Starting phenix.real_space_refine on Thu Jan 15 23:41:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dee_27391/01_2026/8dee_27391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dee_27391/01_2026/8dee_27391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dee_27391/01_2026/8dee_27391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dee_27391/01_2026/8dee_27391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dee_27391/01_2026/8dee_27391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dee_27391/01_2026/8dee_27391.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.025 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 188 5.16 5 C 19468 2.51 5 N 5324 2.21 5 O 5736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30716 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3324 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3181 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "F" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3324 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "G" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3181 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "I" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "J" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3324 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "K" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3181 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "M" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "N" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3324 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "O" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3181 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 27, 'TRANS': 380} Chain: "R" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Time building chain proxies: 7.95, per 1000 atoms: 0.26 Number of scatterers: 30716 At special positions: 0 Unit cell: (199.2, 173.055, 197.955, 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 188 16.00 O 5736 8.00 N 5324 7.00 C 19468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.03 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 269 " distance=2.03 Simple disulfide: pdb=" SG CYS G 204 " - pdb=" SG CYS G 229 " distance=2.04 Simple disulfide: pdb=" SG CYS G 206 " - pdb=" SG CYS G 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 127 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.03 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 108 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 269 " distance=2.03 Simple disulfide: pdb=" SG CYS K 204 " - pdb=" SG CYS K 229 " distance=2.03 Simple disulfide: pdb=" SG CYS K 206 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 114 " distance=2.03 Simple disulfide: pdb=" SG CYS N 62 " - pdb=" SG CYS N 94 " distance=2.04 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 259 " - pdb=" SG CYS N 271 " distance=2.03 Simple disulfide: pdb=" SG CYS N 301 " - pdb=" SG CYS N 376 " distance=2.03 Simple disulfide: pdb=" SG CYS N 306 " - pdb=" SG CYS N 380 " distance=2.03 Simple disulfide: pdb=" SG CYS N 328 " - pdb=" SG CYS N 370 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 127 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 28 " distance=2.07 Simple disulfide: pdb=" SG CYS O 94 " - pdb=" SG CYS O 108 " distance=2.03 Simple disulfide: pdb=" SG CYS O 155 " - pdb=" SG CYS O 269 " distance=2.03 Simple disulfide: pdb=" SG CYS O 204 " - pdb=" SG CYS O 229 " distance=2.03 Simple disulfide: pdb=" SG CYS O 206 " - pdb=" SG CYS O 223 " distance=2.03 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7376 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 89 sheets defined 13.1% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.254A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 116' Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.650A pdb=" N ALA A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL A 402 " --> pdb=" O GLN A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.853A pdb=" N ALA A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 354 through 366 removed outlier: 3.721A pdb=" N ILE B 360 " --> pdb=" O HIS B 356 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 365 " --> pdb=" O HIS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 401 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.854A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 116 removed outlier: 4.252A pdb=" N THR F 115 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 116 " --> pdb=" O ASP F 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 112 through 116' Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.523A pdb=" N THR F 254 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.907A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 403 through 439 removed outlier: 3.604A pdb=" N ALA F 417 " --> pdb=" O LEU F 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 227 No H-bonds generated for 'chain 'G' and resid 225 through 227' Processing helix chain 'G' and resid 354 through 366 Processing helix chain 'G' and resid 366 through 405 Proline residue: G 402 - end of helix Processing helix chain 'G' and resid 413 through 420 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'J' and resid 112 through 116 removed outlier: 4.068A pdb=" N THR J 115 " --> pdb=" O PRO J 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE J 116 " --> pdb=" O ASP J 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 112 through 116' Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 403 through 438 removed outlier: 3.797A pdb=" N ALA J 417 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 366 removed outlier: 3.846A pdb=" N ILE K 360 " --> pdb=" O HIS K 356 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 365 " --> pdb=" O HIS K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 405 removed outlier: 3.595A pdb=" N VAL K 371 " --> pdb=" O PRO K 367 " (cutoff:3.500A) Proline residue: K 402 - end of helix removed outlier: 4.257A pdb=" N LEU K 405 " --> pdb=" O THR K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 420 Processing helix chain 'M' and resid 143 through 149 Processing helix chain 'M' and resid 165 through 169 removed outlier: 3.810A pdb=" N MET M 168 " --> pdb=" O PRO M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 116 removed outlier: 3.786A pdb=" N THR N 115 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 246 Processing helix chain 'N' and resid 250 through 254 Processing helix chain 'N' and resid 255 through 259 removed outlier: 3.937A pdb=" N GLY N 258 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS N 259 " --> pdb=" O PRO N 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 255 through 259' Processing helix chain 'N' and resid 403 through 438 removed outlier: 4.379A pdb=" N ALA N 417 " --> pdb=" O LEU N 413 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER N 418 " --> pdb=" O PHE N 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 227 No H-bonds generated for 'chain 'O' and resid 225 through 227' Processing helix chain 'O' and resid 354 through 366 removed outlier: 3.990A pdb=" N ILE O 360 " --> pdb=" O HIS O 356 " (cutoff:3.500A) Processing helix chain 'O' and resid 366 through 405 Proline residue: O 402 - end of helix removed outlier: 3.880A pdb=" N LEU O 405 " --> pdb=" O THR O 401 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 420 Processing helix chain 'R' and resid 144 through 149 removed outlier: 3.853A pdb=" N ALA R 148 " --> pdb=" O GLN R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 removed outlier: 4.174A pdb=" N SER R 170 " --> pdb=" O ASN R 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.952A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.465A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU A 129 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 48 removed outlier: 6.259A pdb=" N LYS A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS A 123 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.735A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.919A pdb=" N VAL A 108 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP A 75 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.263A pdb=" N SER A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.242A pdb=" N LEU B 288 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE B 322 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 290 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG B 320 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA B 292 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR B 318 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG B 294 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY B 316 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 38 removed outlier: 8.949A pdb=" N ILE B 34 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER B 51 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N ILE B 48 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N GLN B 107 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 11.677A pdb=" N VAL B 50 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N LEU B 105 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N ALA B 52 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE B 103 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 70 Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 89 removed outlier: 4.361A pdb=" N ASP B 112 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 151 through 158 Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AC1, first strand: chain 'B' and resid 183 through 186 removed outlier: 4.283A pdb=" N VAL B 190 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 209 through 214 Processing sheet with id=AC3, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.652A pdb=" N PHE E 112 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR E 123 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 114 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR E 123 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 182 through 186 removed outlier: 9.556A pdb=" N ALA E 190 " --> pdb=" O PRO E 201 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE E 198 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 240 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 225 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N TRP E 242 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA E 223 " --> pdb=" O TRP E 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 213 through 215 removed outlier: 3.685A pdb=" N ALA E 223 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA E 223 " --> pdb=" O TRP E 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N TRP E 242 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 225 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 240 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.968A pdb=" N LYS F 160 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 15 through 19 removed outlier: 5.488A pdb=" N ILE F 31 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU F 129 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 15 through 19 Processing sheet with id=AC9, first strand: chain 'F' and resid 42 through 48 removed outlier: 3.552A pdb=" N LYS F 123 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA F 119 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.707A pdb=" N GLN F 59 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 51 through 54 removed outlier: 4.886A pdb=" N VAL F 108 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP F 75 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'F' and resid 296 through 303 Processing sheet with id=AD6, first strand: chain 'F' and resid 330 through 332 Processing sheet with id=AD7, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'F' and resid 387 through 388 removed outlier: 7.271A pdb=" N LEU G 288 " --> pdb=" O PHE G 322 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE G 322 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU G 290 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG G 320 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA G 292 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR G 318 " --> pdb=" O ALA G 292 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG G 294 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY G 316 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AE1, first strand: chain 'G' and resid 34 through 38 removed outlier: 8.971A pdb=" N ILE G 34 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 51 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN G 36 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 16.783A pdb=" N GLN G 49 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 13.827A pdb=" N TYR G 69 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 12.490A pdb=" N SER G 51 " --> pdb=" O PHE G 67 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N PHE G 67 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 12.082A pdb=" N GLN G 53 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N THR G 65 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY G 55 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 34 through 38 removed outlier: 8.971A pdb=" N ILE G 34 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 51 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN G 36 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR G 102 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ALA G 52 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS G 100 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N PHE G 54 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N GLY G 98 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 15.648A pdb=" N TYR G 56 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 17.709A pdb=" N ARG G 96 " --> pdb=" O TYR G 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 86 through 89 removed outlier: 4.387A pdb=" N ASP G 112 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 151 through 158 Processing sheet with id=AE5, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AE6, first strand: chain 'G' and resid 183 through 186 Processing sheet with id=AE7, first strand: chain 'G' and resid 209 through 214 Processing sheet with id=AE8, first strand: chain 'I' and resid 140 through 141 removed outlier: 5.814A pdb=" N PHE I 112 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR I 123 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE I 114 " --> pdb=" O ASN I 121 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR I 123 " --> pdb=" O PRO I 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 249 through 251 removed outlier: 6.810A pdb=" N VAL I 240 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL I 225 " --> pdb=" O VAL I 240 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA I 223 " --> pdb=" O ILE I 214 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA I 190 " --> pdb=" O PRO I 201 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE I 198 " --> pdb=" O LEU I 237 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 2 through 8 removed outlier: 4.072A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.472A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU J 129 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.305A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.707A pdb=" N GLN J 59 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AF7, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AF8, first strand: chain 'J' and resid 219 through 221 Processing sheet with id=AF9, first strand: chain 'J' and resid 298 through 306 removed outlier: 3.679A pdb=" N GLU J 298 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 330 through 332 Processing sheet with id=AG2, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'J' and resid 387 through 388 removed outlier: 5.671A pdb=" N ARG K 294 " --> pdb=" O ILE K 314 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE K 314 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR K 296 " --> pdb=" O GLU K 312 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU K 312 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU K 298 " --> pdb=" O THR K 310 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR K 310 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'K' and resid 34 through 38 removed outlier: 8.628A pdb=" N ILE K 34 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER K 51 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN K 36 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR K 102 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N ALA K 52 " --> pdb=" O LYS K 100 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS K 100 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N PHE K 54 " --> pdb=" O GLY K 98 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N GLY K 98 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE K 88 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG K 96 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N ILE K 86 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS K 131 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N THR K 115 " --> pdb=" O VAL K 129 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL K 129 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER K 117 " --> pdb=" O CYS K 127 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N CYS K 127 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR K 119 " --> pdb=" O ASN K 125 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN K 125 " --> pdb=" O THR K 119 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 66 through 70 Processing sheet with id=AG7, first strand: chain 'K' and resid 151 through 158 Processing sheet with id=AG8, first strand: chain 'K' and resid 240 through 241 Processing sheet with id=AG9, first strand: chain 'K' and resid 183 through 186 removed outlier: 4.291A pdb=" N VAL K 190 " --> pdb=" O MET K 220 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 209 through 214 Processing sheet with id=AH2, first strand: chain 'M' and resid 111 through 116 removed outlier: 6.613A pdb=" N LEU M 116 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL M 120 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR M 123 " --> pdb=" O PRO M 134 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 174 through 175 removed outlier: 6.711A pdb=" N GLN M 174 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA M 223 " --> pdb=" O GLN M 174 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N VAL M 222 " --> pdb=" O TRP M 242 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP M 242 " --> pdb=" O VAL M 222 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 224 " --> pdb=" O VAL M 240 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER M 238 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY M 228 " --> pdb=" O ALA M 236 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA M 236 " --> pdb=" O GLY M 228 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN M 230 " --> pdb=" O ARG M 234 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG M 234 " --> pdb=" O ASN M 230 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 182 through 186 removed outlier: 9.502A pdb=" N ALA M 190 " --> pdb=" O PRO M 201 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE M 198 " --> pdb=" O LEU M 237 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG M 234 " --> pdb=" O ASN M 230 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN M 230 " --> pdb=" O ARG M 234 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA M 236 " --> pdb=" O GLY M 228 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY M 228 " --> pdb=" O ALA M 236 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER M 238 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE M 224 " --> pdb=" O VAL M 240 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP M 242 " --> pdb=" O VAL M 222 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N VAL M 222 " --> pdb=" O TRP M 242 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 2 through 8 removed outlier: 3.985A pdb=" N LYS N 160 " --> pdb=" O ASP N 281 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 15 through 19 removed outlier: 5.500A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 128 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER N 41 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 140 through 147 removed outlier: 6.659A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER N 41 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 128 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.569A pdb=" N GLN N 59 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 51 through 54 Processing sheet with id=AI1, first strand: chain 'N' and resid 203 through 204 Processing sheet with id=AI2, first strand: chain 'N' and resid 219 through 221 Processing sheet with id=AI3, first strand: chain 'N' and resid 296 through 303 Processing sheet with id=AI4, first strand: chain 'N' and resid 330 through 332 Processing sheet with id=AI5, first strand: chain 'N' and resid 387 through 388 Processing sheet with id=AI6, first strand: chain 'N' and resid 387 through 388 removed outlier: 7.228A pdb=" N LEU O 288 " --> pdb=" O PHE O 322 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE O 322 " --> pdb=" O LEU O 288 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU O 290 " --> pdb=" O ARG O 320 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG O 320 " --> pdb=" O LEU O 290 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ALA O 292 " --> pdb=" O THR O 318 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR O 318 " --> pdb=" O ALA O 292 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG O 294 " --> pdb=" O GLY O 316 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLY O 316 " --> pdb=" O ARG O 294 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 17 through 19 Processing sheet with id=AI8, first strand: chain 'O' and resid 34 through 38 removed outlier: 8.954A pdb=" N ILE O 34 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER O 51 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN O 36 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TYR O 102 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N ALA O 52 " --> pdb=" O LYS O 100 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS O 100 " --> pdb=" O ALA O 52 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N PHE O 54 " --> pdb=" O GLY O 98 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N GLY O 98 " --> pdb=" O PHE O 54 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 66 through 70 Processing sheet with id=AJ1, first strand: chain 'O' and resid 86 through 89 removed outlier: 4.198A pdb=" N ASP O 112 " --> pdb=" O LYS O 131 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 151 through 158 Processing sheet with id=AJ3, first strand: chain 'O' and resid 240 through 241 Processing sheet with id=AJ4, first strand: chain 'O' and resid 183 through 186 removed outlier: 4.716A pdb=" N VAL O 190 " --> pdb=" O MET O 220 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 209 through 214 Processing sheet with id=AJ6, first strand: chain 'R' and resid 140 through 141 removed outlier: 3.802A pdb=" N GLY R 122 " --> pdb=" O ILE R 114 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU R 116 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR R 123 " --> pdb=" O PRO R 134 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 249 through 251 removed outlier: 4.957A pdb=" N PHE R 198 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ALA R 190 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA R 223 " --> pdb=" O ILE R 214 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'R' and resid 249 through 251 removed outlier: 6.661A pdb=" N VAL R 240 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL R 225 " --> pdb=" O VAL R 240 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3261 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: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9990 1.35 - 1.48: 8075 1.48 - 1.61: 13211 1.61 - 1.74: 4 1.74 - 1.87: 236 Bond restraints: 31516 Sorted by residual: bond pdb=" CB PRO M 253 " pdb=" CG PRO M 253 " ideal model delta sigma weight residual 1.492 1.665 -0.173 5.00e-02 4.00e+02 1.20e+01 bond pdb=" CB PRO A 8 " pdb=" CG PRO A 8 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.10e+01 bond pdb=" N PRO M 201 " pdb=" CD PRO M 201 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.16e+00 bond pdb=" C THR K 401 " pdb=" N PRO K 402 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 7.23e+00 bond pdb=" CB PRO M 134 " pdb=" CG PRO M 134 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.06e+00 ... (remaining 31511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 42400 3.02 - 6.04: 478 6.04 - 9.06: 24 9.06 - 12.09: 5 12.09 - 15.11: 5 Bond angle restraints: 42912 Sorted by residual: angle pdb=" CA PRO M 201 " pdb=" N PRO M 201 " pdb=" CD PRO M 201 " ideal model delta sigma weight residual 112.00 96.89 15.11 1.40e+00 5.10e-01 1.16e+02 angle pdb=" CA PRO M 253 " pdb=" N PRO M 253 " pdb=" CD PRO M 253 " ideal model delta sigma weight residual 112.00 98.45 13.55 1.40e+00 5.10e-01 9.36e+01 angle pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" CD PRO A 8 " ideal model delta sigma weight residual 112.00 99.34 12.66 1.40e+00 5.10e-01 8.17e+01 angle pdb=" CA PRO M 134 " pdb=" N PRO M 134 " pdb=" CD PRO M 134 " ideal model delta sigma weight residual 112.00 99.81 12.19 1.40e+00 5.10e-01 7.58e+01 angle pdb=" N VAL M 200 " pdb=" CA VAL M 200 " pdb=" C VAL M 200 " ideal model delta sigma weight residual 109.01 103.43 5.58 1.13e+00 7.83e-01 2.44e+01 ... (remaining 42907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16430 17.96 - 35.92: 1891 35.92 - 53.88: 463 53.88 - 71.84: 79 71.84 - 89.79: 26 Dihedral angle restraints: 18889 sinusoidal: 7365 harmonic: 11524 Sorted by residual: dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 28 " pdb=" CB CYS O 28 " ideal model delta sinusoidal sigma weight residual -86.00 -8.54 -77.46 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS F 63 " pdb=" SG CYS F 63 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 27.70 65.30 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -144.88 58.88 1 1.00e+01 1.00e-02 4.64e+01 ... (remaining 18886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4088 0.064 - 0.128: 641 0.128 - 0.192: 80 0.192 - 0.256: 4 0.256 - 0.320: 3 Chirality restraints: 4816 Sorted by residual: chirality pdb=" CA PRO M 201 " pdb=" N PRO M 201 " pdb=" C PRO M 201 " pdb=" CB PRO M 201 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PRO M 134 " pdb=" N PRO M 134 " pdb=" C PRO M 134 " pdb=" CB PRO M 134 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PRO M 253 " pdb=" N PRO M 253 " pdb=" C PRO M 253 " pdb=" CB PRO M 253 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4813 not shown) Planarity restraints: 5508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 200 " 0.094 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO M 201 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO M 201 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 201 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 7 " 0.081 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 8 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 252 " 0.060 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO M 253 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO M 253 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO M 253 " 0.045 5.00e-02 4.00e+02 ... (remaining 5505 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 361 2.62 - 3.19: 26006 3.19 - 3.76: 45971 3.76 - 4.33: 61902 4.33 - 4.90: 107236 Nonbonded interactions: 241476 Sorted by model distance: nonbonded pdb=" OG SER J 360 " pdb=" O GLN J 362 " model vdw 2.049 3.040 nonbonded pdb=" O PRO J 383 " pdb=" OG SER K 346 " model vdw 2.069 3.040 nonbonded pdb=" OG SER K 71 " pdb=" OD1 ASP K 73 " model vdw 2.109 3.040 nonbonded pdb=" OG SER B 41 " pdb=" OD1 ASP B 43 " model vdw 2.112 3.040 nonbonded pdb=" OG SER R 210 " pdb=" O TRP R 259 " model vdw 2.116 3.040 ... (remaining 241471 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 34.230 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.650 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 31567 Z= 0.180 Angle : 0.766 15.108 43014 Z= 0.408 Chirality : 0.048 0.320 4816 Planarity : 0.006 0.128 5508 Dihedral : 16.101 89.794 11360 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 0.24 % Allowed : 22.65 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3976 helix: 3.09 (0.25), residues: 404 sheet: -0.18 (0.15), residues: 1272 loop : -0.66 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 220 TYR 0.025 0.001 TYR K 168 PHE 0.037 0.001 PHE K 54 TRP 0.022 0.001 TRP M 186 HIS 0.017 0.001 HIS K 259 Details of bonding type rmsd covalent geometry : bond 0.00428 (31516) covalent geometry : angle 0.76257 (42912) SS BOND : bond 0.00737 ( 51) SS BOND : angle 1.64390 ( 102) hydrogen bonds : bond 0.10980 ( 1164) hydrogen bonds : angle 6.24634 ( 3261) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 411 time to evaluate : 1.251 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: B 36 ASN cc_start: 0.8477 (m110) cc_final: 0.8224 (m-40) REVERT: G 83 MET cc_start: 0.8920 (tpp) cc_final: 0.8677 (tpp) REVERT: G 225 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8332 (mmpt) REVERT: G 330 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7730 (tt0) REVERT: I 202 ARG cc_start: 0.7533 (ttp80) cc_final: 0.6981 (ttp80) REVERT: J 411 LEU cc_start: 0.8723 (mm) cc_final: 0.8499 (mt) REVERT: K 36 ASN cc_start: 0.8849 (m-40) cc_final: 0.8272 (m110) REVERT: M 214 ILE cc_start: 0.7072 (mm) cc_final: 0.6839 (pt) REVERT: N 2 GLU cc_start: 0.7702 (tt0) cc_final: 0.7380 (tt0) REVERT: O 53 GLN cc_start: 0.6592 (mm110) cc_final: 0.6051 (mm110) outliers start: 8 outliers final: 2 residues processed: 416 average time/residue: 0.2174 time to fit residues: 142.0009 Evaluate side-chains 388 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain N residue 230 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN E 185 ASN F 59 GLN ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 ASN K 255 GLN N 235 GLN O 255 GLN O 259 HIS ** R 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109019 restraints weight = 50173.440| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.99 r_work: 0.3154 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31567 Z= 0.114 Angle : 0.558 7.691 43014 Z= 0.289 Chirality : 0.044 0.285 4816 Planarity : 0.004 0.058 5508 Dihedral : 4.685 40.135 4319 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 2.64 % Allowed : 21.02 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3976 helix: 2.68 (0.25), residues: 428 sheet: -0.10 (0.14), residues: 1356 loop : -0.63 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 306 TYR 0.019 0.001 TYR F 308 PHE 0.018 0.001 PHE K 54 TRP 0.017 0.001 TRP M 186 HIS 0.008 0.001 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00271 (31516) covalent geometry : angle 0.55726 (42912) SS BOND : bond 0.00257 ( 51) SS BOND : angle 0.87777 ( 102) hydrogen bonds : bond 0.03210 ( 1164) hydrogen bonds : angle 5.10536 ( 3261) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 400 time to evaluate : 1.163 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 160 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7764 (mmpt) REVERT: A 364 ASN cc_start: 0.8886 (t0) cc_final: 0.8628 (m-40) REVERT: I 133 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7781 (tmtt) REVERT: I 160 GLU cc_start: 0.8062 (pm20) cc_final: 0.7695 (pm20) REVERT: I 168 MET cc_start: 0.9009 (mtp) cc_final: 0.8788 (mtp) REVERT: I 184 TYR cc_start: 0.7023 (m-80) cc_final: 0.6602 (m-80) REVERT: I 202 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7393 (ttp80) REVERT: J 88 MET cc_start: 0.7819 (mtt) cc_final: 0.7589 (mtt) REVERT: J 411 LEU cc_start: 0.8718 (mm) cc_final: 0.8474 (mt) REVERT: K 248 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6301 (ptt180) REVERT: N 414 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7374 (m-80) outliers start: 89 outliers final: 48 residues processed: 472 average time/residue: 0.2044 time to fit residues: 153.0027 Evaluate side-chains 429 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 379 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 228 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain R residue 157 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 136 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 chunk 257 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111796 restraints weight = 49942.425| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.42 r_work: 0.3233 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31567 Z= 0.163 Angle : 0.563 8.096 43014 Z= 0.291 Chirality : 0.044 0.204 4816 Planarity : 0.004 0.056 5508 Dihedral : 4.643 46.103 4317 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 3.95 % Allowed : 20.90 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3976 helix: 2.67 (0.24), residues: 440 sheet: -0.10 (0.14), residues: 1364 loop : -0.71 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 23 TYR 0.022 0.001 TYR F 308 PHE 0.014 0.001 PHE K 54 TRP 0.020 0.001 TRP M 186 HIS 0.010 0.001 HIS O 259 Details of bonding type rmsd covalent geometry : bond 0.00383 (31516) covalent geometry : angle 0.56162 (42912) SS BOND : bond 0.00345 ( 51) SS BOND : angle 0.93173 ( 102) hydrogen bonds : bond 0.03157 ( 1164) hydrogen bonds : angle 4.97013 ( 3261) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 390 time to evaluate : 1.144 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 364 ASN cc_start: 0.8872 (t0) cc_final: 0.8606 (m-40) REVERT: A 372 LYS cc_start: 0.8289 (tppp) cc_final: 0.8031 (mtpp) REVERT: F 95 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.4747 (p90) REVERT: F 209 ASP cc_start: 0.8614 (p0) cc_final: 0.8362 (p0) REVERT: G 225 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8417 (mtmt) REVERT: I 115 MET cc_start: 0.7816 (tpp) cc_final: 0.7242 (tpp) REVERT: I 133 LYS cc_start: 0.7992 (tmtt) cc_final: 0.7747 (tmtt) REVERT: I 160 GLU cc_start: 0.7846 (pm20) cc_final: 0.7381 (pm20) REVERT: I 168 MET cc_start: 0.9071 (mtp) cc_final: 0.8851 (mtp) REVERT: I 175 TYR cc_start: 0.5365 (OUTLIER) cc_final: 0.4809 (p90) REVERT: I 184 TYR cc_start: 0.7257 (m-80) cc_final: 0.6829 (m-80) REVERT: I 202 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7527 (ttp80) REVERT: J 88 MET cc_start: 0.7850 (mtt) cc_final: 0.7630 (mtt) REVERT: J 218 ASP cc_start: 0.8804 (t70) cc_final: 0.8561 (t70) REVERT: J 411 LEU cc_start: 0.8649 (mm) cc_final: 0.8428 (mt) REVERT: K 163 GLU cc_start: 0.8027 (pm20) cc_final: 0.7363 (pp20) REVERT: M 112 PHE cc_start: 0.7692 (t80) cc_final: 0.7374 (t80) REVERT: N 414 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.6990 (t80) REVERT: O 105 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8142 (tt) REVERT: R 140 LYS cc_start: 0.8555 (tptt) cc_final: 0.8322 (tptt) outliers start: 133 outliers final: 87 residues processed: 499 average time/residue: 0.1997 time to fit residues: 159.2513 Evaluate side-chains 471 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 380 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 230 HIS Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain R residue 157 TYR Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 173 optimal weight: 0.3980 chunk 359 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 160 HIS F 235 GLN J 118 HIS R 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108160 restraints weight = 49326.989| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.38 r_work: 0.3137 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 31567 Z= 0.341 Angle : 0.688 8.675 43014 Z= 0.358 Chirality : 0.048 0.230 4816 Planarity : 0.005 0.058 5508 Dihedral : 5.211 55.966 4317 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 5.79 % Allowed : 21.05 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3976 helix: 2.45 (0.24), residues: 440 sheet: -0.47 (0.14), residues: 1356 loop : -0.93 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 248 TYR 0.031 0.002 TYR F 308 PHE 0.022 0.002 PHE F 51 TRP 0.022 0.002 TRP M 186 HIS 0.008 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00793 (31516) covalent geometry : angle 0.68619 (42912) SS BOND : bond 0.00619 ( 51) SS BOND : angle 1.32051 ( 102) hydrogen bonds : bond 0.03668 ( 1164) hydrogen bonds : angle 5.29845 ( 3261) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 381 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LYS cc_start: 0.8363 (tppp) cc_final: 0.8108 (mtpp) REVERT: B 248 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (ptp-170) REVERT: B 258 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8710 (mp) REVERT: E 174 GLN cc_start: 0.7409 (tp40) cc_final: 0.7097 (tm-30) REVERT: F 209 ASP cc_start: 0.8684 (p0) cc_final: 0.8451 (p0) REVERT: F 347 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8315 (t) REVERT: F 374 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8549 (p) REVERT: G 369 TYR cc_start: 0.8467 (m-80) cc_final: 0.8164 (m-80) REVERT: I 115 MET cc_start: 0.7910 (tpp) cc_final: 0.7520 (tpp) REVERT: I 168 MET cc_start: 0.9104 (mtp) cc_final: 0.8866 (mtp) REVERT: I 184 TYR cc_start: 0.7656 (m-80) cc_final: 0.7008 (m-80) REVERT: I 243 ASN cc_start: 0.7941 (t0) cc_final: 0.7434 (t0) REVERT: J 160 LYS cc_start: 0.8180 (tptt) cc_final: 0.7904 (tptt) REVERT: J 411 LEU cc_start: 0.8742 (mm) cc_final: 0.8511 (mt) REVERT: K 163 GLU cc_start: 0.8085 (pm20) cc_final: 0.7541 (pp20) REVERT: K 248 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.6477 (ptt180) REVERT: M 166 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: M 214 ILE cc_start: 0.7137 (mm) cc_final: 0.6599 (pt) REVERT: N 414 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7072 (t80) REVERT: O 83 MET cc_start: 0.8558 (mmp) cc_final: 0.8320 (mmp) REVERT: O 173 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7080 (ptp90) REVERT: R 140 LYS cc_start: 0.8482 (tptt) cc_final: 0.8220 (tptt) outliers start: 195 outliers final: 141 residues processed: 538 average time/residue: 0.1981 time to fit residues: 170.9462 Evaluate side-chains 511 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 362 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 166 GLN Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 125 HIS Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 301 CYS Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 357 SER Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 173 ARG Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 383 VAL Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 chunk 375 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 235 GLN N 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109970 restraints weight = 48695.775| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.54 r_work: 0.3174 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31567 Z= 0.159 Angle : 0.581 7.835 43014 Z= 0.301 Chirality : 0.045 0.213 4816 Planarity : 0.004 0.055 5508 Dihedral : 4.934 59.569 4317 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 4.78 % Allowed : 22.51 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 3976 helix: 2.62 (0.24), residues: 428 sheet: -0.37 (0.14), residues: 1355 loop : -0.77 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 306 TYR 0.029 0.001 TYR N 273 PHE 0.022 0.001 PHE F 95 TRP 0.017 0.001 TRP M 186 HIS 0.007 0.001 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00371 (31516) covalent geometry : angle 0.57976 (42912) SS BOND : bond 0.00365 ( 51) SS BOND : angle 0.97840 ( 102) hydrogen bonds : bond 0.03137 ( 1164) hydrogen bonds : angle 5.02997 ( 3261) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 381 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LYS cc_start: 0.8316 (tppp) cc_final: 0.8048 (mtpp) REVERT: B 258 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8687 (mp) REVERT: F 209 ASP cc_start: 0.8658 (p0) cc_final: 0.8452 (p0) REVERT: F 298 GLU cc_start: 0.8282 (pt0) cc_final: 0.8028 (pt0) REVERT: F 302 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9021 (p) REVERT: G 369 TYR cc_start: 0.8315 (m-80) cc_final: 0.7984 (m-80) REVERT: I 115 MET cc_start: 0.7886 (tpp) cc_final: 0.7552 (tpp) REVERT: I 168 MET cc_start: 0.9069 (mtp) cc_final: 0.8835 (mtp) REVERT: I 175 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4872 (p90) REVERT: I 243 ASN cc_start: 0.8158 (t0) cc_final: 0.7574 (t0) REVERT: J 196 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8630 (mtmm) REVERT: J 411 LEU cc_start: 0.8708 (mm) cc_final: 0.8501 (mt) REVERT: K 23 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7977 (tmm-80) REVERT: K 163 GLU cc_start: 0.7977 (pm20) cc_final: 0.7411 (pp20) REVERT: K 248 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.6314 (ptt180) REVERT: M 112 PHE cc_start: 0.7490 (t80) cc_final: 0.7165 (t80) REVERT: M 166 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: M 214 ILE cc_start: 0.7059 (mm) cc_final: 0.6491 (pt) REVERT: N 414 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7034 (t80) REVERT: O 83 MET cc_start: 0.8482 (mmp) cc_final: 0.8241 (mmp) REVERT: R 140 LYS cc_start: 0.8517 (tptt) cc_final: 0.8249 (tptt) REVERT: R 192 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8157 (tm-30) outliers start: 161 outliers final: 123 residues processed: 517 average time/residue: 0.2012 time to fit residues: 165.3093 Evaluate side-chains 494 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 365 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 166 GLN Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 230 HIS Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 247 SER Chi-restraints excluded: chain N residue 271 CYS Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 357 SER Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 383 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 189 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 342 optimal weight: 0.8980 chunk 290 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 235 GLN O 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108491 restraints weight = 48833.638| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.35 r_work: 0.3155 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31567 Z= 0.235 Angle : 0.624 9.183 43014 Z= 0.322 Chirality : 0.046 0.236 4816 Planarity : 0.004 0.055 5508 Dihedral : 4.974 36.223 4316 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 5.76 % Allowed : 22.18 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 3976 helix: 2.61 (0.24), residues: 428 sheet: -0.39 (0.14), residues: 1327 loop : -0.87 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 326 TYR 0.032 0.002 TYR N 273 PHE 0.025 0.002 PHE F 95 TRP 0.028 0.001 TRP M 186 HIS 0.007 0.001 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00548 (31516) covalent geometry : angle 0.62165 (42912) SS BOND : bond 0.00455 ( 51) SS BOND : angle 1.19693 ( 102) hydrogen bonds : bond 0.03266 ( 1164) hydrogen bonds : angle 5.08438 ( 3261) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 381 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LYS cc_start: 0.8331 (tppp) cc_final: 0.8069 (mtpp) REVERT: F 209 ASP cc_start: 0.8697 (p0) cc_final: 0.8487 (p0) REVERT: G 36 ASN cc_start: 0.8820 (m-40) cc_final: 0.8581 (m-40) REVERT: G 203 GLU cc_start: 0.7331 (pp20) cc_final: 0.7017 (pp20) REVERT: G 238 LYS cc_start: 0.5559 (tptt) cc_final: 0.5006 (tptt) REVERT: G 369 TYR cc_start: 0.8432 (m-80) cc_final: 0.8098 (m-80) REVERT: I 115 MET cc_start: 0.7854 (tpp) cc_final: 0.7594 (tpp) REVERT: I 168 MET cc_start: 0.9103 (mtp) cc_final: 0.8881 (mtp) REVERT: I 243 ASN cc_start: 0.8072 (t0) cc_final: 0.7537 (t0) REVERT: J 30 GLU cc_start: 0.7597 (tp30) cc_final: 0.7304 (tp30) REVERT: J 160 LYS cc_start: 0.8175 (tptt) cc_final: 0.7854 (tptt) REVERT: J 196 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8629 (mtmm) REVERT: J 411 LEU cc_start: 0.8731 (mm) cc_final: 0.8515 (mt) REVERT: K 163 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7784 (pp20) REVERT: K 248 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.6373 (ptt180) REVERT: M 112 PHE cc_start: 0.7883 (t80) cc_final: 0.7558 (t80) REVERT: M 166 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: M 214 ILE cc_start: 0.7073 (mm) cc_final: 0.6523 (pt) REVERT: N 174 ASP cc_start: 0.8233 (t0) cc_final: 0.8006 (t0) REVERT: N 208 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8441 (mm) REVERT: N 414 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7034 (t80) REVERT: O 83 MET cc_start: 0.8474 (mmp) cc_final: 0.8261 (mmp) REVERT: O 173 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7026 (ptp90) REVERT: R 140 LYS cc_start: 0.8512 (tptt) cc_final: 0.8242 (tptt) REVERT: R 172 THR cc_start: 0.8764 (p) cc_final: 0.8261 (t) REVERT: R 243 ASN cc_start: 0.8383 (t0) cc_final: 0.8000 (t0) outliers start: 194 outliers final: 160 residues processed: 546 average time/residue: 0.1982 time to fit residues: 173.3884 Evaluate side-chains 534 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 368 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 228 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 166 GLN Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 230 HIS Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 247 SER Chi-restraints excluded: chain N residue 271 CYS Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 301 CYS Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 357 SER Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain N residue 435 ILE Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain O residue 24 HIS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 173 ARG Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 383 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 69 optimal weight: 0.8980 chunk 352 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 396 GLN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.147542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110088 restraints weight = 48941.389| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.39 r_work: 0.3195 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31567 Z= 0.118 Angle : 0.581 9.043 43014 Z= 0.299 Chirality : 0.044 0.220 4816 Planarity : 0.004 0.054 5508 Dihedral : 4.720 38.588 4316 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 4.45 % Allowed : 23.25 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3976 helix: 2.76 (0.24), residues: 428 sheet: -0.31 (0.15), residues: 1295 loop : -0.76 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 326 TYR 0.031 0.001 TYR N 273 PHE 0.044 0.001 PHE F 95 TRP 0.030 0.001 TRP M 186 HIS 0.007 0.001 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00280 (31516) covalent geometry : angle 0.57887 (42912) SS BOND : bond 0.00354 ( 51) SS BOND : angle 1.26901 ( 102) hydrogen bonds : bond 0.02932 ( 1164) hydrogen bonds : angle 4.88506 ( 3261) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 378 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 LYS cc_start: 0.8327 (tppp) cc_final: 0.8056 (mtpp) REVERT: B 258 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8804 (mp) REVERT: F 209 ASP cc_start: 0.8669 (p0) cc_final: 0.8442 (p0) REVERT: F 302 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9075 (p) REVERT: G 36 ASN cc_start: 0.8853 (m-40) cc_final: 0.8614 (m-40) REVERT: G 203 GLU cc_start: 0.7427 (pp20) cc_final: 0.7182 (pp20) REVERT: G 225 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8276 (mtmt) REVERT: G 238 LYS cc_start: 0.5471 (tptt) cc_final: 0.4878 (tptt) REVERT: I 115 MET cc_start: 0.7864 (tpp) cc_final: 0.7515 (tpp) REVERT: I 175 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4850 (p90) REVERT: I 243 ASN cc_start: 0.8240 (t0) cc_final: 0.7668 (t0) REVERT: J 30 GLU cc_start: 0.7622 (tp30) cc_final: 0.7267 (tp30) REVERT: J 160 LYS cc_start: 0.8089 (tptt) cc_final: 0.7859 (tptt) REVERT: J 196 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8631 (mtmm) REVERT: J 352 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (tp) REVERT: J 411 LEU cc_start: 0.8670 (mm) cc_final: 0.8470 (mt) REVERT: K 23 ARG cc_start: 0.8252 (tmm-80) cc_final: 0.7997 (tmm-80) REVERT: K 248 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.6235 (ptt180) REVERT: M 112 PHE cc_start: 0.8129 (t80) cc_final: 0.7808 (t80) REVERT: M 166 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: M 214 ILE cc_start: 0.7065 (mm) cc_final: 0.6497 (pt) REVERT: N 160 LYS cc_start: 0.8592 (tptt) cc_final: 0.8251 (mmtt) REVERT: N 174 ASP cc_start: 0.8220 (t0) cc_final: 0.7972 (t0) REVERT: N 414 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7009 (t80) REVERT: O 396 ARG cc_start: 0.7528 (ttm170) cc_final: 0.7086 (mmm-85) REVERT: R 115 MET cc_start: 0.8302 (mpp) cc_final: 0.8102 (mmp) REVERT: R 140 LYS cc_start: 0.8564 (tptt) cc_final: 0.8283 (tptt) REVERT: R 243 ASN cc_start: 0.8394 (t0) cc_final: 0.8007 (t0) outliers start: 150 outliers final: 123 residues processed: 504 average time/residue: 0.2029 time to fit residues: 163.2291 Evaluate side-chains 501 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 371 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 435 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 228 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 352 ILE Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 166 GLN Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 230 HIS Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 271 CYS Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain O residue 24 HIS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain R residue 157 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 134 optimal weight: 2.9990 chunk 372 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 174 optimal weight: 0.0770 chunk 203 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106870 restraints weight = 49333.315| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.54 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 31567 Z= 0.287 Angle : 0.667 9.830 43014 Z= 0.344 Chirality : 0.047 0.247 4816 Planarity : 0.005 0.055 5508 Dihedral : 5.042 38.322 4316 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 5.61 % Allowed : 22.33 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 3976 helix: 2.47 (0.24), residues: 444 sheet: -0.50 (0.14), residues: 1341 loop : -0.89 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 326 TYR 0.033 0.002 TYR N 273 PHE 0.024 0.002 PHE N 170 TRP 0.029 0.002 TRP M 186 HIS 0.018 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00666 (31516) covalent geometry : angle 0.66327 (42912) SS BOND : bond 0.00590 ( 51) SS BOND : angle 1.50027 ( 102) hydrogen bonds : bond 0.03427 ( 1164) hydrogen bonds : angle 5.10789 ( 3261) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 379 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 209 ASP cc_start: 0.8715 (p0) cc_final: 0.8489 (p0) REVERT: F 347 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8328 (t) REVERT: G 203 GLU cc_start: 0.7560 (pp20) cc_final: 0.7295 (pp20) REVERT: G 238 LYS cc_start: 0.5678 (tptt) cc_final: 0.5294 (tptt) REVERT: G 369 TYR cc_start: 0.8472 (m-80) cc_final: 0.8132 (m-80) REVERT: I 115 MET cc_start: 0.7796 (tpp) cc_final: 0.7474 (tpp) REVERT: I 243 ASN cc_start: 0.8217 (t0) cc_final: 0.7680 (t0) REVERT: J 160 LYS cc_start: 0.8255 (tptt) cc_final: 0.7883 (tptt) REVERT: J 352 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8540 (tp) REVERT: J 411 LEU cc_start: 0.8720 (mm) cc_final: 0.8498 (mt) REVERT: K 23 ARG cc_start: 0.8376 (tmm-80) cc_final: 0.8086 (tmm-80) REVERT: K 163 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7956 (pp20) REVERT: K 248 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6524 (ptt180) REVERT: M 112 PHE cc_start: 0.8021 (t80) cc_final: 0.7736 (t80) REVERT: M 214 ILE cc_start: 0.7169 (mm) cc_final: 0.6666 (pt) REVERT: N 160 LYS cc_start: 0.8596 (tptt) cc_final: 0.8369 (mmtt) REVERT: N 174 ASP cc_start: 0.8326 (t0) cc_final: 0.8082 (t0) REVERT: N 208 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8424 (mm) REVERT: N 414 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7070 (t80) REVERT: O 83 MET cc_start: 0.8583 (mmp) cc_final: 0.8204 (mmp) REVERT: O 173 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7100 (ptp90) REVERT: O 320 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.9199 (mmt-90) REVERT: O 344 GLN cc_start: 0.8595 (tt0) cc_final: 0.8329 (mt0) REVERT: R 140 LYS cc_start: 0.8589 (tptt) cc_final: 0.8316 (tptt) REVERT: R 172 THR cc_start: 0.8807 (p) cc_final: 0.8322 (t) REVERT: R 186 TRP cc_start: 0.8294 (t60) cc_final: 0.7760 (t60) REVERT: R 243 ASN cc_start: 0.8493 (t0) cc_final: 0.8085 (t0) outliers start: 189 outliers final: 158 residues processed: 538 average time/residue: 0.1964 time to fit residues: 168.3035 Evaluate side-chains 535 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 369 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 352 ILE Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 230 HIS Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 247 SER Chi-restraints excluded: chain N residue 271 CYS Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 301 CYS Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 357 SER Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain N residue 435 ILE Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 24 HIS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 173 ARG Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 320 ARG Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 383 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 253 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 241 optimal weight: 0.8980 chunk 323 optimal weight: 0.0010 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108599 restraints weight = 49165.737| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.40 r_work: 0.3183 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31567 Z= 0.148 Angle : 0.608 14.899 43014 Z= 0.311 Chirality : 0.045 0.232 4816 Planarity : 0.004 0.054 5508 Dihedral : 4.843 35.929 4316 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 4.69 % Allowed : 22.98 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 3976 helix: 2.64 (0.24), residues: 432 sheet: -0.34 (0.15), residues: 1284 loop : -0.82 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 220 TYR 0.029 0.001 TYR N 273 PHE 0.029 0.001 PHE F 95 TRP 0.032 0.001 TRP M 186 HIS 0.012 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00349 (31516) covalent geometry : angle 0.60601 (42912) SS BOND : bond 0.00379 ( 51) SS BOND : angle 1.16843 ( 102) hydrogen bonds : bond 0.03062 ( 1164) hydrogen bonds : angle 4.92326 ( 3261) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 378 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8839 (mp) REVERT: F 209 ASP cc_start: 0.8635 (p0) cc_final: 0.8408 (p0) REVERT: F 302 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9074 (p) REVERT: F 347 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8294 (t) REVERT: G 203 GLU cc_start: 0.7451 (pp20) cc_final: 0.7225 (pp20) REVERT: G 238 LYS cc_start: 0.5639 (tptt) cc_final: 0.4823 (tptt) REVERT: G 369 TYR cc_start: 0.8321 (m-80) cc_final: 0.7981 (m-80) REVERT: I 175 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.4776 (p90) REVERT: I 243 ASN cc_start: 0.8240 (t0) cc_final: 0.7682 (t0) REVERT: J 160 LYS cc_start: 0.8089 (tptt) cc_final: 0.7664 (tptt) REVERT: J 196 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8598 (mtmm) REVERT: K 23 ARG cc_start: 0.8203 (tmm-80) cc_final: 0.7874 (tmm-80) REVERT: K 163 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: K 248 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6229 (ptt180) REVERT: M 166 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: M 214 ILE cc_start: 0.7142 (mm) cc_final: 0.6583 (pt) REVERT: N 208 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8382 (mm) REVERT: N 414 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6993 (t80) REVERT: O 83 MET cc_start: 0.8469 (mmp) cc_final: 0.8103 (mmp) REVERT: O 396 ARG cc_start: 0.7472 (ttm170) cc_final: 0.6988 (mmm-85) REVERT: R 140 LYS cc_start: 0.8534 (tptt) cc_final: 0.8255 (tptt) REVERT: R 186 TRP cc_start: 0.8204 (t60) cc_final: 0.7821 (t60) REVERT: R 243 ASN cc_start: 0.8420 (t0) cc_final: 0.8038 (t0) outliers start: 158 outliers final: 141 residues processed: 514 average time/residue: 0.2052 time to fit residues: 168.8746 Evaluate side-chains 519 residues out of total 3368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 369 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 63 CYS Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 259 CYS Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 CYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 407 TRP Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 228 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 387 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 411 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain J residue 259 CYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 353 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 248 ARG Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 166 GLN Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 238 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 94 CYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 230 HIS Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 271 CYS Chi-restraints excluded: chain N residue 279 SER Chi-restraints excluded: chain N residue 293 SER Chi-restraints excluded: chain N residue 316 LEU Chi-restraints excluded: chain N residue 317 THR Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 414 PHE Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain O residue 164 THR Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 HIS Chi-restraints excluded: chain O residue 305 LEU Chi-restraints excluded: chain O residue 310 THR Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7757 > 50: distance: 30 - 45: 26.066 distance: 33 - 37: 25.941 distance: 37 - 38: 9.635 distance: 38 - 39: 15.301 distance: 38 - 41: 7.596 distance: 39 - 40: 40.650 distance: 39 - 45: 10.658 distance: 40 - 55: 14.345 distance: 41 - 42: 20.368 distance: 42 - 43: 18.069 distance: 42 - 44: 42.098 distance: 45 - 46: 18.145 distance: 46 - 47: 9.596 distance: 46 - 49: 11.286 distance: 47 - 48: 21.157 distance: 47 - 50: 14.164 distance: 50 - 51: 13.473 distance: 51 - 52: 4.340 distance: 51 - 54: 18.679 distance: 52 - 53: 27.660 distance: 52 - 55: 24.306 distance: 55 - 56: 18.503 distance: 56 - 57: 16.849 distance: 56 - 59: 7.991 distance: 57 - 58: 22.515 distance: 57 - 62: 11.265 distance: 59 - 60: 15.130 distance: 59 - 61: 26.067 distance: 62 - 63: 20.427 distance: 63 - 64: 15.156 distance: 63 - 66: 9.145 distance: 64 - 65: 9.723 distance: 64 - 71: 15.634 distance: 66 - 67: 11.775 distance: 67 - 68: 8.071 distance: 68 - 69: 15.942 distance: 69 - 70: 24.942 distance: 71 - 72: 24.039 distance: 72 - 73: 23.132 distance: 72 - 75: 19.602 distance: 73 - 74: 11.294 distance: 75 - 76: 6.570 distance: 76 - 77: 22.255 distance: 76 - 78: 39.489 distance: 79 - 80: 12.624 distance: 79 - 141: 20.833 distance: 80 - 81: 10.341 distance: 80 - 83: 3.223 distance: 81 - 82: 39.975 distance: 81 - 88: 12.350 distance: 82 - 138: 26.983 distance: 83 - 84: 25.733 distance: 84 - 85: 25.542 distance: 85 - 86: 16.107 distance: 86 - 87: 14.482 distance: 88 - 89: 17.462 distance: 89 - 90: 19.060 distance: 89 - 92: 20.793 distance: 90 - 91: 11.288 distance: 90 - 97: 26.742 distance: 92 - 93: 43.659 distance: 93 - 94: 26.721 distance: 94 - 95: 23.833 distance: 95 - 96: 45.744 distance: 97 - 98: 20.249 distance: 97 - 130: 26.961 distance: 98 - 99: 28.338 distance: 98 - 101: 17.544 distance: 99 - 100: 42.810 distance: 99 - 102: 4.027 distance: 100 - 127: 31.627 distance: 102 - 103: 38.780 distance: 103 - 104: 22.570 distance: 103 - 106: 17.983 distance: 104 - 105: 16.239 distance: 104 - 108: 27.376 distance: 106 - 107: 18.924