Starting phenix.real_space_refine on Fri Mar 6 15:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffe_31566/03_2026/7ffe_31566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffe_31566/03_2026/7ffe_31566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ffe_31566/03_2026/7ffe_31566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffe_31566/03_2026/7ffe_31566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ffe_31566/03_2026/7ffe_31566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffe_31566/03_2026/7ffe_31566.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 240 5.16 5 C 20973 2.51 5 N 5656 2.21 5 O 6194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33063 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 28, 'TRANS': 411} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3257 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 30, 'TRANS': 385} Chain breaks: 1 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "N" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3229 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3243 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 30, 'TRANS': 383} Chain breaks: 1 Chain: "R" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3249 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain breaks: 1 Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Time building chain proxies: 7.35, per 1000 atoms: 0.22 Number of scatterers: 33063 At special positions: 0 Unit cell: (153.12, 209.88, 217.8, 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 240 16.00 O 6194 8.00 N 5656 7.00 C 20973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7958 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 92 sheets defined 16.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.093A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.858A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.238A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.542A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.729A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.648A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.567A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.588A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.758A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.544A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 351 through 363 removed outlier: 3.784A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.863A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 416 Processing helix chain 'K' and resid 114 through 123 Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.786A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 removed outlier: 3.729A pdb=" N LEU N 5 " --> pdb=" O THR N 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.803A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.514A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.617A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.504A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.573A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.901A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 440 removed outlier: 3.538A pdb=" N LYS O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.592A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.207A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.530A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.772A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.735A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 409 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.591A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.100A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.655A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.734A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.099A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.752A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.308A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.647A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.697A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.406A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AC4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 148 removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 170 Processing sheet with id=AC7, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.539A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.775A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD3, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.339A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD6, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD7, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE1, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.588A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.504A pdb=" N ILE J 110 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE4, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE5, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.533A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE7, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.983A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.657A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AF2, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AF3, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.493A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 213 through 217 current: chain 'K' and resid 239 through 245 removed outlier: 6.158A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AF6, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.554A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AF9, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AG1, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AG2, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.715A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.683A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AG5, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AG6, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AG7, first strand: chain 'O' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 27 through 42 current: chain 'O' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 141 through 147 current: chain 'O' and resid 183 through 185 Processing sheet with id=AG8, first strand: chain 'O' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 51 through 55 current: chain 'O' and resid 101 through 110 No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.890A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AH2, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AH3, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AH4, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.013A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AH6, first strand: chain 'O' and resid 364 through 369 Processing sheet with id=AH7, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AH8, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AH9, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.624A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AI2, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AI3, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.785A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AI6, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AI7, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AI8, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AJ1, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AJ2, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.630A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.878A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.563A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AJ6, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.656A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AJ8, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AJ9, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.517A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2604 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: 5.96 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10549 1.34 - 1.47: 8346 1.47 - 1.59: 14710 1.59 - 1.72: 1 1.72 - 1.84: 320 Bond restraints: 33926 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.088 1.08e-02 8.57e+03 6.64e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.311 -0.076 1.21e-02 6.83e+03 3.99e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.88e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.064 1.22e-02 6.72e+03 2.74e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.507 -0.043 1.25e-02 6.40e+03 1.18e+01 ... (remaining 33921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 45613 3.17 - 6.34: 489 6.34 - 9.51: 77 9.51 - 12.68: 6 12.68 - 15.86: 3 Bond angle restraints: 46188 Sorted by residual: angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.30 -15.86 1.93e+00 2.68e-01 6.75e+01 angle pdb=" N GLU R 148 " pdb=" CA GLU R 148 " pdb=" C GLU R 148 " ideal model delta sigma weight residual 107.69 119.41 -11.72 2.01e+00 2.48e-01 3.40e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.03 -7.26 1.25e+00 6.40e-01 3.37e+01 angle pdb=" N VAL N 179 " pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 109.80 117.18 -7.38 1.33e+00 5.65e-01 3.08e+01 angle pdb=" N THR R 140 " pdb=" CA THR R 140 " pdb=" C THR R 140 " ideal model delta sigma weight residual 114.56 108.31 6.25 1.27e+00 6.20e-01 2.42e+01 ... (remaining 46183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 19653 17.61 - 35.22: 604 35.22 - 52.83: 122 52.83 - 70.44: 26 70.44 - 88.05: 7 Dihedral angle restraints: 20412 sinusoidal: 7991 harmonic: 12421 Sorted by residual: dihedral pdb=" CA ILE G 369 " pdb=" C ILE G 369 " pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta harmonic sigma weight residual -180.00 -129.96 -50.04 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA ASN B 264 " pdb=" C ASN B 264 " pdb=" N PRO B 265 " pdb=" CA PRO B 265 " ideal model delta harmonic sigma weight residual 180.00 131.47 48.53 0 5.00e+00 4.00e-02 9.42e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 27 " pdb=" CB CYS N 27 " ideal model delta sinusoidal sigma weight residual 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 20409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4546 0.091 - 0.182: 573 0.182 - 0.273: 25 0.273 - 0.364: 3 0.364 - 0.455: 2 Chirality restraints: 5149 Sorted by residual: chirality pdb=" CB ILE B 369 " pdb=" CA ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CG2 ILE B 369 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CG LEU I 31 " pdb=" CB LEU I 31 " pdb=" CD1 LEU I 31 " pdb=" CD2 LEU I 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASP N 175 " pdb=" N ASP N 175 " pdb=" C ASP N 175 " pdb=" CB ASP N 175 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5146 not shown) Planarity restraints: 5938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO C 265 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " -0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 236 " 0.039 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP J 236 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 236 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 236 " 0.019 2.00e-02 2.50e+03 ... (remaining 5935 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3632 2.75 - 3.29: 28457 3.29 - 3.82: 52554 3.82 - 4.36: 60171 4.36 - 4.90: 108010 Nonbonded interactions: 252824 Sorted by model distance: nonbonded pdb=" NZ LYS K 146 " pdb=" O ARG N 401 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR N 359 " pdb=" O ALA O 401 " model vdw 2.257 3.040 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.267 3.040 nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.267 3.040 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.274 3.040 ... (remaining 252819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' selection = chain 'S' } ncs_group { reference = (chain 'B' and resid 1 through 440) selection = (chain 'C' and resid 1 through 440) selection = chain 'G' selection = (chain 'O' and resid 1 through 440) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'P' selection = chain 'T' } ncs_group { reference = (chain 'J' and (resid 2 through 55 or resid 62 through 419)) selection = chain 'N' selection = (chain 'Q' and (resid 2 through 55 or resid 62 through 419)) selection = (chain 'R' and (resid 2 through 55 or resid 62 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.140 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.008 0.469 33979 Z= 0.343 Angle : 0.951 33.278 46294 Z= 0.517 Chirality : 0.058 0.455 5149 Planarity : 0.008 0.102 5938 Dihedral : 9.400 88.052 12295 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 0.28 % Allowed : 2.21 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.13 % 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: -3.34 (0.11), residues: 4235 helix: -2.31 (0.16), residues: 574 sheet: -1.64 (0.13), residues: 1237 loop : -2.58 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 21 TYR 0.040 0.003 TYR C 308 PHE 0.031 0.004 PHE Q 328 TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS N 28 Details of bonding type rmsd covalent geometry : bond 0.00748 (33926) covalent geometry : angle 0.93245 (46188) SS BOND : bond 0.06455 ( 53) SS BOND : angle 4.04846 ( 106) hydrogen bonds : bond 0.20899 ( 1004) hydrogen bonds : angle 8.39291 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1004 time to evaluate : 1.104 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: B 15 TYR cc_start: 0.7934 (t80) cc_final: 0.6926 (t80) REVERT: B 75 ASP cc_start: 0.8485 (t0) cc_final: 0.8136 (t0) REVERT: B 191 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 409 TRP cc_start: 0.8110 (m100) cc_final: 0.7529 (m100) REVERT: F 130 ILE cc_start: 0.7231 (mm) cc_final: 0.6914 (mt) REVERT: F 151 MET cc_start: 0.6361 (mmt) cc_final: 0.5894 (mmt) REVERT: F 199 TYR cc_start: 0.7194 (m-80) cc_final: 0.6450 (m-80) REVERT: G 95 PHE cc_start: 0.7608 (p90) cc_final: 0.7407 (p90) REVERT: I 15 PRO cc_start: 0.7205 (Cg_exo) cc_final: 0.6949 (Cg_endo) REVERT: J 239 ASN cc_start: 0.8120 (t0) cc_final: 0.7848 (t0) REVERT: J 389 PHE cc_start: 0.8133 (t80) cc_final: 0.7894 (t80) REVERT: J 392 SER cc_start: 0.8162 (m) cc_final: 0.7756 (t) REVERT: K 122 LEU cc_start: 0.6433 (mt) cc_final: 0.5962 (mt) REVERT: K 126 LYS cc_start: 0.6054 (mppt) cc_final: 0.5517 (mttp) REVERT: K 132 LEU cc_start: 0.7751 (tp) cc_final: 0.7544 (tt) REVERT: K 159 ASN cc_start: 0.6216 (t0) cc_final: 0.5787 (t0) REVERT: K 162 LEU cc_start: 0.8725 (mt) cc_final: 0.8455 (mt) REVERT: K 187 ASP cc_start: 0.8400 (m-30) cc_final: 0.8151 (t0) REVERT: K 192 THR cc_start: 0.7789 (t) cc_final: 0.7422 (t) REVERT: K 193 HIS cc_start: 0.7421 (p-80) cc_final: 0.7007 (p-80) REVERT: K 231 LEU cc_start: 0.6770 (mt) cc_final: 0.5977 (mm) REVERT: K 236 ARG cc_start: 0.5252 (mtm180) cc_final: 0.5026 (mtm180) REVERT: K 267 TYR cc_start: 0.3122 (t80) cc_final: 0.2847 (t80) REVERT: O 162 THR cc_start: 0.9146 (m) cc_final: 0.8869 (p) REVERT: O 284 ASP cc_start: 0.8277 (m-30) cc_final: 0.7655 (m-30) REVERT: Q 207 ILE cc_start: 0.7794 (tt) cc_final: 0.7530 (tt) REVERT: S 122 LEU cc_start: 0.7959 (mt) cc_final: 0.7485 (mt) REVERT: S 126 LYS cc_start: 0.4861 (mppt) cc_final: 0.4658 (mtmt) REVERT: S 151 MET cc_start: 0.4300 (mmt) cc_final: 0.3453 (mmp) REVERT: S 159 ASN cc_start: 0.5810 (t0) cc_final: 0.5328 (t0) REVERT: S 180 VAL cc_start: 0.6121 (t) cc_final: 0.5435 (t) REVERT: S 211 ASN cc_start: 0.7662 (m-40) cc_final: 0.7403 (m-40) REVERT: S 214 PHE cc_start: 0.5787 (m-80) cc_final: 0.5250 (m-10) REVERT: S 231 LEU cc_start: 0.6916 (mt) cc_final: 0.6319 (mm) REVERT: S 241 VAL cc_start: 0.6758 (t) cc_final: 0.6505 (p) REVERT: S 242 LEU cc_start: 0.5238 (mt) cc_final: 0.4329 (mm) outliers start: 10 outliers final: 3 residues processed: 1009 average time/residue: 0.2235 time to fit residues: 350.9131 Evaluate side-chains 535 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 532 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 159 ASN A 197 GLN A 204 HIS A 246 ASN A 271 ASN B 43 ASN B 125 HIS B 304 ASN B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN C 43 ASN C 130 GLN C 140 HIS C 304 ASN C 360 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN G 43 ASN G 264 ASN G 360 ASN G 390 HIS G 394 HIS G 396 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN ** J 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 HIS K 197 GLN K 203 HIS K 271 ASN N 7 ASN N 121 HIS N 156 HIS ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 HIS O 43 ASN O 360 ASN O 394 HIS O 396 GLN Q 52 GLN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 HIS Q 159 GLN ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN Q 232 GLN R 160 ASN ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 GLN R 332 ASN ** S 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102319 restraints weight = 59295.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100351 restraints weight = 31783.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101136 restraints weight = 30468.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101728 restraints weight = 23391.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101867 restraints weight = 21460.864| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 33979 Z= 0.153 Angle : 0.670 11.898 46294 Z= 0.350 Chirality : 0.045 0.171 5149 Planarity : 0.006 0.085 5938 Dihedral : 6.067 75.643 4637 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 2.19 % Allowed : 9.68 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.08 % 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: -2.13 (0.12), residues: 4235 helix: -0.15 (0.21), residues: 564 sheet: -1.03 (0.14), residues: 1239 loop : -1.99 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 250 TYR 0.023 0.001 TYR S 177 PHE 0.036 0.002 PHE F 189 TRP 0.025 0.002 TRP F 202 HIS 0.010 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00346 (33926) covalent geometry : angle 0.66453 (46188) SS BOND : bond 0.00376 ( 53) SS BOND : angle 1.87717 ( 106) hydrogen bonds : bond 0.03773 ( 1004) hydrogen bonds : angle 5.95330 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 568 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7042 (m-10) cc_final: 0.6824 (m-10) REVERT: A 177 TYR cc_start: 0.7423 (p90) cc_final: 0.7006 (p90) REVERT: A 197 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6163 (tt0) REVERT: B 183 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: B 377 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7951 (mttm) REVERT: B 409 TRP cc_start: 0.8086 (m100) cc_final: 0.7293 (m100) REVERT: C 51 TYR cc_start: 0.8560 (p90) cc_final: 0.8241 (p90) REVERT: C 79 LYS cc_start: 0.8923 (tttt) cc_final: 0.8701 (tttp) REVERT: C 233 TYR cc_start: 0.8895 (p90) cc_final: 0.8636 (p90) REVERT: C 366 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8066 (mtp85) REVERT: F 184 MET cc_start: 0.9056 (mtp) cc_final: 0.8798 (mtp) REVERT: F 199 TYR cc_start: 0.7974 (m-80) cc_final: 0.6691 (m-80) REVERT: F 202 TRP cc_start: 0.8735 (t60) cc_final: 0.7844 (t60) REVERT: G 75 ASP cc_start: 0.8762 (t0) cc_final: 0.8484 (t0) REVERT: G 125 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7695 (p90) REVERT: I 33 MET cc_start: 0.7950 (ptp) cc_final: 0.7604 (ptp) REVERT: J 113 GLU cc_start: 0.6370 (pt0) cc_final: 0.6056 (pt0) REVERT: J 256 HIS cc_start: 0.7022 (p90) cc_final: 0.6686 (p90) REVERT: J 389 PHE cc_start: 0.8319 (t80) cc_final: 0.7921 (t80) REVERT: J 392 SER cc_start: 0.7982 (m) cc_final: 0.7547 (t) REVERT: K 118 MET cc_start: 0.8239 (ttp) cc_final: 0.7469 (tmm) REVERT: K 120 MET cc_start: 0.8087 (mmm) cc_final: 0.7804 (mmp) REVERT: K 131 MET cc_start: 0.8605 (mmm) cc_final: 0.8374 (mmm) REVERT: K 159 ASN cc_start: 0.8201 (t0) cc_final: 0.7830 (t0) REVERT: K 183 ASN cc_start: 0.9104 (p0) cc_final: 0.8850 (p0) REVERT: K 193 HIS cc_start: 0.8227 (p-80) cc_final: 0.7927 (p-80) REVERT: K 197 GLN cc_start: 0.8882 (tt0) cc_final: 0.8565 (tp40) REVERT: K 209 TYR cc_start: 0.8645 (t80) cc_final: 0.8173 (t80) REVERT: L 6 MET cc_start: 0.5578 (mmp) cc_final: 0.5310 (mmm) REVERT: N 94 ASP cc_start: 0.7035 (t0) cc_final: 0.6831 (t0) REVERT: O 144 THR cc_start: 0.8836 (m) cc_final: 0.8323 (p) REVERT: O 366 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8301 (ttp-170) REVERT: O 377 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8206 (ttmm) REVERT: P 14 PHE cc_start: 0.6161 (p90) cc_final: 0.5905 (p90) REVERT: P 26 LYS cc_start: 0.7546 (mttp) cc_final: 0.7141 (mttm) REVERT: Q 112 MET cc_start: 0.8714 (ttp) cc_final: 0.8472 (ttp) REVERT: Q 201 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8302 (tm-30) REVERT: R 167 MET cc_start: 0.8222 (mmp) cc_final: 0.7892 (mmm) REVERT: S 159 ASN cc_start: 0.8456 (t0) cc_final: 0.8092 (t0) REVERT: S 241 VAL cc_start: 0.8632 (t) cc_final: 0.8002 (p) REVERT: S 242 LEU cc_start: 0.8544 (mt) cc_final: 0.8328 (mm) REVERT: S 258 TRP cc_start: 0.8097 (m-90) cc_final: 0.7411 (m-90) REVERT: S 267 TYR cc_start: 0.7817 (t80) cc_final: 0.7534 (t80) REVERT: S 270 GLU cc_start: 0.8477 (pp20) cc_final: 0.8133 (pp20) REVERT: T 33 MET cc_start: 0.8214 (ttp) cc_final: 0.7703 (ptm) outliers start: 79 outliers final: 46 residues processed: 617 average time/residue: 0.2033 time to fit residues: 203.2789 Evaluate side-chains 541 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 491 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 233 ASN Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 172 LYS Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 295 THR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 355 VAL Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 402 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 300 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 197 GLN A 203 HIS A 246 ASN B 3 HIS B 130 GLN B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS G 386 HIS J 96 HIS J 160 ASN J 256 HIS K 271 ASN N 160 ASN N 212 ASN O 130 GLN O 396 GLN O 438 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 HIS Q 353 HIS R 168 HIS S 203 HIS S 204 HIS ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099283 restraints weight = 59132.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097191 restraints weight = 31364.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098251 restraints weight = 34547.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098774 restraints weight = 24000.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099891 restraints weight = 21111.780| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33979 Z= 0.147 Angle : 0.615 9.261 46294 Z= 0.318 Chirality : 0.044 0.154 5149 Planarity : 0.005 0.076 5938 Dihedral : 5.566 77.402 4636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.03 % Favored : 94.90 % Rotamer: Outliers : 2.88 % Allowed : 10.57 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.57 (0.12), residues: 4235 helix: 0.55 (0.23), residues: 572 sheet: -0.70 (0.14), residues: 1243 loop : -1.66 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 250 TYR 0.020 0.001 TYR O 308 PHE 0.027 0.002 PHE F 189 TRP 0.036 0.002 TRP A 202 HIS 0.007 0.001 HIS Q 305 Details of bonding type rmsd covalent geometry : bond 0.00340 (33926) covalent geometry : angle 0.61230 (46188) SS BOND : bond 0.00226 ( 53) SS BOND : angle 1.37583 ( 106) hydrogen bonds : bond 0.03318 ( 1004) hydrogen bonds : angle 5.43404 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 529 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.6231 (tmm) cc_final: 0.6005 (mtt) REVERT: A 136 ILE cc_start: 0.8469 (mt) cc_final: 0.8146 (mm) REVERT: A 139 TYR cc_start: 0.7239 (m-10) cc_final: 0.7004 (m-10) REVERT: A 177 TYR cc_start: 0.7574 (p90) cc_final: 0.7107 (p90) REVERT: A 202 TRP cc_start: 0.8310 (t60) cc_final: 0.7944 (t60) REVERT: B 183 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: B 377 LYS cc_start: 0.8391 (ptpp) cc_final: 0.7727 (mttm) REVERT: B 409 TRP cc_start: 0.8132 (m100) cc_final: 0.7791 (m100) REVERT: B 433 MET cc_start: 0.6314 (mmp) cc_final: 0.5876 (tmm) REVERT: C 327 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8463 (pttt) REVERT: C 366 ARG cc_start: 0.8333 (mtp85) cc_final: 0.8130 (mtp85) REVERT: C 439 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7927 (tm-30) REVERT: F 199 TYR cc_start: 0.8006 (m-80) cc_final: 0.6985 (m-80) REVERT: F 202 TRP cc_start: 0.8688 (t60) cc_final: 0.7677 (t60) REVERT: F 215 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.7732 (p) REVERT: F 250 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7167 (tpp80) REVERT: F 270 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7671 (mt-10) REVERT: G 6 THR cc_start: 0.9259 (m) cc_final: 0.8997 (p) REVERT: G 115 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8437 (mt) REVERT: G 125 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7901 (p90) REVERT: G 151 GLU cc_start: 0.7838 (mp0) cc_final: 0.7634 (mp0) REVERT: I 33 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8078 (ptp) REVERT: J 67 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.8103 (ttp-170) REVERT: J 113 GLU cc_start: 0.6667 (pt0) cc_final: 0.6267 (pt0) REVERT: J 239 ASN cc_start: 0.8860 (t0) cc_final: 0.8568 (t0) REVERT: J 256 HIS cc_start: 0.7077 (p-80) cc_final: 0.6704 (p-80) REVERT: J 392 SER cc_start: 0.8058 (m) cc_final: 0.7565 (t) REVERT: K 118 MET cc_start: 0.8076 (ttp) cc_final: 0.7744 (tmm) REVERT: K 159 ASN cc_start: 0.8565 (t0) cc_final: 0.8150 (t0) REVERT: K 183 ASN cc_start: 0.9134 (p0) cc_final: 0.8893 (p0) REVERT: K 193 HIS cc_start: 0.8308 (p-80) cc_final: 0.7922 (p-80) REVERT: K 197 GLN cc_start: 0.8860 (tt0) cc_final: 0.8358 (tp40) REVERT: K 202 TRP cc_start: 0.7475 (t60) cc_final: 0.6902 (t60) REVERT: K 209 TYR cc_start: 0.8695 (t80) cc_final: 0.7305 (t80) REVERT: K 257 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7096 (ptp) REVERT: K 274 GLN cc_start: 0.9405 (mt0) cc_final: 0.9191 (mt0) REVERT: L 6 MET cc_start: 0.5603 (mmp) cc_final: 0.5318 (mmm) REVERT: O 144 THR cc_start: 0.8899 (m) cc_final: 0.8554 (p) REVERT: O 366 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8340 (mtp85) REVERT: O 377 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8274 (ttmm) REVERT: P 6 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6780 (tpt) REVERT: P 14 PHE cc_start: 0.6478 (p90) cc_final: 0.6113 (p90) REVERT: P 29 GLU cc_start: 0.8512 (mp0) cc_final: 0.8279 (mp0) REVERT: P 43 TYR cc_start: 0.7182 (t80) cc_final: 0.6935 (t80) REVERT: P 47 LEU cc_start: 0.8368 (tp) cc_final: 0.7825 (tp) REVERT: Q 37 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8205 (mmmt) REVERT: Q 160 ASN cc_start: 0.7469 (t160) cc_final: 0.7264 (t0) REVERT: Q 167 MET cc_start: 0.8652 (mmt) cc_final: 0.8357 (mmt) REVERT: Q 201 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7996 (tm-30) REVERT: Q 323 GLU cc_start: 0.8075 (tp30) cc_final: 0.7770 (tp30) REVERT: R 88 ARG cc_start: 0.5623 (mmt180) cc_final: 0.5404 (mmt180) REVERT: S 159 ASN cc_start: 0.8667 (t0) cc_final: 0.8137 (t0) REVERT: S 177 TYR cc_start: 0.8352 (p90) cc_final: 0.8084 (p90) REVERT: S 191 TYR cc_start: 0.8814 (p90) cc_final: 0.8602 (p90) REVERT: S 241 VAL cc_start: 0.8904 (t) cc_final: 0.8266 (p) REVERT: S 258 TRP cc_start: 0.8085 (m-90) cc_final: 0.7592 (m-90) REVERT: S 267 TYR cc_start: 0.7792 (t80) cc_final: 0.7528 (t80) outliers start: 104 outliers final: 69 residues processed: 592 average time/residue: 0.2004 time to fit residues: 194.1720 Evaluate side-chains 561 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 485 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 233 ASN Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 24 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 295 THR Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 438 ASN Chi-restraints excluded: chain P residue 6 MET Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 355 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain S residue 261 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 289 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 327 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 356 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN B 130 GLN B 386 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 394 HIS F 137 ASN F 246 ASN K 271 ASN O 125 HIS O 130 GLN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 288 HIS R 96 HIS R 168 HIS S 137 ASN S 204 HIS S 271 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093714 restraints weight = 58907.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090977 restraints weight = 32968.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092223 restraints weight = 38213.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092702 restraints weight = 24728.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093415 restraints weight = 21761.426| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 33979 Z= 0.259 Angle : 0.674 8.980 46294 Z= 0.350 Chirality : 0.047 0.272 5149 Planarity : 0.005 0.082 5938 Dihedral : 5.675 79.843 4636 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 3.73 % Allowed : 11.34 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.34 (0.13), residues: 4235 helix: 1.00 (0.23), residues: 571 sheet: -0.60 (0.15), residues: 1243 loop : -1.55 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 362 TYR 0.028 0.002 TYR O 308 PHE 0.022 0.002 PHE F 189 TRP 0.022 0.002 TRP A 202 HIS 0.008 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00618 (33926) covalent geometry : angle 0.67085 (46188) SS BOND : bond 0.00439 ( 53) SS BOND : angle 1.58786 ( 106) hydrogen bonds : bond 0.03548 ( 1004) hydrogen bonds : angle 5.37405 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 497 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.8512 (mt) cc_final: 0.8258 (mm) REVERT: A 157 ILE cc_start: 0.8211 (mp) cc_final: 0.7959 (mm) REVERT: A 177 TYR cc_start: 0.7662 (p90) cc_final: 0.7236 (p90) REVERT: A 230 ILE cc_start: 0.8251 (mt) cc_final: 0.7918 (tt) REVERT: B 183 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: B 377 LYS cc_start: 0.8444 (ptpp) cc_final: 0.7779 (mttm) REVERT: B 409 TRP cc_start: 0.8248 (m100) cc_final: 0.7932 (m100) REVERT: B 433 MET cc_start: 0.6190 (mmp) cc_final: 0.5939 (tmm) REVERT: C 191 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: C 327 LYS cc_start: 0.9010 (ptmt) cc_final: 0.8555 (pttt) REVERT: C 366 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7933 (mtp85) REVERT: C 439 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8125 (tm-30) REVERT: F 174 ASP cc_start: 0.8006 (t0) cc_final: 0.7791 (t0) REVERT: F 202 TRP cc_start: 0.8767 (t60) cc_final: 0.7727 (t60) REVERT: F 215 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7975 (p) REVERT: F 250 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7179 (tpp80) REVERT: F 258 TRP cc_start: 0.7783 (m-90) cc_final: 0.7297 (m-90) REVERT: F 270 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8026 (mt-10) REVERT: G 2 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7846 (mm-30) REVERT: G 6 THR cc_start: 0.9382 (m) cc_final: 0.9093 (p) REVERT: G 115 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8552 (mt) REVERT: I 33 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (ptp) REVERT: J 113 GLU cc_start: 0.6952 (pt0) cc_final: 0.6641 (pt0) REVERT: J 392 SER cc_start: 0.7626 (m) cc_final: 0.7030 (t) REVERT: K 159 ASN cc_start: 0.8529 (t0) cc_final: 0.8219 (t0) REVERT: K 174 ASP cc_start: 0.8702 (t0) cc_final: 0.8384 (t0) REVERT: K 193 HIS cc_start: 0.8271 (p-80) cc_final: 0.7819 (p-80) REVERT: K 202 TRP cc_start: 0.7736 (t60) cc_final: 0.7127 (t60) REVERT: L 29 GLU cc_start: 0.8828 (pp20) cc_final: 0.8422 (pp20) REVERT: N 94 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: N 323 GLU cc_start: 0.7871 (pm20) cc_final: 0.7594 (pm20) REVERT: O 140 HIS cc_start: 0.7193 (m90) cc_final: 0.6948 (m170) REVERT: O 144 THR cc_start: 0.8792 (m) cc_final: 0.8444 (p) REVERT: P 14 PHE cc_start: 0.6241 (p90) cc_final: 0.5867 (p90) REVERT: P 26 LYS cc_start: 0.7923 (mttm) cc_final: 0.7681 (ptpt) REVERT: P 29 GLU cc_start: 0.8665 (mp0) cc_final: 0.8061 (mp0) REVERT: Q 37 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8204 (mmmt) REVERT: Q 137 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6987 (mt-10) REVERT: Q 167 MET cc_start: 0.8578 (mmt) cc_final: 0.8132 (mmt) REVERT: Q 201 GLU cc_start: 0.8551 (tm-30) cc_final: 0.7903 (tm-30) REVERT: Q 401 ARG cc_start: 0.8556 (mtm180) cc_final: 0.8282 (mtp85) REVERT: S 116 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6306 (mt0) REVERT: S 159 ASN cc_start: 0.8723 (t0) cc_final: 0.8299 (t0) REVERT: S 177 TYR cc_start: 0.8474 (p90) cc_final: 0.8228 (p90) REVERT: S 241 VAL cc_start: 0.9100 (t) cc_final: 0.8809 (p) REVERT: S 258 TRP cc_start: 0.8176 (m-90) cc_final: 0.7928 (m-90) REVERT: S 267 TYR cc_start: 0.8145 (t80) cc_final: 0.7720 (t80) REVERT: S 274 GLN cc_start: 0.8576 (mt0) cc_final: 0.8224 (mt0) outliers start: 135 outliers final: 95 residues processed: 580 average time/residue: 0.1936 time to fit residues: 183.1741 Evaluate side-chains 559 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 458 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 233 ASN Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 398 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 51 TYR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 295 THR Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 137 ASN Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 261 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 201 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 358 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 403 optimal weight: 30.0000 chunk 71 optimal weight: 0.7980 chunk 293 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS F 246 ASN ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 GLN ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN N 141 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 256 HIS Q 353 HIS R 168 HIS ** S 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095548 restraints weight = 58459.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093285 restraints weight = 30744.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094722 restraints weight = 31403.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094813 restraints weight = 22899.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096079 restraints weight = 20492.511| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33979 Z= 0.124 Angle : 0.606 11.600 46294 Z= 0.312 Chirality : 0.044 0.171 5149 Planarity : 0.004 0.076 5938 Dihedral : 5.371 79.953 4630 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.52 % Allowed : 13.53 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -1.09 (0.13), residues: 4235 helix: 1.19 (0.23), residues: 572 sheet: -0.50 (0.14), residues: 1286 loop : -1.35 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 289 TYR 0.025 0.001 TYR R 363 PHE 0.018 0.001 PHE L 14 TRP 0.018 0.001 TRP A 202 HIS 0.010 0.001 HIS S 203 Details of bonding type rmsd covalent geometry : bond 0.00286 (33926) covalent geometry : angle 0.60086 (46188) SS BOND : bond 0.00309 ( 53) SS BOND : angle 1.77730 ( 106) hydrogen bonds : bond 0.02908 ( 1004) hydrogen bonds : angle 5.23987 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 481 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.8509 (mt) cc_final: 0.8284 (mm) REVERT: A 151 MET cc_start: 0.7165 (mmm) cc_final: 0.6946 (mmm) REVERT: A 177 TYR cc_start: 0.7568 (p90) cc_final: 0.7115 (p90) REVERT: A 197 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6579 (tt0) REVERT: A 230 ILE cc_start: 0.8175 (mt) cc_final: 0.7864 (tt) REVERT: B 183 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6975 (tt0) REVERT: B 373 TYR cc_start: 0.8368 (m-10) cc_final: 0.7918 (m-10) REVERT: B 409 TRP cc_start: 0.8137 (m100) cc_final: 0.7849 (m100) REVERT: B 433 MET cc_start: 0.6274 (mmp) cc_final: 0.5689 (tmm) REVERT: C 66 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: C 327 LYS cc_start: 0.9029 (ptmt) cc_final: 0.8583 (pttt) REVERT: C 407 TRP cc_start: 0.9069 (OUTLIER) cc_final: 0.8422 (m100) REVERT: F 130 ILE cc_start: 0.7891 (mt) cc_final: 0.7669 (mp) REVERT: F 174 ASP cc_start: 0.8065 (t0) cc_final: 0.7827 (t0) REVERT: F 202 TRP cc_start: 0.8770 (t60) cc_final: 0.7713 (t60) REVERT: F 215 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8028 (p) REVERT: F 250 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7349 (tpp80) REVERT: F 258 TRP cc_start: 0.7732 (m-90) cc_final: 0.7287 (m-90) REVERT: F 270 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8001 (mt-10) REVERT: G 2 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7905 (mm-30) REVERT: G 6 THR cc_start: 0.9386 (m) cc_final: 0.9116 (p) REVERT: G 115 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8529 (mt) REVERT: G 125 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (p90) REVERT: I 33 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8448 (ptp) REVERT: I 45 GLU cc_start: 0.8449 (mp0) cc_final: 0.8157 (mp0) REVERT: I 48 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8038 (mt-10) REVERT: J 392 SER cc_start: 0.7553 (m) cc_final: 0.6990 (t) REVERT: K 159 ASN cc_start: 0.8535 (t0) cc_final: 0.8199 (t0) REVERT: K 174 ASP cc_start: 0.8688 (t0) cc_final: 0.8343 (t0) REVERT: K 176 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8072 (mt-10) REVERT: K 193 HIS cc_start: 0.8249 (p-80) cc_final: 0.7834 (p-80) REVERT: K 197 GLN cc_start: 0.8769 (tp40) cc_final: 0.8527 (tp40) REVERT: K 202 TRP cc_start: 0.7585 (t60) cc_final: 0.7062 (t60) REVERT: K 209 TYR cc_start: 0.8746 (t80) cc_final: 0.8375 (t80) REVERT: K 257 MET cc_start: 0.7491 (ptt) cc_final: 0.7057 (ptp) REVERT: L 26 LYS cc_start: 0.7089 (mtpp) cc_final: 0.6765 (ptpp) REVERT: L 29 GLU cc_start: 0.8816 (pp20) cc_final: 0.8168 (pp20) REVERT: L 51 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5933 (p) REVERT: N 24 VAL cc_start: 0.9439 (t) cc_final: 0.9223 (m) REVERT: N 94 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: N 231 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8559 (mm) REVERT: N 323 GLU cc_start: 0.7886 (pm20) cc_final: 0.7534 (pm20) REVERT: O 126 THR cc_start: 0.8680 (m) cc_final: 0.8261 (p) REVERT: O 144 THR cc_start: 0.8785 (m) cc_final: 0.8423 (p) REVERT: P 14 PHE cc_start: 0.6300 (p90) cc_final: 0.6038 (p90) REVERT: P 26 LYS cc_start: 0.7945 (mttm) cc_final: 0.7678 (ptpt) REVERT: P 29 GLU cc_start: 0.8651 (mp0) cc_final: 0.8125 (mp0) REVERT: P 31 LEU cc_start: 0.8204 (mt) cc_final: 0.7885 (mt) REVERT: Q 37 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8256 (mmmt) REVERT: Q 167 MET cc_start: 0.8531 (mmt) cc_final: 0.8052 (mmt) REVERT: Q 201 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7690 (tm-30) REVERT: R 88 ARG cc_start: 0.5052 (mmt180) cc_final: 0.4403 (mmt180) REVERT: R 94 ASP cc_start: 0.6973 (m-30) cc_final: 0.6576 (m-30) REVERT: S 116 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6493 (mt0) REVERT: S 159 ASN cc_start: 0.8754 (t0) cc_final: 0.8311 (t0) REVERT: S 177 TYR cc_start: 0.8387 (p90) cc_final: 0.8057 (p90) REVERT: S 241 VAL cc_start: 0.9186 (t) cc_final: 0.8895 (p) REVERT: S 266 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8242 (ttpt) REVERT: S 267 TYR cc_start: 0.7997 (t80) cc_final: 0.7613 (t80) REVERT: S 274 GLN cc_start: 0.8613 (mt0) cc_final: 0.8246 (mt0) outliers start: 91 outliers final: 60 residues processed: 538 average time/residue: 0.1971 time to fit residues: 172.3401 Evaluate side-chains 524 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 452 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain S residue 261 LYS Chi-restraints excluded: chain S residue 266 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 164 optimal weight: 0.5980 chunk 304 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 282 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN B 10 GLN B 235 GLN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 GLN K 182 GLN ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095325 restraints weight = 58730.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092777 restraints weight = 33028.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093922 restraints weight = 37308.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094405 restraints weight = 24975.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095542 restraints weight = 21859.666| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33979 Z= 0.140 Angle : 0.599 13.121 46294 Z= 0.307 Chirality : 0.044 0.182 5149 Planarity : 0.004 0.077 5938 Dihedral : 5.245 80.454 4630 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 2.99 % Allowed : 13.39 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.96 (0.13), residues: 4235 helix: 1.31 (0.23), residues: 573 sheet: -0.38 (0.15), residues: 1243 loop : -1.29 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 213 TYR 0.020 0.001 TYR O 308 PHE 0.018 0.001 PHE L 14 TRP 0.017 0.001 TRP A 202 HIS 0.007 0.001 HIS S 203 Details of bonding type rmsd covalent geometry : bond 0.00329 (33926) covalent geometry : angle 0.59537 (46188) SS BOND : bond 0.00248 ( 53) SS BOND : angle 1.42555 ( 106) hydrogen bonds : bond 0.02914 ( 1004) hydrogen bonds : angle 5.11893 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 482 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6378 (tp) cc_final: 0.5987 (tt) REVERT: A 136 ILE cc_start: 0.8560 (mt) cc_final: 0.8285 (mm) REVERT: A 177 TYR cc_start: 0.7376 (p90) cc_final: 0.7019 (p90) REVERT: A 230 ILE cc_start: 0.8376 (mt) cc_final: 0.8089 (tt) REVERT: B 183 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: B 373 TYR cc_start: 0.8357 (m-10) cc_final: 0.7851 (m-10) REVERT: B 409 TRP cc_start: 0.8129 (m100) cc_final: 0.7863 (m100) REVERT: B 433 MET cc_start: 0.6206 (mmp) cc_final: 0.5631 (tmm) REVERT: C 66 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: C 99 GLU cc_start: 0.8080 (mp0) cc_final: 0.7663 (mp0) REVERT: C 327 LYS cc_start: 0.8996 (ptmt) cc_final: 0.8561 (pttt) REVERT: C 407 TRP cc_start: 0.9086 (OUTLIER) cc_final: 0.8353 (m100) REVERT: F 130 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7524 (mp) REVERT: F 202 TRP cc_start: 0.8752 (t60) cc_final: 0.7704 (t60) REVERT: F 208 GLN cc_start: 0.6893 (mp10) cc_final: 0.6260 (mp10) REVERT: F 215 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7988 (p) REVERT: F 250 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7112 (tpp80) REVERT: F 258 TRP cc_start: 0.7748 (m-90) cc_final: 0.7419 (m-90) REVERT: F 270 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8038 (mt-10) REVERT: G 2 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7926 (mm-30) REVERT: G 6 THR cc_start: 0.9385 (m) cc_final: 0.9122 (p) REVERT: G 115 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8550 (mt) REVERT: I 48 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8041 (mt-10) REVERT: J 392 SER cc_start: 0.7848 (m) cc_final: 0.7310 (t) REVERT: K 159 ASN cc_start: 0.8615 (t0) cc_final: 0.8317 (t0) REVERT: K 174 ASP cc_start: 0.8724 (t0) cc_final: 0.8332 (t0) REVERT: K 193 HIS cc_start: 0.8309 (p-80) cc_final: 0.7926 (p-80) REVERT: K 202 TRP cc_start: 0.7547 (t60) cc_final: 0.7093 (t60) REVERT: K 209 TYR cc_start: 0.8746 (t80) cc_final: 0.8369 (t80) REVERT: K 257 MET cc_start: 0.7497 (ptt) cc_final: 0.7077 (ptp) REVERT: K 274 GLN cc_start: 0.9392 (mt0) cc_final: 0.8829 (tt0) REVERT: L 6 MET cc_start: 0.5729 (mmp) cc_final: 0.4598 (mmt) REVERT: L 26 LYS cc_start: 0.7153 (mtpp) cc_final: 0.6924 (ptpp) REVERT: L 29 GLU cc_start: 0.8821 (pp20) cc_final: 0.8163 (pp20) REVERT: L 51 VAL cc_start: 0.6221 (OUTLIER) cc_final: 0.5966 (p) REVERT: N 24 VAL cc_start: 0.9421 (t) cc_final: 0.9216 (m) REVERT: N 69 ASP cc_start: 0.7617 (t70) cc_final: 0.7368 (t70) REVERT: N 94 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6921 (m-30) REVERT: N 231 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8669 (mm) REVERT: N 323 GLU cc_start: 0.7915 (pm20) cc_final: 0.7575 (pm20) REVERT: O 56 ASP cc_start: 0.8177 (t0) cc_final: 0.7824 (m-30) REVERT: O 126 THR cc_start: 0.8696 (m) cc_final: 0.8274 (p) REVERT: O 144 THR cc_start: 0.8818 (m) cc_final: 0.8492 (p) REVERT: P 14 PHE cc_start: 0.6340 (p90) cc_final: 0.5948 (p90) REVERT: P 26 LYS cc_start: 0.7923 (mttm) cc_final: 0.7614 (ptpt) REVERT: P 29 GLU cc_start: 0.8638 (mp0) cc_final: 0.8053 (mp0) REVERT: P 31 LEU cc_start: 0.8265 (mt) cc_final: 0.7846 (mt) REVERT: Q 113 GLU cc_start: 0.8105 (pt0) cc_final: 0.7818 (pt0) REVERT: Q 167 MET cc_start: 0.8492 (mmt) cc_final: 0.7988 (mmt) REVERT: Q 201 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7554 (tm-30) REVERT: R 94 ASP cc_start: 0.7115 (m-30) cc_final: 0.6694 (m-30) REVERT: S 116 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6357 (mt0) REVERT: S 159 ASN cc_start: 0.8875 (t0) cc_final: 0.8437 (t0) REVERT: S 177 TYR cc_start: 0.8399 (p90) cc_final: 0.8097 (p90) REVERT: S 209 TYR cc_start: 0.7463 (t80) cc_final: 0.6861 (t80) REVERT: S 241 VAL cc_start: 0.9261 (t) cc_final: 0.8970 (p) REVERT: S 266 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8241 (ttpt) REVERT: S 274 GLN cc_start: 0.8620 (mt0) cc_final: 0.8260 (mt0) REVERT: T 33 MET cc_start: 0.8430 (ptm) cc_final: 0.8109 (ptm) outliers start: 108 outliers final: 80 residues processed: 552 average time/residue: 0.1914 time to fit residues: 172.1148 Evaluate side-chains 544 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 454 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain S residue 261 LYS Chi-restraints excluded: chain S residue 266 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 337 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 341 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 394 HIS F 246 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 GLN ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093688 restraints weight = 59079.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091248 restraints weight = 32180.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092292 restraints weight = 37093.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092878 restraints weight = 24634.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094060 restraints weight = 21472.338| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33979 Z= 0.201 Angle : 0.637 13.688 46294 Z= 0.327 Chirality : 0.045 0.167 5149 Planarity : 0.004 0.076 5938 Dihedral : 5.341 81.647 4630 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 3.32 % Allowed : 13.83 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.93 (0.13), residues: 4235 helix: 1.45 (0.23), residues: 564 sheet: -0.44 (0.15), residues: 1267 loop : -1.24 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 213 TYR 0.030 0.002 TYR S 191 PHE 0.018 0.002 PHE L 14 TRP 0.017 0.001 TRP G 409 HIS 0.008 0.001 HIS Q 168 Details of bonding type rmsd covalent geometry : bond 0.00479 (33926) covalent geometry : angle 0.63317 (46188) SS BOND : bond 0.00411 ( 53) SS BOND : angle 1.51307 ( 106) hydrogen bonds : bond 0.03126 ( 1004) hydrogen bonds : angle 5.14811 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 478 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8044 (tmm) cc_final: 0.7195 (ppp) REVERT: A 136 ILE cc_start: 0.8551 (mt) cc_final: 0.8286 (mm) REVERT: A 151 MET cc_start: 0.6792 (mmm) cc_final: 0.6534 (mmm) REVERT: A 177 TYR cc_start: 0.7327 (p90) cc_final: 0.7079 (p90) REVERT: A 197 GLN cc_start: 0.7500 (mt0) cc_final: 0.7255 (tt0) REVERT: A 230 ILE cc_start: 0.8357 (mt) cc_final: 0.8065 (tt) REVERT: B 183 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: B 233 TYR cc_start: 0.9026 (p90) cc_final: 0.8644 (p90) REVERT: B 373 TYR cc_start: 0.8397 (m-10) cc_final: 0.7935 (m-10) REVERT: B 409 TRP cc_start: 0.8158 (m100) cc_final: 0.7885 (m100) REVERT: B 433 MET cc_start: 0.6219 (mmp) cc_final: 0.5651 (tmm) REVERT: C 66 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: C 99 GLU cc_start: 0.8015 (mp0) cc_final: 0.7728 (mp0) REVERT: C 327 LYS cc_start: 0.9024 (ptmt) cc_final: 0.8585 (pttt) REVERT: C 407 TRP cc_start: 0.9148 (OUTLIER) cc_final: 0.8648 (m100) REVERT: F 130 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7496 (mp) REVERT: F 151 MET cc_start: 0.7085 (mmt) cc_final: 0.6868 (mmt) REVERT: F 202 TRP cc_start: 0.8716 (t60) cc_final: 0.7624 (t60) REVERT: F 208 GLN cc_start: 0.7061 (mp10) cc_final: 0.6461 (mp10) REVERT: F 215 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7963 (p) REVERT: F 250 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7134 (tpp80) REVERT: F 258 TRP cc_start: 0.7833 (m-90) cc_final: 0.7578 (m-90) REVERT: G 2 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7938 (mm-30) REVERT: G 6 THR cc_start: 0.9383 (m) cc_final: 0.9132 (p) REVERT: G 115 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8575 (mt) REVERT: I 26 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7167 (mmtm) REVERT: I 48 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8118 (mt-10) REVERT: J 392 SER cc_start: 0.7643 (m) cc_final: 0.7072 (t) REVERT: K 151 MET cc_start: 0.8517 (mmt) cc_final: 0.8169 (mmt) REVERT: K 159 ASN cc_start: 0.8484 (t0) cc_final: 0.8116 (t0) REVERT: K 174 ASP cc_start: 0.8807 (t0) cc_final: 0.8446 (t0) REVERT: K 183 ASN cc_start: 0.9234 (p0) cc_final: 0.8975 (p0) REVERT: K 193 HIS cc_start: 0.8258 (p-80) cc_final: 0.7743 (p-80) REVERT: K 197 GLN cc_start: 0.8559 (tp40) cc_final: 0.8056 (mm-40) REVERT: K 202 TRP cc_start: 0.7746 (t60) cc_final: 0.7176 (t60) REVERT: K 209 TYR cc_start: 0.8750 (t80) cc_final: 0.8001 (t80) REVERT: L 29 GLU cc_start: 0.8887 (pp20) cc_final: 0.8498 (pp20) REVERT: L 51 VAL cc_start: 0.6157 (OUTLIER) cc_final: 0.5867 (p) REVERT: N 24 VAL cc_start: 0.9406 (t) cc_final: 0.9192 (m) REVERT: N 69 ASP cc_start: 0.7672 (t70) cc_final: 0.7392 (t70) REVERT: N 94 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: N 110 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8498 (tt) REVERT: N 231 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8831 (mm) REVERT: O 56 ASP cc_start: 0.8285 (t0) cc_final: 0.8032 (m-30) REVERT: O 126 THR cc_start: 0.8770 (m) cc_final: 0.8347 (p) REVERT: O 144 THR cc_start: 0.8768 (m) cc_final: 0.8487 (p) REVERT: O 436 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8570 (mt) REVERT: P 9 LEU cc_start: 0.6339 (mp) cc_final: 0.5305 (tt) REVERT: P 14 PHE cc_start: 0.5959 (p90) cc_final: 0.5705 (p90) REVERT: P 26 LYS cc_start: 0.7930 (mttm) cc_final: 0.7669 (ptpt) REVERT: P 29 GLU cc_start: 0.8702 (mp0) cc_final: 0.8038 (mp0) REVERT: P 31 LEU cc_start: 0.8289 (mt) cc_final: 0.8008 (mt) REVERT: Q 167 MET cc_start: 0.8340 (mmt) cc_final: 0.7689 (mmt) REVERT: Q 201 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7580 (tm-30) REVERT: R 94 ASP cc_start: 0.7286 (m-30) cc_final: 0.6766 (m-30) REVERT: R 167 MET cc_start: 0.8374 (mmp) cc_final: 0.8146 (mmp) REVERT: S 116 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6453 (mt0) REVERT: S 159 ASN cc_start: 0.8881 (t0) cc_final: 0.8513 (t0) REVERT: S 177 TYR cc_start: 0.8423 (p90) cc_final: 0.8179 (p90) REVERT: S 215 THR cc_start: 0.8999 (p) cc_final: 0.8736 (t) REVERT: S 241 VAL cc_start: 0.9282 (t) cc_final: 0.8995 (p) REVERT: S 266 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8231 (ttpt) outliers start: 120 outliers final: 87 residues processed: 559 average time/residue: 0.1888 time to fit residues: 172.8679 Evaluate side-chains 555 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 456 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 353 HIS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain S residue 266 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 96 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 419 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093162 restraints weight = 58580.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090562 restraints weight = 35262.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091673 restraints weight = 41487.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092228 restraints weight = 25995.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093159 restraints weight = 22570.842| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 33979 Z= 0.243 Angle : 0.679 13.964 46294 Z= 0.348 Chirality : 0.046 0.176 5149 Planarity : 0.005 0.076 5938 Dihedral : 5.501 83.284 4630 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 3.51 % Allowed : 14.33 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.97 (0.13), residues: 4235 helix: 1.43 (0.23), residues: 569 sheet: -0.33 (0.15), residues: 1152 loop : -1.33 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 213 TYR 0.028 0.002 TYR S 191 PHE 0.026 0.002 PHE C 95 TRP 0.020 0.002 TRP G 409 HIS 0.007 0.001 HIS J 28 Details of bonding type rmsd covalent geometry : bond 0.00579 (33926) covalent geometry : angle 0.67487 (46188) SS BOND : bond 0.00330 ( 53) SS BOND : angle 1.61976 ( 106) hydrogen bonds : bond 0.03355 ( 1004) hydrogen bonds : angle 5.22814 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 474 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7987 (tmm) cc_final: 0.7434 (mtt) REVERT: A 177 TYR cc_start: 0.7681 (p90) cc_final: 0.7292 (p90) REVERT: A 197 GLN cc_start: 0.7575 (mt0) cc_final: 0.7343 (tt0) REVERT: A 230 ILE cc_start: 0.8447 (mt) cc_final: 0.8142 (tt) REVERT: B 183 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: B 373 TYR cc_start: 0.8434 (m-10) cc_final: 0.8044 (m-10) REVERT: B 409 TRP cc_start: 0.8239 (m100) cc_final: 0.7978 (m100) REVERT: C 66 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (mp10) REVERT: C 327 LYS cc_start: 0.9044 (ptmt) cc_final: 0.8605 (pttt) REVERT: C 407 TRP cc_start: 0.9133 (OUTLIER) cc_final: 0.8562 (m100) REVERT: F 130 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7584 (mp) REVERT: F 202 TRP cc_start: 0.8741 (t60) cc_final: 0.7695 (t60) REVERT: F 208 GLN cc_start: 0.7145 (mp10) cc_final: 0.6836 (mp10) REVERT: F 215 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8036 (p) REVERT: G 2 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7971 (mm-30) REVERT: G 6 THR cc_start: 0.9374 (m) cc_final: 0.9133 (p) REVERT: G 115 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8591 (mt) REVERT: I 26 LYS cc_start: 0.7545 (mmtm) cc_final: 0.7257 (mmtm) REVERT: I 45 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: J 392 SER cc_start: 0.7776 (m) cc_final: 0.7164 (t) REVERT: K 159 ASN cc_start: 0.8471 (t0) cc_final: 0.8191 (t0) REVERT: K 174 ASP cc_start: 0.8915 (t0) cc_final: 0.8598 (t0) REVERT: K 183 ASN cc_start: 0.9244 (p0) cc_final: 0.9003 (p0) REVERT: K 193 HIS cc_start: 0.8299 (p-80) cc_final: 0.7795 (p-80) REVERT: K 197 GLN cc_start: 0.8529 (tp40) cc_final: 0.8107 (mm-40) REVERT: K 202 TRP cc_start: 0.7795 (t60) cc_final: 0.7557 (t60) REVERT: K 209 TYR cc_start: 0.8765 (t80) cc_final: 0.8102 (t80) REVERT: L 6 MET cc_start: 0.5789 (mmp) cc_final: 0.4551 (mmt) REVERT: L 29 GLU cc_start: 0.8841 (pp20) cc_final: 0.8540 (pp20) REVERT: L 52 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7519 (mtpt) REVERT: N 69 ASP cc_start: 0.7819 (t70) cc_final: 0.7557 (t70) REVERT: N 110 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8578 (tt) REVERT: N 128 GLU cc_start: 0.7518 (tt0) cc_final: 0.7305 (tt0) REVERT: O 56 ASP cc_start: 0.8236 (t0) cc_final: 0.7997 (m-30) REVERT: O 126 THR cc_start: 0.8833 (m) cc_final: 0.8422 (p) REVERT: O 144 THR cc_start: 0.8787 (m) cc_final: 0.8490 (p) REVERT: O 436 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (mt) REVERT: P 14 PHE cc_start: 0.6085 (p90) cc_final: 0.5764 (p90) REVERT: P 29 GLU cc_start: 0.8577 (mp0) cc_final: 0.8246 (mp0) REVERT: Q 137 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6954 (mt-10) REVERT: Q 167 MET cc_start: 0.8175 (mmt) cc_final: 0.7689 (mmt) REVERT: Q 201 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7537 (tm-30) REVERT: Q 401 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8346 (mtt180) REVERT: R 94 ASP cc_start: 0.7299 (m-30) cc_final: 0.6828 (m-30) REVERT: S 116 GLN cc_start: 0.7599 (mm-40) cc_final: 0.6854 (mt0) REVERT: S 159 ASN cc_start: 0.9000 (t0) cc_final: 0.8672 (t0) REVERT: S 177 TYR cc_start: 0.8464 (p90) cc_final: 0.8139 (p90) REVERT: S 192 THR cc_start: 0.9131 (t) cc_final: 0.8636 (m) REVERT: S 266 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8182 (ttpt) REVERT: T 40 ASN cc_start: 0.8499 (t0) cc_final: 0.8072 (t0) outliers start: 127 outliers final: 98 residues processed: 559 average time/residue: 0.1877 time to fit residues: 172.4104 Evaluate side-chains 557 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 449 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain N residue 287 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 353 HIS Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 137 ASN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 189 PHE Chi-restraints excluded: chain S residue 197 GLN Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain S residue 266 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 373 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 375 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 GLN K 182 GLN K 197 GLN Q 96 HIS ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094826 restraints weight = 58694.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092255 restraints weight = 32289.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093598 restraints weight = 35072.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093886 restraints weight = 24166.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094340 restraints weight = 21283.812| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33979 Z= 0.120 Angle : 0.627 14.857 46294 Z= 0.317 Chirality : 0.044 0.181 5149 Planarity : 0.004 0.072 5938 Dihedral : 5.296 82.911 4630 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 2.66 % Allowed : 15.57 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.86 (0.13), residues: 4235 helix: 1.47 (0.23), residues: 576 sheet: -0.35 (0.15), residues: 1213 loop : -1.20 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 213 TYR 0.028 0.001 TYR S 191 PHE 0.019 0.001 PHE L 14 TRP 0.029 0.001 TRP F 258 HIS 0.006 0.001 HIS R 168 Details of bonding type rmsd covalent geometry : bond 0.00276 (33926) covalent geometry : angle 0.62417 (46188) SS BOND : bond 0.00289 ( 53) SS BOND : angle 1.40336 ( 106) hydrogen bonds : bond 0.02827 ( 1004) hydrogen bonds : angle 5.09848 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 472 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8060 (tmm) cc_final: 0.7572 (mpp) REVERT: A 177 TYR cc_start: 0.7383 (p90) cc_final: 0.7158 (p90) REVERT: A 197 GLN cc_start: 0.7486 (mt0) cc_final: 0.7235 (tt0) REVERT: A 230 ILE cc_start: 0.8316 (mt) cc_final: 0.8044 (tt) REVERT: B 53 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9091 (p) REVERT: B 183 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: B 373 TYR cc_start: 0.8439 (m-10) cc_final: 0.7992 (m-10) REVERT: B 409 TRP cc_start: 0.8103 (m100) cc_final: 0.7851 (m100) REVERT: B 433 MET cc_start: 0.6295 (mmp) cc_final: 0.5753 (tmm) REVERT: C 66 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: C 327 LYS cc_start: 0.9034 (ptmt) cc_final: 0.8582 (pttt) REVERT: C 407 TRP cc_start: 0.9084 (OUTLIER) cc_final: 0.8617 (m100) REVERT: F 130 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7411 (mp) REVERT: F 151 MET cc_start: 0.7156 (mmt) cc_final: 0.6930 (mmt) REVERT: F 174 ASP cc_start: 0.8108 (t0) cc_final: 0.7888 (t0) REVERT: F 202 TRP cc_start: 0.8704 (t60) cc_final: 0.7628 (t60) REVERT: G 2 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7912 (mm-30) REVERT: G 6 THR cc_start: 0.9402 (m) cc_final: 0.9148 (p) REVERT: G 115 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8577 (mt) REVERT: I 26 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7135 (mmtm) REVERT: I 45 GLU cc_start: 0.8224 (pm20) cc_final: 0.7923 (mp0) REVERT: J 113 GLU cc_start: 0.7132 (pt0) cc_final: 0.6812 (pt0) REVERT: J 177 SER cc_start: 0.8792 (m) cc_final: 0.8448 (t) REVERT: J 392 SER cc_start: 0.7651 (m) cc_final: 0.7094 (t) REVERT: K 118 MET cc_start: 0.7870 (tmm) cc_final: 0.6925 (ppp) REVERT: K 120 MET cc_start: 0.8098 (mmm) cc_final: 0.7717 (mmt) REVERT: K 159 ASN cc_start: 0.8604 (t0) cc_final: 0.8357 (t0) REVERT: K 174 ASP cc_start: 0.8861 (t0) cc_final: 0.8546 (t0) REVERT: K 193 HIS cc_start: 0.8290 (p-80) cc_final: 0.7735 (p-80) REVERT: K 197 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: K 202 TRP cc_start: 0.7699 (t60) cc_final: 0.7486 (t60) REVERT: K 209 TYR cc_start: 0.8696 (t80) cc_final: 0.7875 (t80) REVERT: K 257 MET cc_start: 0.7465 (ptt) cc_final: 0.7056 (ptp) REVERT: L 6 MET cc_start: 0.5693 (mmp) cc_final: 0.4540 (mmt) REVERT: L 29 GLU cc_start: 0.8828 (pp20) cc_final: 0.8521 (pp20) REVERT: L 51 VAL cc_start: 0.6511 (OUTLIER) cc_final: 0.6229 (p) REVERT: N 10 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7661 (tptt) REVERT: N 69 ASP cc_start: 0.7824 (t70) cc_final: 0.7527 (t70) REVERT: N 110 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8487 (tt) REVERT: N 216 GLN cc_start: 0.7579 (mm-40) cc_final: 0.6880 (mm-40) REVERT: O 56 ASP cc_start: 0.8320 (t0) cc_final: 0.8046 (m-30) REVERT: O 126 THR cc_start: 0.8802 (m) cc_final: 0.8398 (p) REVERT: O 144 THR cc_start: 0.8795 (m) cc_final: 0.8568 (p) REVERT: O 436 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8557 (mt) REVERT: P 14 PHE cc_start: 0.5537 (p90) cc_final: 0.5280 (p90) REVERT: P 29 GLU cc_start: 0.8793 (mp0) cc_final: 0.8332 (mp0) REVERT: Q 113 GLU cc_start: 0.8000 (pt0) cc_final: 0.7601 (pt0) REVERT: Q 167 MET cc_start: 0.8261 (mmt) cc_final: 0.7954 (mmt) REVERT: Q 201 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7475 (tm-30) REVERT: R 369 LEU cc_start: 0.7709 (tp) cc_final: 0.7263 (tt) REVERT: S 116 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6668 (mt0) REVERT: S 159 ASN cc_start: 0.8900 (t0) cc_final: 0.8527 (t0) REVERT: S 177 TYR cc_start: 0.8371 (p90) cc_final: 0.8158 (p90) REVERT: S 236 ARG cc_start: 0.7302 (mtm180) cc_final: 0.7064 (mtm180) REVERT: T 40 ASN cc_start: 0.8474 (t0) cc_final: 0.8012 (t0) outliers start: 96 outliers final: 73 residues processed: 533 average time/residue: 0.1920 time to fit residues: 167.0567 Evaluate side-chains 533 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 450 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain K residue 197 GLN Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 189 PHE Chi-restraints excluded: chain S residue 197 GLN Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 287 optimal weight: 1.9990 chunk 262 optimal weight: 0.4980 chunk 356 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 386 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 372 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 290 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 362 HIS ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 ASN K 182 GLN K 271 ASN K 274 GLN S 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095825 restraints weight = 59051.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093767 restraints weight = 30377.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095008 restraints weight = 31763.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095282 restraints weight = 22772.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096623 restraints weight = 20309.462| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 33979 Z= 0.108 Angle : 0.615 15.223 46294 Z= 0.311 Chirality : 0.044 0.188 5149 Planarity : 0.004 0.077 5938 Dihedral : 5.126 82.402 4630 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.29 % Favored : 94.69 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.74 (0.13), residues: 4235 helix: 1.46 (0.23), residues: 587 sheet: -0.18 (0.15), residues: 1194 loop : -1.16 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 213 TYR 0.029 0.001 TYR S 191 PHE 0.021 0.001 PHE G 398 TRP 0.019 0.001 TRP S 258 HIS 0.005 0.001 HIS K 193 Details of bonding type rmsd covalent geometry : bond 0.00244 (33926) covalent geometry : angle 0.61232 (46188) SS BOND : bond 0.00274 ( 53) SS BOND : angle 1.41386 ( 106) hydrogen bonds : bond 0.02703 ( 1004) hydrogen bonds : angle 5.00642 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 474 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8064 (tmm) cc_final: 0.7575 (mpp) REVERT: A 151 MET cc_start: 0.6981 (mmm) cc_final: 0.6686 (mmm) REVERT: A 174 ASP cc_start: 0.7459 (t0) cc_final: 0.7216 (m-30) REVERT: A 197 GLN cc_start: 0.7360 (mt0) cc_final: 0.7133 (tt0) REVERT: A 230 ILE cc_start: 0.8284 (mt) cc_final: 0.8018 (tt) REVERT: A 255 VAL cc_start: 0.8605 (t) cc_final: 0.8329 (p) REVERT: A 257 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5928 (mpp) REVERT: B 7 MET cc_start: 0.7452 (tpp) cc_final: 0.7178 (tpt) REVERT: B 15 TYR cc_start: 0.7843 (t80) cc_final: 0.7612 (t80) REVERT: B 53 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8986 (p) REVERT: B 183 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: B 233 TYR cc_start: 0.8889 (p90) cc_final: 0.8506 (p90) REVERT: B 366 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8251 (ttp80) REVERT: B 373 TYR cc_start: 0.8369 (m-10) cc_final: 0.7858 (m-10) REVERT: B 409 TRP cc_start: 0.8113 (m100) cc_final: 0.7829 (m100) REVERT: C 66 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8347 (mp10) REVERT: C 241 GLU cc_start: 0.8587 (tp30) cc_final: 0.8206 (tp30) REVERT: C 327 LYS cc_start: 0.9007 (ptmt) cc_final: 0.8611 (pttt) REVERT: C 407 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8441 (m100) REVERT: F 130 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7373 (mp) REVERT: F 202 TRP cc_start: 0.8783 (t60) cc_final: 0.7686 (t60) REVERT: G 2 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7881 (mm-30) REVERT: G 6 THR cc_start: 0.9402 (m) cc_final: 0.9143 (p) REVERT: G 115 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8602 (mt) REVERT: G 241 GLU cc_start: 0.7903 (tp30) cc_final: 0.7476 (tp30) REVERT: I 26 LYS cc_start: 0.7407 (mmtm) cc_final: 0.7113 (mmtm) REVERT: I 45 GLU cc_start: 0.8151 (pm20) cc_final: 0.7883 (mp0) REVERT: J 113 GLU cc_start: 0.7173 (pt0) cc_final: 0.6819 (pt0) REVERT: J 177 SER cc_start: 0.8777 (m) cc_final: 0.8458 (t) REVERT: J 392 SER cc_start: 0.7812 (m) cc_final: 0.7332 (t) REVERT: K 118 MET cc_start: 0.7976 (tmm) cc_final: 0.6962 (ppp) REVERT: K 159 ASN cc_start: 0.8598 (t0) cc_final: 0.8313 (t0) REVERT: K 174 ASP cc_start: 0.8814 (t0) cc_final: 0.8505 (t0) REVERT: K 193 HIS cc_start: 0.8330 (p-80) cc_final: 0.7728 (p-80) REVERT: K 202 TRP cc_start: 0.7590 (t60) cc_final: 0.7385 (t60) REVERT: K 257 MET cc_start: 0.7386 (ptt) cc_final: 0.6970 (ptp) REVERT: L 6 MET cc_start: 0.5848 (mmp) cc_final: 0.4823 (mmt) REVERT: L 29 GLU cc_start: 0.8856 (pp20) cc_final: 0.8543 (pp20) REVERT: L 51 VAL cc_start: 0.6524 (OUTLIER) cc_final: 0.5159 (p) REVERT: L 52 LYS cc_start: 0.7049 (mtpt) cc_final: 0.6790 (mppt) REVERT: N 10 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7478 (tptt) REVERT: N 69 ASP cc_start: 0.7781 (t70) cc_final: 0.7443 (t70) REVERT: N 216 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6830 (mm-40) REVERT: O 56 ASP cc_start: 0.8288 (t0) cc_final: 0.8037 (m-30) REVERT: O 126 THR cc_start: 0.8748 (m) cc_final: 0.8336 (p) REVERT: O 436 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8532 (mt) REVERT: P 8 LEU cc_start: 0.8202 (mt) cc_final: 0.7716 (tt) REVERT: P 29 GLU cc_start: 0.8887 (mp0) cc_final: 0.8269 (mp0) REVERT: Q 113 GLU cc_start: 0.8030 (pt0) cc_final: 0.7577 (pt0) REVERT: Q 167 MET cc_start: 0.8293 (mmt) cc_final: 0.8066 (mmt) REVERT: Q 201 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7412 (tm-30) REVERT: R 94 ASP cc_start: 0.7145 (m-30) cc_final: 0.6713 (m-30) REVERT: R 369 LEU cc_start: 0.7666 (tp) cc_final: 0.7316 (tt) REVERT: S 116 GLN cc_start: 0.7545 (mm-40) cc_final: 0.6752 (mt0) REVERT: S 159 ASN cc_start: 0.8856 (t0) cc_final: 0.8451 (t0) REVERT: T 40 ASN cc_start: 0.8418 (t0) cc_final: 0.7927 (t0) outliers start: 82 outliers final: 65 residues processed: 529 average time/residue: 0.1887 time to fit residues: 163.6141 Evaluate side-chains 523 residues out of total 3615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 449 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 380 CYS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain S residue 137 ASN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 197 GLN Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 421 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 412 optimal weight: 6.9990 chunk 363 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 GLN K 197 GLN K 271 ASN K 274 GLN S 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097540 restraints weight = 56889.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.095723 restraints weight = 32849.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096099 restraints weight = 31737.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096508 restraints weight = 27227.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097463 restraints weight = 22329.645| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33979 Z= 0.194 Angle : 0.656 14.308 46294 Z= 0.334 Chirality : 0.046 0.274 5149 Planarity : 0.005 0.077 5938 Dihedral : 5.260 83.081 4630 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 2.57 % Allowed : 16.04 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % 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: -0.79 (0.13), residues: 4235 helix: 1.49 (0.23), residues: 582 sheet: -0.29 (0.15), residues: 1183 loop : -1.16 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 366 TYR 0.028 0.002 TYR A 177 PHE 0.018 0.002 PHE L 14 TRP 0.017 0.001 TRP G 409 HIS 0.006 0.001 HIS J 28 Details of bonding type rmsd covalent geometry : bond 0.00464 (33926) covalent geometry : angle 0.65253 (46188) SS BOND : bond 0.00339 ( 53) SS BOND : angle 1.56228 ( 106) hydrogen bonds : bond 0.03052 ( 1004) hydrogen bonds : angle 5.03568 ( 2604) =============================================================================== Job complete usr+sys time: 5972.54 seconds wall clock time: 103 minutes 53.22 seconds (6233.22 seconds total)