117 ASP cc_start: 0.7513 (t0) cc_final: 0.7305 (t0) REVERT: J 160 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7434 (ttpp) REVERT: J 216 ASN cc_start: 0.7852 (t0) cc_final: 0.7643 (t0) REVERT: J 218 ASN cc_start: 0.8408 (t0) cc_final: 0.8155 (t0) REVERT: J 241 GLU cc_start: 0.7130 (tp30) cc_final: 0.6886 (tp30) REVERT: J 242 GLN cc_start: 0.8456 (tp40) cc_final: 0.8053 (tp40) REVERT: J 311 ASP cc_start: 0.7637 (t0) cc_final: 0.7165 (t0) REVERT: J 338 THR cc_start: 0.7983 (m) cc_final: 0.7586 (p) REVERT: J 340 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7487 (ttmm) REVERT: J 357 SER cc_start: 0.8399 (t) cc_final: 0.7938 (t) REVERT: J 387 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7809 (mt) REVERT: K 37 LYS cc_start: 0.7775 (mmmt) cc_final: 0.7473 (tppt) REVERT: K 42 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6867 (t70) REVERT: K 144 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6628 (mm-30) REVERT: K 239 ASN cc_start: 0.7808 (t0) cc_final: 0.7488 (m110) REVERT: K 242 LYS cc_start: 0.8339 (mmtp) cc_final: 0.8123 (mptt) REVERT: K 252 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7532 (mmtm) REVERT: K 254 LYS cc_start: 0.7419 (pttt) cc_final: 0.7201 (ptmm) REVERT: K 283 VAL cc_start: 0.8537 (t) cc_final: 0.8251 (p) REVERT: T 11 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6933 (tt) REVERT: U 71 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7272 (ttpp) REVERT: U 96 HIS cc_start: 0.7641 (t-90) cc_final: 0.7346 (t70) REVERT: U 97 PHE cc_start: 0.8340 (t80) cc_final: 0.8070 (t80) REVERT: V 63 SER cc_start: 0.6572 (p) cc_final: 0.6203 (p) outliers start: 121 outliers final: 97 residues processed: 729 average time/residue: 0.4216 time to fit residues: 491.1632 Evaluate side-chains 769 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 665 time to evaluate : 5.658 ------------------------------------------------------------------------------- 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 87 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain B residue 41 HIS 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 285 LEU 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 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 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 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 339 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 ILE 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 130 GLN 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 353 THR Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 42 ASP 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 L residue 69 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 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 28 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 222 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 381 HIS G 81 GLN G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN J 66 GLN J 381 HIS K 71 HIS ** L 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 = 0.3507 r_free = 0.3507 target = 0.126992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104546 restraints weight = 33337.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107729 restraints weight = 15649.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109686 restraints weight = 9102.047| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21242 Z= 0.201 Angle : 0.730 19.662 28851 Z= 0.416 Chirality : 0.046 0.186 3220 Planarity : 0.005 0.052 3703 Dihedral : 6.120 40.505 2695 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.11 % Favored : 91.82 % Rotamer: Outliers : 4.95 % Allowed : 17.98 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2677 helix: 1.64 (1.06), residues: 24 sheet: -0.59 (0.15), residues: 1096 loop : -2.28 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 103 HIS 0.010 0.001 HIS S 96 PHE 0.048 0.002 PHE J 398 TYR 0.017 0.001 TYR U 35 ARG 0.000 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 590) hydrogen bonds : angle 5.60668 ( 1590) SS BOND : bond 0.00418 ( 44) SS BOND : angle 1.25677 ( 88) covalent geometry : bond 0.00421 (21198) covalent geometry : angle 0.72751 (28763) *********************** 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 783 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 669 time to evaluate : 3.009 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: 0.8141 (mtpt) cc_final: 0.7846 (mtpp) REVERT: A 76 GLU cc_start: 0.7031 (tp30) cc_final: 0.6807 (tp30) REVERT: A 99 GLU cc_start: 0.8331 (pm20) cc_final: 0.7859 (pm20) REVERT: A 105 LYS cc_start: 0.8407 (mttt) cc_final: 0.7563 (ttmm) REVERT: A 137 VAL cc_start: 0.8421 (t) cc_final: 0.8123 (p) REVERT: A 143 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7782 (m) REVERT: A 196 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7101 (mm-40) REVERT: A 203 ILE cc_start: 0.8287 (mm) cc_final: 0.7992 (tp) REVERT: A 208 VAL cc_start: 0.8989 (p) cc_final: 0.8739 (p) REVERT: A 225 LYS cc_start: 0.7798 (ttpp) cc_final: 0.7319 (ttmm) REVERT: A 357 SER cc_start: 0.8595 (t) cc_final: 0.8165 (p) REVERT: A 360 ASN cc_start: 0.7255 (m-40) cc_final: 0.6861 (m-40) REVERT: A 399 THR cc_start: 0.7703 (m) cc_final: 0.7337 (p) REVERT: B 37 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7857 (mmtp) REVERT: B 137 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6906 (mt-10) REVERT: B 144 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6691 (mm-30) REVERT: B 245 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7113 (ttpp) REVERT: B 255 LEU cc_start: 0.7824 (mp) cc_final: 0.7500 (mt) REVERT: B 286 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7655 (mtpp) REVERT: F 52 LYS cc_start: 0.8230 (tttt) cc_final: 0.7768 (ttpp) REVERT: F 76 GLU cc_start: 0.7141 (tp30) cc_final: 0.6714 (tp30) REVERT: F 79 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8225 (ttmm) REVERT: F 99 GLU cc_start: 0.8409 (pm20) cc_final: 0.8173 (pm20) REVERT: F 105 LYS cc_start: 0.8424 (mttt) cc_final: 0.7936 (mtpt) REVERT: F 125 HIS cc_start: 0.7329 (p90) cc_final: 0.7082 (p90) REVERT: F 133 LEU cc_start: 0.7958 (mt) cc_final: 0.7674 (mm) REVERT: F 151 GLU cc_start: 0.7017 (pm20) cc_final: 0.6775 (pm20) REVERT: F 156 PHE cc_start: 0.7022 (p90) cc_final: 0.6549 (p90) REVERT: F 217 THR cc_start: 0.8734 (p) cc_final: 0.8326 (t) REVERT: F 241 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6669 (mm-30) REVERT: F 317 THR cc_start: 0.7896 (m) cc_final: 0.7615 (p) REVERT: F 340 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7818 (ttmm) REVERT: G 49 THR cc_start: 0.7874 (t) cc_final: 0.7475 (p) REVERT: G 66 MET cc_start: 0.8239 (ttt) cc_final: 0.7768 (ttt) REVERT: G 252 LYS cc_start: 0.8168 (mppt) cc_final: 0.7619 (mmtm) REVERT: G 254 LYS cc_start: 0.7555 (ttpt) cc_final: 0.7271 (tttm) REVERT: G 265 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7791 (mmmt) REVERT: G 277 THR cc_start: 0.8156 (m) cc_final: 0.7633 (p) REVERT: G 323 GLU cc_start: 0.7101 (pp20) cc_final: 0.6434 (pp20) REVERT: J 31 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7760 (pt) REVERT: J 37 LYS cc_start: 0.8626 (mttt) cc_final: 0.8414 (mttp) REVERT: J 42 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8252 (p) REVERT: J 52 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7776 (ptpt) REVERT: J 77 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7465 (mm-40) REVERT: J 99 GLU cc_start: 0.8420 (pm20) cc_final: 0.7689 (pm20) REVERT: J 105 LYS cc_start: 0.8325 (mttt) cc_final: 0.7798 (mtmt) REVERT: J 117 ASP cc_start: 0.7422 (t0) cc_final: 0.7188 (t0) REVERT: J 160 LYS cc_start: 0.7746 (ttpp) cc_final: 0.7419 (ttpp) REVERT: J 216 ASN cc_start: 0.7832 (t0) cc_final: 0.7567 (t0) REVERT: J 218 ASN cc_start: 0.8383 (t0) cc_final: 0.8050 (t0) REVERT: J 241 GLU cc_start: 0.7130 (tp30) cc_final: 0.6700 (tp30) REVERT: J 242 GLN cc_start: 0.8380 (tp40) cc_final: 0.8051 (tp40) REVERT: J 245 LYS cc_start: 0.8186 (ptpp) cc_final: 0.7776 (ptpp) REVERT: J 311 ASP cc_start: 0.7626 (t0) cc_final: 0.7180 (t0) REVERT: J 338 THR cc_start: 0.7954 (m) cc_final: 0.7544 (p) REVERT: J 340 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7460 (ttmm) REVERT: J 357 SER cc_start: 0.8330 (t) cc_final: 0.7868 (t) REVERT: J 387 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7739 (mt) REVERT: K 37 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7457 (tppt) REVERT: K 42 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6781 (t70) REVERT: K 49 THR cc_start: 0.8498 (p) cc_final: 0.8047 (t) REVERT: K 81 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7580 (mm110) REVERT: K 144 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6671 (mm-30) REVERT: K 242 LYS cc_start: 0.8354 (mmtp) cc_final: 0.8123 (mptt) REVERT: K 252 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7566 (mmtm) REVERT: K 254 LYS cc_start: 0.7410 (pttt) cc_final: 0.7163 (ptmm) REVERT: K 283 VAL cc_start: 0.8540 (t) cc_final: 0.8238 (p) REVERT: T 11 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6907 (tt) REVERT: U 71 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7215 (ttpp) REVERT: U 96 HIS cc_start: 0.7636 (t-90) cc_final: 0.7349 (t70) REVERT: U 97 PHE cc_start: 0.8331 (t80) cc_final: 0.8037 (t80) REVERT: V 63 SER cc_start: 0.6528 (p) cc_final: 0.6151 (p) outliers start: 114 outliers final: 97 residues processed: 724 average time/residue: 0.4543 time to fit residues: 519.7215 Evaluate side-chains 754 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 651 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 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 370 CYS Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain B residue 41 HIS 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 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 62 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 208 VAL 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 G residue 73 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 ASP 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 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 31 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 ILE 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 146 VAL Chi-restraints excluded: chain J residue 183 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 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 42 ASP 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 307 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 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 28 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 10 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 222 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS B 81 GLN B 121 HIS B 305 HIS F 16 ASN F 100 ASN F 102 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 HIS ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN J 20 ASN J 270 ASN J 381 HIS K 81 GLN K 159 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103636 restraints weight = 33374.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106626 restraints weight = 16127.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108521 restraints weight = 9591.314| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21242 Z= 0.249 Angle : 0.769 21.234 28851 Z= 0.434 Chirality : 0.047 0.201 3220 Planarity : 0.005 0.054 3703 Dihedral : 6.289 40.738 2695 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.23 % Favored : 90.66 % Rotamer: Outliers : 5.13 % Allowed : 17.81 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.16), residues: 2677 helix: 0.90 (1.06), residues: 27 sheet: -0.57 (0.16), residues: 1092 loop : -2.31 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 103 HIS 0.010 0.001 HIS S 96 PHE 0.048 0.002 PHE J 398 TYR 0.018 0.002 TYR B 15 ARG 0.000 0.000 ARG F 289 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 590) hydrogen bonds : angle 5.73791 ( 1590) SS BOND : bond 0.00581 ( 44) SS BOND : angle 1.46990 ( 88) covalent geometry : bond 0.00540 (21198) covalent geometry : angle 0.76595 (28763) ********************** 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 777 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 659 time to evaluate : 2.275 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: 0.8162 (mtpt) cc_final: 0.7868 (mtpp) REVERT: A 76 GLU cc_start: 0.6968 (tp30) cc_final: 0.6706 (tp30) REVERT: A 99 GLU cc_start: 0.8332 (pm20) cc_final: 0.7950 (pm20) REVERT: A 105 LYS cc_start: 0.8402 (mttt) cc_final: 0.7617 (ttmm) REVERT: A 137 VAL cc_start: 0.8442 (t) cc_final: 0.8156 (p) REVERT: A 143 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7827 (m) REVERT: A 153 PRO cc_start: 0.8551 (Cg_endo) cc_final: 0.8287 (Cg_exo) REVERT: A 183 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6441 (mt-10) REVERT: A 196 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7147 (mm-40) REVERT: A 203 ILE cc_start: 0.8330 (mm) cc_final: 0.8038 (tp) REVERT: A 208 VAL cc_start: 0.8986 (p) cc_final: 0.8734 (p) REVERT: A 225 LYS cc_start: 0.7807 (ttpp) cc_final: 0.7349 (ttmm) REVERT: A 357 SER cc_start: 0.8619 (t) cc_final: 0.8154 (p) REVERT: A 360 ASN cc_start: 0.7269 (m-40) cc_final: 0.6944 (m-40) REVERT: B 37 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7814 (mmtp) REVERT: B 137 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 144 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 245 LYS cc_start: 0.7459 (ttpt) cc_final: 0.7127 (ttpp) REVERT: B 255 LEU cc_start: 0.7872 (mp) cc_final: 0.7537 (mt) REVERT: B 286 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7623 (mtpp) REVERT: F 52 LYS cc_start: 0.8235 (tttt) cc_final: 0.7805 (ttpp) REVERT: F 76 GLU cc_start: 0.7082 (tp30) cc_final: 0.6694 (tp30) REVERT: F 79 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8088 (ttmm) REVERT: F 99 GLU cc_start: 0.8345 (pm20) cc_final: 0.8082 (pm20) REVERT: F 105 LYS cc_start: 0.8400 (mttt) cc_final: 0.8006 (mtpt) REVERT: F 125 HIS cc_start: 0.7260 (p90) cc_final: 0.7048 (p90) REVERT: F 133 LEU cc_start: 0.8022 (mt) cc_final: 0.7741 (mm) REVERT: F 151 GLU cc_start: 0.7060 (pm20) cc_final: 0.6827 (pm20) REVERT: F 156 PHE cc_start: 0.7078 (p90) cc_final: 0.6635 (p90) REVERT: F 217 THR cc_start: 0.8727 (p) cc_final: 0.8340 (t) REVERT: F 241 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6673 (mm-30) REVERT: F 317 THR cc_start: 0.7945 (m) cc_final: 0.7676 (p) REVERT: F 340 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7882 (ttmm) REVERT: G 49 THR cc_start: 0.7905 (t) cc_final: 0.7502 (p) REVERT: G 66 MET cc_start: 0.8153 (ttt) cc_final: 0.7815 (ttt) REVERT: G 252 LYS cc_start: 0.8138 (mppt) cc_final: 0.7491 (mmtm) REVERT: G 254 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7268 (tttm) REVERT: G 265 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7914 (mmmt) REVERT: G 277 THR cc_start: 0.8179 (m) cc_final: 0.7632 (p) REVERT: G 323 GLU cc_start: 0.7043 (pp20) cc_final: 0.6398 (pp20) REVERT: J 31 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7863 (pt) REVERT: J 35 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7794 (tttp) REVERT: J 42 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8256 (p) REVERT: J 52 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7859 (ptmt) REVERT: J 77 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7478 (mm-40) REVERT: J 99 GLU cc_start: 0.8412 (pm20) cc_final: 0.7753 (pm20) REVERT: J 105 LYS cc_start: 0.8330 (mttt) cc_final: 0.7819 (mtmt) REVERT: J 160 LYS cc_start: 0.7713 (ttpp) cc_final: 0.7409 (ttpp) REVERT: J 241 GLU cc_start: 0.7173 (tp30) cc_final: 0.6469 (tp30) REVERT: J 242 GLN cc_start: 0.8420 (tp40) cc_final: 0.8021 (tp40) REVERT: J 245 LYS cc_start: 0.8188 (ptpp) cc_final: 0.7750 (ptpp) REVERT: J 269 GLU cc_start: 0.7292 (tt0) cc_final: 0.6807 (tt0) REVERT: J 311 ASP cc_start: 0.7650 (t0) cc_final: 0.7244 (t0) REVERT: J 340 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7512 (ttmm) REVERT: J 387 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7866 (mt) REVERT: K 37 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7465 (tppt) REVERT: K 42 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6778 (t70) REVERT: K 144 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6626 (mm-30) REVERT: K 242 LYS cc_start: 0.8362 (mmtp) cc_final: 0.8162 (mptt) REVERT: K 252 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7544 (mmtm) REVERT: K 254 LYS cc_start: 0.7386 (pttt) cc_final: 0.7165 (ptmm) REVERT: K 283 VAL cc_start: 0.8536 (t) cc_final: 0.8255 (p) REVERT: T 11 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6961 (tt) REVERT: U 71 LYS cc_start: 0.7593 (ttpp) cc_final: 0.7265 (ttpp) REVERT: U 96 HIS cc_start: 0.7701 (t-90) cc_final: 0.7411 (t70) REVERT: U 97 PHE cc_start: 0.8366 (t80) cc_final: 0.8080 (t80) outliers start: 118 outliers final: 101 residues processed: 715 average time/residue: 0.3405 time to fit residues: 383.9017 Evaluate side-chains 761 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 654 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 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 370 CYS Chi-restraints excluded: chain A residue 381 HIS Chi-restraints excluded: chain B residue 41 HIS 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 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 62 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 208 VAL 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 G residue 73 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 108 ASP 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 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 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 31 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 ILE 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 130 GLN Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 183 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 381 HIS Chi-restraints excluded: chain J residue 387 ILE Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain K residue 42 ASP 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 297 THR 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 100 PHE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain T residue 4 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 171 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 222 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 390 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 121 HIS F 16 ASN F 102 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN J 20 ASN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 HIS K 71 HIS K 305 HIS ** L 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 = 0.3506 r_free = 0.3506 target = 0.126900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104536 restraints weight = 33340.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107749 restraints weight = 15605.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109582 restraints weight = 9064.211| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21242 Z= 0.193 Angle : 0.736 20.022 28851 Z= 0.418 Chirality : 0.046 0.172 3220 Planarity : 0.005 0.053 3703 Dihedral : 6.058 40.411 2695 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 4.82 % Allowed : 18.64 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.76 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2677 helix: -1.13 (0.84), residues: 42 sheet: -0.47 (0.16), residues: 1078 loop : -2.23 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 89 HIS 0.011 0.001 HIS S 96 PHE 0.050 0.002 PHE J 398 TYR 0.021 0.001 TYR J 308 ARG 0.000 0.000 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 590) hydrogen bonds : angle 5.56932 ( 1590) SS BOND : bond 0.00433 ( 44) SS BOND : angle 1.27430 ( 88) covalent geometry : bond 0.00404 (21198) covalent geometry : angle 0.73417 (28763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9737.50 seconds wall clock time: 178 minutes 32.81 seconds (10712.81 seconds total)