Starting phenix.real_space_refine on Fri Jan 17 04:52:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b41_44164/01_2025/9b41_44164.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b41_44164/01_2025/9b41_44164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b41_44164/01_2025/9b41_44164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b41_44164/01_2025/9b41_44164.map" model { file = "/net/cci-nas-00/data/ceres_data/9b41_44164/01_2025/9b41_44164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b41_44164/01_2025/9b41_44164.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 180 5.16 5 C 35256 2.51 5 N 9468 2.21 5 O 10704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 55608 Number of models: 1 Model: "" Number of chains: 24 Chain: "L" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "B" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "C" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "D" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "F" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "G" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "H" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "I" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "J" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "K" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3441 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain: "M" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "N" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "O" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "P" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "Q" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "R" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "T" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "U" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "V" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "W" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Chain: "X" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 145} Time building chain proxies: 24.43, per 1000 atoms: 0.44 Number of scatterers: 55608 At special positions: 0 Unit cell: (167.5, 164.82, 195.64, 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 180 16.00 O 10704 8.00 N 9468 7.00 C 35256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.25 Conformation dependent library (CDL) restraints added in 5.8 seconds 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13080 Finding SS restraints... Secondary structure from input PDB file: 317 helices and 49 sheets defined 57.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'L' and resid 96 through 104 Processing helix chain 'L' and resid 110 through 118 Processing helix chain 'L' and resid 120 through 129 Processing helix chain 'L' and resid 131 through 137 removed outlier: 4.260A pdb=" N ASN L 137 " --> pdb=" O ASP L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 164 Processing helix chain 'L' and resid 164 through 179 Processing helix chain 'L' and resid 194 through 198 removed outlier: 3.795A pdb=" N LYS L 198 " --> pdb=" O TYR L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 221 Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 278 through 284 Processing helix chain 'L' and resid 285 through 303 removed outlier: 3.795A pdb=" N ALA L 297 " --> pdb=" O THR L 293 " (cutoff:3.500A) Proline residue: L 298 - end of helix removed outlier: 3.614A pdb=" N SER L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 320 removed outlier: 4.140A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN L 319 " --> pdb=" O LYS L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 333 Processing helix chain 'L' and resid 357 through 374 removed outlier: 3.877A pdb=" N ILE L 361 " --> pdb=" O ASP L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 392 through 401 Processing helix chain 'L' and resid 401 through 424 removed outlier: 3.522A pdb=" N SER L 405 " --> pdb=" O GLU L 401 " (cutoff:3.500A) Proline residue: L 413 - end of helix Processing helix chain 'L' and resid 443 through 465 Processing helix chain 'L' and resid 468 through 478 removed outlier: 3.708A pdb=" N VAL L 472 " --> pdb=" O SER L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 528 removed outlier: 3.659A pdb=" N ASN L 502 " --> pdb=" O MET L 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.546A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 131 through 137 removed outlier: 4.445A pdb=" N ASN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.772A pdb=" N LYS A 198 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 265 through 273 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 278 through 303 removed outlier: 5.515A pdb=" N GLU A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.631A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.828A pdb=" N ILE A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 402 through 424 Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 443 through 465 Processing helix chain 'A' and resid 468 through 478 removed outlier: 3.772A pdb=" N VAL A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 528 removed outlier: 3.738A pdb=" N ASN A 502 " --> pdb=" O MET A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 131 through 137 removed outlier: 4.261A pdb=" N ASN B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.807A pdb=" N LYS B 198 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 265 through 273 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 278 through 303 removed outlier: 5.550A pdb=" N GLU B 285 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Proline residue: B 298 - end of helix removed outlier: 3.662A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 4.238A pdb=" N ALA B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 357 through 374 removed outlier: 3.798A pdb=" N ILE B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 367 " --> pdb=" O MET B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 402 through 424 Proline residue: B 413 - end of helix removed outlier: 3.590A pdb=" N LYS B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 465 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.850A pdb=" N VAL B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 528 removed outlier: 3.667A pdb=" N ASN B 502 " --> pdb=" O MET B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 3.502A pdb=" N SER C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.330A pdb=" N ASN C 137 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 164 Processing helix chain 'C' and resid 164 through 179 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.796A pdb=" N LYS C 198 " --> pdb=" O TYR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 285 through 303 removed outlier: 3.772A pdb=" N ALA C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Proline residue: C 298 - end of helix removed outlier: 3.614A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 4.112A pdb=" N ALA C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 357 through 374 removed outlier: 3.875A pdb=" N ILE C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'C' and resid 401 through 424 removed outlier: 3.604A pdb=" N SER C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 443 through 465 Processing helix chain 'C' and resid 468 through 478 removed outlier: 3.747A pdb=" N VAL C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 528 removed outlier: 3.624A pdb=" N ASN C 502 " --> pdb=" O MET C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.512A pdb=" N SER D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 131 through 137 removed outlier: 4.451A pdb=" N ASN D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 164 through 179 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.784A pdb=" N LYS D 198 " --> pdb=" O TYR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 265 through 273 Proline residue: D 270 - end of helix Processing helix chain 'D' and resid 278 through 303 removed outlier: 5.477A pdb=" N GLU D 285 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG D 286 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.617A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.995A pdb=" N ALA D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.759A pdb=" N ASN D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 374 removed outlier: 3.768A pdb=" N ILE D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 392 through 401 Processing helix chain 'D' and resid 402 through 424 Proline residue: D 413 - end of helix Processing helix chain 'D' and resid 443 through 465 Processing helix chain 'D' and resid 468 through 478 removed outlier: 3.749A pdb=" N VAL D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 528 removed outlier: 3.750A pdb=" N ASN D 502 " --> pdb=" O MET D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 120 through 129 Processing helix chain 'E' and resid 131 through 137 removed outlier: 4.263A pdb=" N ASN E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 164 Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 194 through 198 removed outlier: 3.806A pdb=" N LYS E 198 " --> pdb=" O TYR E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 221 Processing helix chain 'E' and resid 265 through 273 Proline residue: E 270 - end of helix Processing helix chain 'E' and resid 278 through 303 removed outlier: 5.528A pdb=" N GLU E 285 " --> pdb=" O GLN E 281 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG E 286 " --> pdb=" O ARG E 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Proline residue: E 298 - end of helix removed outlier: 3.768A pdb=" N SER E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 320 removed outlier: 4.425A pdb=" N ALA E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 357 through 374 removed outlier: 3.915A pdb=" N ILE E 361 " --> pdb=" O ASP E 357 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN E 367 " --> pdb=" O MET E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 392 through 401 Processing helix chain 'E' and resid 402 through 424 Proline residue: E 413 - end of helix removed outlier: 3.611A pdb=" N LYS E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 465 Processing helix chain 'E' and resid 468 through 478 removed outlier: 3.754A pdb=" N VAL E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 528 removed outlier: 3.650A pdb=" N ASN E 502 " --> pdb=" O MET E 498 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 528 " --> pdb=" O GLU E 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.590A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 120 through 129 Processing helix chain 'F' and resid 131 through 137 removed outlier: 4.352A pdb=" N ASN F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 164 Processing helix chain 'F' and resid 164 through 179 Processing helix chain 'F' and resid 194 through 198 removed outlier: 3.813A pdb=" N LYS F 198 " --> pdb=" O TYR F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 278 through 283 Processing helix chain 'F' and resid 285 through 303 removed outlier: 3.770A pdb=" N ALA F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Proline residue: F 298 - end of helix removed outlier: 3.596A pdb=" N SER F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 320 removed outlier: 4.155A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN F 319 " --> pdb=" O LYS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 Processing helix chain 'F' and resid 357 through 374 removed outlier: 3.889A pdb=" N ILE F 361 " --> pdb=" O ASP F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 392 through 400 Processing helix chain 'F' and resid 401 through 424 removed outlier: 3.552A pdb=" N SER F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) Proline residue: F 413 - end of helix Processing helix chain 'F' and resid 443 through 465 Processing helix chain 'F' and resid 468 through 478 removed outlier: 3.672A pdb=" N VAL F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 528 removed outlier: 3.661A pdb=" N ASN F 502 " --> pdb=" O MET F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 removed outlier: 3.532A pdb=" N SER G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 120 through 129 Processing helix chain 'G' and resid 131 through 137 removed outlier: 4.262A pdb=" N ASN G 137 " --> pdb=" O ASP G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 164 through 179 Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.779A pdb=" N LYS G 198 " --> pdb=" O TYR G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'G' and resid 265 through 273 Proline residue: G 270 - end of helix Processing helix chain 'G' and resid 278 through 284 Processing helix chain 'G' and resid 285 through 303 removed outlier: 3.761A pdb=" N ALA G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Proline residue: G 298 - end of helix removed outlier: 3.636A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 320 removed outlier: 4.069A pdb=" N ALA G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN G 319 " --> pdb=" O LYS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 357 through 374 removed outlier: 3.825A pdb=" N ILE G 361 " --> pdb=" O ASP G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 381 Processing helix chain 'G' and resid 392 through 401 Processing helix chain 'G' and resid 401 through 424 Proline residue: G 413 - end of helix Processing helix chain 'G' and resid 443 through 465 Processing helix chain 'G' and resid 468 through 478 removed outlier: 3.741A pdb=" N VAL G 472 " --> pdb=" O SER G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 528 removed outlier: 3.729A pdb=" N ASN G 502 " --> pdb=" O MET G 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 120 through 129 Processing helix chain 'H' and resid 131 through 137 removed outlier: 4.266A pdb=" N ASN H 137 " --> pdb=" O ASP H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 164 Processing helix chain 'H' and resid 164 through 179 Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.807A pdb=" N LYS H 198 " --> pdb=" O TYR H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 221 Processing helix chain 'H' and resid 265 through 273 Proline residue: H 270 - end of helix Processing helix chain 'H' and resid 278 through 303 removed outlier: 5.590A pdb=" N GLU H 285 " --> pdb=" O GLN H 281 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG H 286 " --> pdb=" O ARG H 282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL H 287 " --> pdb=" O ILE H 283 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR H 288 " --> pdb=" O TYR H 284 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Proline residue: H 298 - end of helix removed outlier: 3.712A pdb=" N SER H 303 " --> pdb=" O LEU H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 320 removed outlier: 4.273A pdb=" N ALA H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 333 Processing helix chain 'H' and resid 357 through 374 removed outlier: 3.809A pdb=" N ILE H 361 " --> pdb=" O ASP H 357 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 367 " --> pdb=" O MET H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 381 Processing helix chain 'H' and resid 392 through 401 Processing helix chain 'H' and resid 402 through 424 Proline residue: H 413 - end of helix removed outlier: 3.615A pdb=" N LYS H 424 " --> pdb=" O LEU H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 465 Processing helix chain 'H' and resid 468 through 478 removed outlier: 3.777A pdb=" N VAL H 472 " --> pdb=" O SER H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 528 removed outlier: 3.633A pdb=" N ASN H 502 " --> pdb=" O MET H 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 removed outlier: 3.556A pdb=" N SER I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 120 through 129 Processing helix chain 'I' and resid 131 through 137 removed outlier: 4.324A pdb=" N ASN I 137 " --> pdb=" O ASP I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 164 Processing helix chain 'I' and resid 164 through 179 Processing helix chain 'I' and resid 194 through 198 removed outlier: 3.795A pdb=" N LYS I 198 " --> pdb=" O TYR I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 221 Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 278 through 283 Processing helix chain 'I' and resid 285 through 303 removed outlier: 3.763A pdb=" N ALA I 297 " --> pdb=" O THR I 293 " (cutoff:3.500A) Proline residue: I 298 - end of helix removed outlier: 3.601A pdb=" N SER I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 320 removed outlier: 4.244A pdb=" N ALA I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN I 319 " --> pdb=" O LYS I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 333 Processing helix chain 'I' and resid 357 through 374 removed outlier: 3.869A pdb=" N ILE I 361 " --> pdb=" O ASP I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 381 Processing helix chain 'I' and resid 392 through 400 Processing helix chain 'I' and resid 401 through 424 removed outlier: 3.525A pdb=" N SER I 405 " --> pdb=" O GLU I 401 " (cutoff:3.500A) Proline residue: I 413 - end of helix Processing helix chain 'I' and resid 443 through 465 Processing helix chain 'I' and resid 468 through 478 removed outlier: 3.713A pdb=" N VAL I 472 " --> pdb=" O SER I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 528 removed outlier: 3.658A pdb=" N ASN I 502 " --> pdb=" O MET I 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 removed outlier: 3.561A pdb=" N SER J 105 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 118 Processing helix chain 'J' and resid 120 through 129 Processing helix chain 'J' and resid 131 through 137 removed outlier: 4.307A pdb=" N ASN J 137 " --> pdb=" O ASP J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 164 Processing helix chain 'J' and resid 164 through 179 Processing helix chain 'J' and resid 194 through 198 removed outlier: 3.788A pdb=" N LYS J 198 " --> pdb=" O TYR J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 221 Processing helix chain 'J' and resid 265 through 273 Proline residue: J 270 - end of helix Processing helix chain 'J' and resid 278 through 303 removed outlier: 5.489A pdb=" N GLU J 285 " --> pdb=" O GLN J 281 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG J 286 " --> pdb=" O ARG J 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 287 " --> pdb=" O ILE J 283 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR J 288 " --> pdb=" O TYR J 284 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA J 297 " --> pdb=" O THR J 293 " (cutoff:3.500A) Proline residue: J 298 - end of helix removed outlier: 3.625A pdb=" N SER J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 317 Processing helix chain 'J' and resid 321 through 333 Processing helix chain 'J' and resid 357 through 374 removed outlier: 3.802A pdb=" N ILE J 361 " --> pdb=" O ASP J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 381 Processing helix chain 'J' and resid 392 through 401 Processing helix chain 'J' and resid 401 through 424 Proline residue: J 413 - end of helix Processing helix chain 'J' and resid 443 through 465 Processing helix chain 'J' and resid 468 through 478 removed outlier: 3.751A pdb=" N VAL J 472 " --> pdb=" O SER J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 528 removed outlier: 3.739A pdb=" N ASN J 502 " --> pdb=" O MET J 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'K' and resid 120 through 129 Processing helix chain 'K' and resid 131 through 137 removed outlier: 4.261A pdb=" N ASN K 137 " --> pdb=" O ASP K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 164 Processing helix chain 'K' and resid 164 through 179 Processing helix chain 'K' and resid 194 through 198 removed outlier: 3.803A pdb=" N LYS K 198 " --> pdb=" O TYR K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 221 Processing helix chain 'K' and resid 265 through 273 Proline residue: K 270 - end of helix Processing helix chain 'K' and resid 278 through 303 removed outlier: 5.571A pdb=" N GLU K 285 " --> pdb=" O GLN K 281 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG K 286 " --> pdb=" O ARG K 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 287 " --> pdb=" O ILE K 283 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR K 288 " --> pdb=" O TYR K 284 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA K 297 " --> pdb=" O THR K 293 " (cutoff:3.500A) Proline residue: K 298 - end of helix removed outlier: 3.699A pdb=" N SER K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 320 removed outlier: 4.260A pdb=" N ALA K 318 " --> pdb=" O GLU K 314 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 333 Processing helix chain 'K' and resid 357 through 374 removed outlier: 3.800A pdb=" N ILE K 361 " --> pdb=" O ASP K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 381 Processing helix chain 'K' and resid 392 through 401 Processing helix chain 'K' and resid 402 through 424 Proline residue: K 413 - end of helix removed outlier: 3.544A pdb=" N LYS K 424 " --> pdb=" O LEU K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 465 Processing helix chain 'K' and resid 468 through 478 removed outlier: 3.764A pdb=" N VAL K 472 " --> pdb=" O SER K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 528 removed outlier: 3.672A pdb=" N ASN K 502 " --> pdb=" O MET K 498 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 13 Processing helix chain 'M' and resid 14 through 17 Processing helix chain 'M' and resid 23 through 38 removed outlier: 3.881A pdb=" N GLU M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE M 37 " --> pdb=" O ILE M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 74 Processing helix chain 'M' and resid 109 through 117 Processing helix chain 'M' and resid 118 through 132 Processing helix chain 'M' and resid 142 through 147 removed outlier: 3.734A pdb=" N GLY M 146 " --> pdb=" O GLU M 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 13 Processing helix chain 'N' and resid 14 through 17 Processing helix chain 'N' and resid 23 through 38 removed outlier: 3.835A pdb=" N GLU N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE N 37 " --> pdb=" O ILE N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 74 Processing helix chain 'N' and resid 109 through 116 Processing helix chain 'N' and resid 118 through 132 Processing helix chain 'N' and resid 142 through 147 removed outlier: 3.787A pdb=" N GLY N 146 " --> pdb=" O GLU N 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 13 removed outlier: 3.908A pdb=" N PHE O 9 " --> pdb=" O ASP O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 17 Processing helix chain 'O' and resid 23 through 38 removed outlier: 4.008A pdb=" N GLU O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE O 37 " --> pdb=" O ILE O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 74 Processing helix chain 'O' and resid 109 through 117 Processing helix chain 'O' and resid 118 through 132 Processing helix chain 'O' and resid 142 through 147 Processing helix chain 'P' and resid 6 through 13 Processing helix chain 'P' and resid 14 through 17 Processing helix chain 'P' and resid 23 through 38 removed outlier: 3.777A pdb=" N GLU P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE P 37 " --> pdb=" O ILE P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 74 Processing helix chain 'P' and resid 109 through 116 Processing helix chain 'P' and resid 118 through 132 Processing helix chain 'P' and resid 142 through 147 Processing helix chain 'Q' and resid 5 through 13 removed outlier: 4.052A pdb=" N PHE Q 9 " --> pdb=" O ASP Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 17 Processing helix chain 'Q' and resid 23 through 38 removed outlier: 3.866A pdb=" N GLU Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 74 Processing helix chain 'Q' and resid 109 through 117 Processing helix chain 'Q' and resid 118 through 132 Processing helix chain 'Q' and resid 142 through 147 Processing helix chain 'R' and resid 6 through 13 Processing helix chain 'R' and resid 14 through 17 Processing helix chain 'R' and resid 23 through 38 removed outlier: 3.526A pdb=" N LEU R 27 " --> pdb=" O PRO R 23 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 74 Processing helix chain 'R' and resid 109 through 116 Processing helix chain 'R' and resid 118 through 132 Processing helix chain 'R' and resid 142 through 147 Processing helix chain 'S' and resid 5 through 13 removed outlier: 3.851A pdb=" N PHE S 9 " --> pdb=" O ASP S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 17 Processing helix chain 'S' and resid 23 through 38 removed outlier: 3.794A pdb=" N GLU S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE S 37 " --> pdb=" O ILE S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 74 removed outlier: 3.655A pdb=" N GLU S 54 " --> pdb=" O GLY S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 117 Processing helix chain 'S' and resid 118 through 132 Processing helix chain 'S' and resid 142 through 147 removed outlier: 3.633A pdb=" N GLY S 146 " --> pdb=" O GLU S 143 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 13 removed outlier: 3.869A pdb=" N PHE T 9 " --> pdb=" O ASP T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 17 Processing helix chain 'T' and resid 23 through 38 removed outlier: 3.975A pdb=" N GLU T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE T 37 " --> pdb=" O ILE T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 74 Processing helix chain 'T' and resid 109 through 116 Processing helix chain 'T' and resid 118 through 132 Processing helix chain 'T' and resid 142 through 147 Processing helix chain 'U' and resid 5 through 13 removed outlier: 4.022A pdb=" N PHE U 9 " --> pdb=" O ASP U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 17 Processing helix chain 'U' and resid 23 through 38 removed outlier: 3.584A pdb=" N LEU U 27 " --> pdb=" O PRO U 23 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE U 37 " --> pdb=" O ILE U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 74 removed outlier: 3.518A pdb=" N GLU U 54 " --> pdb=" O GLY U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 116 Processing helix chain 'U' and resid 118 through 132 Processing helix chain 'U' and resid 142 through 147 Processing helix chain 'V' and resid 5 through 13 removed outlier: 4.061A pdb=" N PHE V 9 " --> pdb=" O ASP V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 17 Processing helix chain 'V' and resid 23 through 38 removed outlier: 3.981A pdb=" N GLU V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE V 37 " --> pdb=" O ILE V 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 74 removed outlier: 3.625A pdb=" N GLU V 54 " --> pdb=" O GLY V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 116 Processing helix chain 'V' and resid 118 through 132 Processing helix chain 'V' and resid 142 through 147 removed outlier: 3.982A pdb=" N GLY V 146 " --> pdb=" O GLU V 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 13 Processing helix chain 'W' and resid 14 through 17 Processing helix chain 'W' and resid 23 through 38 removed outlier: 3.948A pdb=" N GLU W 36 " --> pdb=" O ASP W 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE W 37 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 74 Processing helix chain 'W' and resid 109 through 117 Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 142 through 147 Processing helix chain 'X' and resid 6 through 13 Processing helix chain 'X' and resid 14 through 17 Processing helix chain 'X' and resid 23 through 38 removed outlier: 3.620A pdb=" N LEU X 27 " --> pdb=" O PRO X 23 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU X 36 " --> pdb=" O ASP X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 74 Processing helix chain 'X' and resid 109 through 116 Processing helix chain 'X' and resid 118 through 132 Processing helix chain 'X' and resid 142 through 147 Processing sheet with id=AA1, first strand: chain 'L' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'L' and resid 210 through 216 removed outlier: 3.820A pdb=" N GLY L 212 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE L 183 " --> pdb=" O ILE L 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 222 through 224 Processing sheet with id=AA4, first strand: chain 'L' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'K' and resid 308 through 309 removed outlier: 6.012A pdb=" N LYS L 340 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 216 removed outlier: 3.770A pdb=" N GLY A 212 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 183 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 222 through 224 removed outlier: 3.575A pdb=" N PHE A 243 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB2, first strand: chain 'B' and resid 210 through 216 removed outlier: 3.743A pdb=" N GLY B 212 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 183 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 222 through 224 Processing sheet with id=AB4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AB5, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB6, first strand: chain 'C' and resid 210 through 216 removed outlier: 3.814A pdb=" N GLY C 212 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 183 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 222 through 224 Processing sheet with id=AB8, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AB9, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC1, first strand: chain 'D' and resid 210 through 216 removed outlier: 3.753A pdb=" N GLY D 212 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 183 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 222 through 224 Processing sheet with id=AC3, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AC4, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AC5, first strand: chain 'E' and resid 210 through 216 removed outlier: 3.732A pdb=" N GLY E 212 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 183 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 222 through 224 Processing sheet with id=AC7, first strand: chain 'E' and resid 308 through 309 Processing sheet with id=AC8, first strand: chain 'F' and resid 139 through 141 Processing sheet with id=AC9, first strand: chain 'F' and resid 210 through 216 removed outlier: 3.795A pdb=" N GLY F 212 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 183 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 222 through 224 Processing sheet with id=AD2, first strand: chain 'F' and resid 308 through 309 Processing sheet with id=AD3, first strand: chain 'G' and resid 139 through 141 Processing sheet with id=AD4, first strand: chain 'G' and resid 210 through 216 removed outlier: 3.773A pdb=" N GLY G 212 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 183 " --> pdb=" O ILE G 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 222 through 224 removed outlier: 3.582A pdb=" N PHE G 243 " --> pdb=" O GLN G 224 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 308 through 309 Processing sheet with id=AD7, first strand: chain 'H' and resid 139 through 141 Processing sheet with id=AD8, first strand: chain 'H' and resid 210 through 216 removed outlier: 3.733A pdb=" N GLY H 212 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 183 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 222 through 224 Processing sheet with id=AE1, first strand: chain 'H' and resid 308 through 309 Processing sheet with id=AE2, first strand: chain 'I' and resid 139 through 141 Processing sheet with id=AE3, first strand: chain 'I' and resid 210 through 216 removed outlier: 3.820A pdb=" N GLY I 212 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE I 183 " --> pdb=" O ILE I 216 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AE5, first strand: chain 'I' and resid 308 through 309 Processing sheet with id=AE6, first strand: chain 'J' and resid 139 through 141 Processing sheet with id=AE7, first strand: chain 'J' and resid 210 through 216 removed outlier: 3.770A pdb=" N GLY J 212 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE J 183 " --> pdb=" O ILE J 216 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 222 through 224 Processing sheet with id=AE9, first strand: chain 'J' and resid 308 through 309 Processing sheet with id=AF1, first strand: chain 'K' and resid 139 through 141 Processing sheet with id=AF2, first strand: chain 'K' and resid 210 through 216 removed outlier: 3.732A pdb=" N GLY K 212 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 183 " --> pdb=" O ILE K 216 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AF4, first strand: chain 'M' and resid 90 through 95 removed outlier: 5.405A pdb=" N THR M 91 " --> pdb=" O LYS M 102 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N THR Q 91 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR R 91 " --> pdb=" O LYS R 102 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR S 91 " --> pdb=" O LYS S 102 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR T 91 " --> pdb=" O LYS T 102 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR U 91 " --> pdb=" O LYS U 102 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR V 91 " --> pdb=" O LYS V 102 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THR W 91 " --> pdb=" O LYS W 102 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR X 91 " --> pdb=" O LYS X 102 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR N 91 " --> pdb=" O LYS N 102 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR O 91 " --> pdb=" O LYS O 102 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N THR P 91 " --> pdb=" O LYS P 102 " (cutoff:3.500A) 2900 hydrogen bonds defined for protein. 8226 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: 21.78 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18396 1.34 - 1.46: 12696 1.46 - 1.58: 25560 1.58 - 1.70: 0 1.70 - 1.83: 312 Bond restraints: 56964 Sorted by residual: bond pdb=" N ILE A 283 " pdb=" CA ILE A 283 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N ILE G 283 " pdb=" CA ILE G 283 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N ILE E 283 " pdb=" CA ILE E 283 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N ILE H 283 " pdb=" CA ILE H 283 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.85e+00 bond pdb=" N ILE B 283 " pdb=" CA ILE B 283 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.72e+00 ... (remaining 56959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 75653 2.39 - 4.77: 1391 4.77 - 7.16: 230 7.16 - 9.55: 49 9.55 - 11.94: 5 Bond angle restraints: 77328 Sorted by residual: angle pdb=" N ASP D 440 " pdb=" CA ASP D 440 " pdb=" C ASP D 440 " ideal model delta sigma weight residual 114.04 108.70 5.34 1.24e+00 6.50e-01 1.85e+01 angle pdb=" N ASP A 440 " pdb=" CA ASP A 440 " pdb=" C ASP A 440 " ideal model delta sigma weight residual 114.04 108.71 5.33 1.24e+00 6.50e-01 1.85e+01 angle pdb=" N ASP C 440 " pdb=" CA ASP C 440 " pdb=" C ASP C 440 " ideal model delta sigma weight residual 114.04 108.85 5.19 1.24e+00 6.50e-01 1.75e+01 angle pdb=" CB MET L 498 " pdb=" CG MET L 498 " pdb=" SD MET L 498 " ideal model delta sigma weight residual 112.70 124.64 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA LYS L 424 " pdb=" CB LYS L 424 " pdb=" CG LYS L 424 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.58e+01 ... (remaining 77323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 28701 17.87 - 35.75: 3962 35.75 - 53.62: 901 53.62 - 71.50: 262 71.50 - 89.37: 62 Dihedral angle restraints: 33888 sinusoidal: 13488 harmonic: 20400 Sorted by residual: dihedral pdb=" CD ARG K 486 " pdb=" NE ARG K 486 " pdb=" CZ ARG K 486 " pdb=" NH1 ARG K 486 " ideal model delta sinusoidal sigma weight residual 0.00 -74.38 74.38 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CA ARG I 486 " pdb=" C ARG I 486 " pdb=" N LEU I 487 " pdb=" CA LEU I 487 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ARG C 486 " pdb=" C ARG C 486 " pdb=" N LEU C 487 " pdb=" CA LEU C 487 " ideal model delta harmonic sigma weight residual -180.00 -151.23 -28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 33885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 6488 0.058 - 0.117: 1504 0.117 - 0.175: 244 0.175 - 0.234: 12 0.234 - 0.292: 8 Chirality restraints: 8256 Sorted by residual: chirality pdb=" CB THR K 488 " pdb=" CA THR K 488 " pdb=" OG1 THR K 488 " pdb=" CG2 THR K 488 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB THR E 488 " pdb=" CA THR E 488 " pdb=" OG1 THR E 488 " pdb=" CG2 THR E 488 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU G 141 " pdb=" CB LEU G 141 " pdb=" CD1 LEU G 141 " pdb=" CD2 LEU G 141 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 8253 not shown) Planarity restraints: 10200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 486 " 1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG K 486 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG K 486 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 486 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG K 486 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 148 " 0.794 9.50e-02 1.11e+02 3.56e-01 7.69e+01 pdb=" NE ARG M 148 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG M 148 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG M 148 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 148 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 282 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C ARG B 282 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG B 282 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE B 283 " 0.024 2.00e-02 2.50e+03 ... (remaining 10197 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4825 2.74 - 3.28: 58164 3.28 - 3.82: 96746 3.82 - 4.36: 115124 4.36 - 4.90: 198396 Nonbonded interactions: 473255 Sorted by model distance: nonbonded pdb=" OG SER C 468 " pdb=" OD1 ASP C 470 " model vdw 2.202 3.040 nonbonded pdb=" OG SER C 425 " pdb=" OE2 GLU C 426 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP F 458 " pdb=" OH TYR G 484 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR O 30 " pdb=" OG SER O 68 " model vdw 2.227 3.040 nonbonded pdb=" ND2 ASN B 295 " pdb=" O ARG V 148 " model vdw 2.228 3.120 ... (remaining 473250 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.060 Extract box with map and model: 1.740 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 98.270 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 56964 Z= 0.266 Angle : 0.793 11.936 77328 Z= 0.415 Chirality : 0.050 0.292 8256 Planarity : 0.009 0.474 10200 Dihedral : 17.580 89.372 20808 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.89 % Allowed : 21.15 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 7032 helix: 0.73 (0.09), residues: 3564 sheet: -1.15 (0.23), residues: 540 loop : -1.40 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP T 155 HIS 0.007 0.001 HIS V 63 PHE 0.018 0.002 PHE W 4 TYR 0.024 0.001 TYR R 22 ARG 0.008 0.001 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 995 time to evaluate : 4.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 168 ASN cc_start: 0.7788 (m110) cc_final: 0.7511 (m110) REVERT: L 386 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7930 (mmmt) REVERT: L 424 LYS cc_start: 0.8270 (tptm) cc_final: 0.7839 (tptt) REVERT: B 164 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.8012 (ptp-110) REVERT: C 168 ASN cc_start: 0.7788 (m110) cc_final: 0.7510 (m110) REVERT: C 320 GLU cc_start: 0.8211 (tt0) cc_final: 0.7858 (tm-30) REVERT: C 386 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7907 (mmmt) REVERT: C 498 MET cc_start: 0.8040 (mmp) cc_final: 0.7794 (mmt) REVERT: D 317 ILE cc_start: 0.9329 (mt) cc_final: 0.9094 (mt) REVERT: E 164 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7991 (ptp-110) REVERT: F 168 ASN cc_start: 0.7786 (m110) cc_final: 0.7502 (m110) REVERT: F 498 MET cc_start: 0.7952 (mmm) cc_final: 0.7559 (mmt) REVERT: I 168 ASN cc_start: 0.7753 (m110) cc_final: 0.7483 (m110) REVERT: I 386 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7956 (mmmt) REVERT: I 424 LYS cc_start: 0.8269 (tptm) cc_final: 0.7836 (tptt) REVERT: I 486 ARG cc_start: 0.7203 (ttt90) cc_final: 0.6757 (ttt90) REVERT: I 498 MET cc_start: 0.7770 (mmm) cc_final: 0.7359 (mmt) REVERT: K 486 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7489 (ptm160) REVERT: M 36 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7827 (mm-30) REVERT: N 145 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8231 (ttt90) REVERT: R 22 TYR cc_start: 0.8839 (m-80) cc_final: 0.8529 (m-80) REVERT: T 5 ASP cc_start: 0.8626 (p0) cc_final: 0.8422 (p0) REVERT: U 143 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8203 (mm-30) REVERT: V 6 GLU cc_start: 0.8237 (pt0) cc_final: 0.7898 (mt-10) REVERT: W 36 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7633 (mm-30) REVERT: X 143 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8445 (mm-30) outliers start: 52 outliers final: 20 residues processed: 1018 average time/residue: 0.5472 time to fit residues: 927.0221 Evaluate side-chains 878 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 857 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 486 ARG Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 129 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 587 optimal weight: 0.7980 chunk 527 optimal weight: 2.9990 chunk 292 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 545 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 406 optimal weight: 0.6980 chunk 632 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 407 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 GLN F 281 GLN F 367 GLN F 407 GLN ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 367 GLN ** H 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 281 GLN I 407 GLN J 367 GLN M 122 GLN N 71 GLN N 109 ASN N 112 GLN P 122 GLN Q 109 ASN ** V 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098579 restraints weight = 97945.919| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.38 r_work: 0.3116 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56964 Z= 0.226 Angle : 0.598 8.771 77328 Z= 0.303 Chirality : 0.044 0.276 8256 Planarity : 0.006 0.069 10200 Dihedral : 4.897 57.725 7711 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.60 % Allowed : 20.16 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.10), residues: 7032 helix: 1.01 (0.09), residues: 3612 sheet: -1.10 (0.24), residues: 540 loop : -1.26 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 155 HIS 0.004 0.001 HIS B 394 PHE 0.019 0.001 PHE S 4 TYR 0.015 0.001 TYR Q 30 ARG 0.005 0.001 ARG L 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 940 time to evaluate : 4.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 164 ARG cc_start: 0.8637 (ptp-110) cc_final: 0.8366 (mtm110) REVERT: L 386 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8109 (mmmt) REVERT: L 424 LYS cc_start: 0.8365 (tptm) cc_final: 0.7904 (tptt) REVERT: A 424 LYS cc_start: 0.8783 (tptt) cc_final: 0.8567 (tptt) REVERT: A 488 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7566 (p) REVERT: B 106 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: B 498 MET cc_start: 0.7537 (tpp) cc_final: 0.6689 (mmm) REVERT: C 168 ASN cc_start: 0.8143 (m110) cc_final: 0.7627 (m110) REVERT: C 320 GLU cc_start: 0.8597 (tt0) cc_final: 0.8392 (tt0) REVERT: C 386 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8082 (mmmt) REVERT: D 317 ILE cc_start: 0.9376 (mt) cc_final: 0.9165 (mt) REVERT: D 488 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7399 (p) REVERT: E 106 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: F 168 ASN cc_start: 0.8168 (m110) cc_final: 0.7644 (m110) REVERT: F 320 GLU cc_start: 0.8549 (tp30) cc_final: 0.8034 (tp30) REVERT: F 498 MET cc_start: 0.7858 (mmm) cc_final: 0.7562 (mmt) REVERT: G 320 GLU cc_start: 0.8607 (tp30) cc_final: 0.8322 (tp30) REVERT: G 324 ASN cc_start: 0.8871 (m-40) cc_final: 0.8610 (m110) REVERT: H 300 LEU cc_start: 0.9099 (tp) cc_final: 0.8805 (tp) REVERT: H 515 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7293 (mtpt) REVERT: I 164 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8180 (mtm110) REVERT: I 168 ASN cc_start: 0.8161 (m110) cc_final: 0.7642 (m110) REVERT: I 335 ASP cc_start: 0.8231 (t0) cc_final: 0.8017 (t70) REVERT: I 386 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8120 (mmmt) REVERT: I 424 LYS cc_start: 0.8384 (tptm) cc_final: 0.7930 (tptt) REVERT: K 106 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: N 148 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7258 (ptt-90) REVERT: O 5 ASP cc_start: 0.8570 (p0) cc_final: 0.8351 (p0) REVERT: O 15 GLU cc_start: 0.9233 (pm20) cc_final: 0.8917 (pm20) REVERT: R 18 ASP cc_start: 0.8849 (t70) cc_final: 0.8642 (t70) REVERT: S 36 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8136 (mm-30) REVERT: T 5 ASP cc_start: 0.8841 (p0) cc_final: 0.8582 (p0) REVERT: T 36 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8371 (mm-30) REVERT: U 15 GLU cc_start: 0.9242 (pm20) cc_final: 0.8965 (pm20) REVERT: X 143 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8558 (mm-30) outliers start: 152 outliers final: 96 residues processed: 1050 average time/residue: 0.5619 time to fit residues: 979.2154 Evaluate side-chains 959 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 856 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 363 MET Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 71 GLN Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 136 PHE Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 99 SER Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain X residue 69 THR Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 133 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 195 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 636 optimal weight: 0.4980 chunk 564 optimal weight: 0.8980 chunk 640 optimal weight: 2.9990 chunk 517 optimal weight: 0.0980 chunk 191 optimal weight: 0.7980 chunk 344 optimal weight: 4.9990 chunk 451 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 407 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN E 407 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 407 GLN I 407 GLN J 324 ASN K 407 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 ASN U 122 GLN V 71 GLN ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096871 restraints weight = 98213.426| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.44 r_work: 0.3133 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56964 Z= 0.175 Angle : 0.562 12.043 77328 Z= 0.280 Chirality : 0.042 0.210 8256 Planarity : 0.005 0.061 10200 Dihedral : 4.608 57.049 7696 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.94 % Allowed : 20.59 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 7032 helix: 1.29 (0.09), residues: 3552 sheet: -1.07 (0.24), residues: 540 loop : -1.18 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 155 HIS 0.003 0.001 HIS X 63 PHE 0.015 0.001 PHE S 4 TYR 0.014 0.001 TYR F 284 ARG 0.005 0.000 ARG J 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 950 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 164 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.8357 (mtm110) REVERT: L 335 ASP cc_start: 0.8232 (t0) cc_final: 0.7994 (t0) REVERT: L 386 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8160 (tttm) REVERT: L 424 LYS cc_start: 0.8442 (tptm) cc_final: 0.7912 (tptm) REVERT: L 498 MET cc_start: 0.8051 (mmm) cc_final: 0.7558 (mmt) REVERT: A 302 MET cc_start: 0.9400 (mmp) cc_final: 0.9183 (mmp) REVERT: A 424 LYS cc_start: 0.8848 (tptt) cc_final: 0.8584 (tptt) REVERT: A 499 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8972 (p) REVERT: B 106 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: B 211 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7979 (mmtm) REVERT: B 268 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9026 (pp) REVERT: B 283 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 417 ARG cc_start: 0.8359 (ttm170) cc_final: 0.8128 (tpp80) REVERT: C 164 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.8105 (ptm-80) REVERT: C 386 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8194 (tttm) REVERT: C 432 LEU cc_start: 0.8970 (mt) cc_final: 0.8766 (mp) REVERT: D 424 LYS cc_start: 0.8753 (tptt) cc_final: 0.8540 (tptt) REVERT: D 488 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7286 (p) REVERT: D 499 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8909 (p) REVERT: E 106 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: E 268 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9028 (pp) REVERT: E 283 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8868 (mt) REVERT: E 417 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8163 (tpp80) REVERT: E 515 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7486 (mtpt) REVERT: F 106 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.6946 (mt0) REVERT: F 164 ARG cc_start: 0.8684 (ptp-110) cc_final: 0.8392 (mtm110) REVERT: F 320 GLU cc_start: 0.8494 (tp30) cc_final: 0.8086 (tp30) REVERT: F 498 MET cc_start: 0.7743 (mmm) cc_final: 0.7540 (mmt) REVERT: F 515 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7940 (mtpt) REVERT: G 320 GLU cc_start: 0.8445 (tp30) cc_final: 0.8170 (tp30) REVERT: G 324 ASN cc_start: 0.8880 (m-40) cc_final: 0.8536 (m110) REVERT: G 424 LYS cc_start: 0.8757 (tptt) cc_final: 0.8525 (tptt) REVERT: H 268 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9032 (pp) REVERT: H 300 LEU cc_start: 0.9070 (tp) cc_final: 0.8768 (tp) REVERT: H 515 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7151 (mtpt) REVERT: I 164 ARG cc_start: 0.8627 (ptp-110) cc_final: 0.8345 (mtm110) REVERT: I 386 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8156 (tttm) REVERT: I 424 LYS cc_start: 0.8453 (tptm) cc_final: 0.7940 (tptm) REVERT: I 486 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6692 (ttt90) REVERT: J 488 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7546 (p) REVERT: J 498 MET cc_start: 0.7765 (mmm) cc_final: 0.7328 (mmm) REVERT: J 499 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8933 (p) REVERT: K 106 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: K 211 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7996 (mmtm) REVERT: K 268 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9024 (pp) REVERT: K 300 LEU cc_start: 0.9066 (tp) cc_final: 0.8789 (tp) REVERT: M 15 GLU cc_start: 0.9236 (pm20) cc_final: 0.8995 (pm20) REVERT: N 7 HIS cc_start: 0.8201 (t70) cc_final: 0.7965 (t70) REVERT: N 15 GLU cc_start: 0.9155 (pm20) cc_final: 0.8858 (pm20) REVERT: N 145 ARG cc_start: 0.8713 (mmm160) cc_final: 0.8364 (mtm180) REVERT: N 148 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7038 (ptt-90) REVERT: O 5 ASP cc_start: 0.8650 (p0) cc_final: 0.8390 (p0) REVERT: O 15 GLU cc_start: 0.9242 (pm20) cc_final: 0.8914 (pm20) REVERT: R 18 ASP cc_start: 0.8908 (t70) cc_final: 0.8648 (t70) REVERT: R 22 TYR cc_start: 0.9040 (m-80) cc_final: 0.8485 (m-80) REVERT: T 5 ASP cc_start: 0.8850 (p0) cc_final: 0.8560 (p0) REVERT: V 5 ASP cc_start: 0.8519 (p0) cc_final: 0.8279 (p0) REVERT: V 36 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8189 (mm-30) REVERT: X 120 TYR cc_start: 0.8853 (m-80) cc_final: 0.8378 (m-80) outliers start: 172 outliers final: 97 residues processed: 1078 average time/residue: 0.5631 time to fit residues: 999.6003 Evaluate side-chains 951 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 834 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 363 MET Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 488 THR Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 136 PHE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 136 PHE Chi-restraints excluded: chain V residue 71 GLN Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 85 THR Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 133 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 678 optimal weight: 2.9990 chunk 458 optimal weight: 4.9990 chunk 507 optimal weight: 4.9990 chunk 579 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 317 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 167 optimal weight: 0.0030 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN A 173 ASN A 281 GLN A 324 ASN A 407 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN D 407 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN G 407 GLN H 281 GLN H 446 GLN I 407 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 ASN ** O 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091869 restraints weight = 98920.363| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.44 r_work: 0.3050 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 56964 Z= 0.314 Angle : 0.606 14.022 77328 Z= 0.304 Chirality : 0.045 0.188 8256 Planarity : 0.005 0.059 10200 Dihedral : 4.601 58.055 7690 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.70 % Allowed : 20.72 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.10), residues: 7032 helix: 1.13 (0.09), residues: 3672 sheet: -1.02 (0.25), residues: 540 loop : -1.17 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 155 HIS 0.005 0.001 HIS S 63 PHE 0.013 0.001 PHE S 4 TYR 0.014 0.001 TYR I 284 ARG 0.005 0.001 ARG G 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 889 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: L 164 ARG cc_start: 0.8685 (ptp-110) cc_final: 0.8378 (mtm110) REVERT: L 268 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8956 (pp) REVERT: L 386 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8268 (tttm) REVERT: L 424 LYS cc_start: 0.8538 (tptm) cc_final: 0.7851 (tptt) REVERT: L 498 MET cc_start: 0.8106 (mmm) cc_final: 0.7654 (mmt) REVERT: A 424 LYS cc_start: 0.8911 (tptt) cc_final: 0.8585 (tptt) REVERT: B 106 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 285 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: B 498 MET cc_start: 0.7629 (tpp) cc_final: 0.7192 (mmm) REVERT: C 106 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: C 164 ARG cc_start: 0.8654 (ptp-110) cc_final: 0.8341 (mtm110) REVERT: C 268 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8948 (pp) REVERT: C 386 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8266 (tttm) REVERT: C 424 LYS cc_start: 0.8855 (tmtt) cc_final: 0.8520 (tptt) REVERT: C 515 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8104 (mtpt) REVERT: D 424 LYS cc_start: 0.8879 (tptt) cc_final: 0.8653 (tptt) REVERT: D 499 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8802 (p) REVERT: E 106 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8433 (mt0) REVERT: F 106 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: F 164 ARG cc_start: 0.8725 (ptp-110) cc_final: 0.8414 (mtm110) REVERT: F 268 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8957 (pp) REVERT: F 320 GLU cc_start: 0.8570 (tp30) cc_final: 0.8245 (tp30) REVERT: F 498 MET cc_start: 0.7864 (mmm) cc_final: 0.7636 (mmt) REVERT: F 515 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7931 (mtpt) REVERT: G 106 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: G 320 GLU cc_start: 0.8543 (tp30) cc_final: 0.8277 (tp30) REVERT: G 324 ASN cc_start: 0.8905 (m-40) cc_final: 0.8543 (m110) REVERT: G 424 LYS cc_start: 0.8859 (tptt) cc_final: 0.8620 (tptt) REVERT: G 499 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8888 (p) REVERT: H 515 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7277 (mtpt) REVERT: I 164 ARG cc_start: 0.8689 (ptp-110) cc_final: 0.8379 (mtm110) REVERT: I 268 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8949 (pp) REVERT: I 386 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8351 (mtpt) REVERT: I 424 LYS cc_start: 0.8566 (tptm) cc_final: 0.7896 (tptt) REVERT: I 486 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7119 (ttt90) REVERT: J 106 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: J 320 GLU cc_start: 0.8417 (tt0) cc_final: 0.7943 (tt0) REVERT: J 424 LYS cc_start: 0.8874 (tptt) cc_final: 0.8649 (tptt) REVERT: J 433 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: K 106 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: K 215 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: K 285 GLU cc_start: 0.7895 (mp0) cc_final: 0.7685 (mp0) REVERT: M 26 ARG cc_start: 0.8995 (ttm-80) cc_final: 0.8761 (ttm-80) REVERT: M 143 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8741 (mm-30) REVERT: N 7 HIS cc_start: 0.8242 (t70) cc_final: 0.7991 (t70) REVERT: N 8 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8576 (tttm) REVERT: N 51 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7181 (pttp) REVERT: N 143 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8512 (tp30) REVERT: N 148 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7067 (ptt-90) REVERT: O 5 ASP cc_start: 0.8754 (p0) cc_final: 0.8538 (p0) REVERT: O 36 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8130 (mm-30) REVERT: P 22 TYR cc_start: 0.9222 (m-80) cc_final: 0.8967 (m-80) REVERT: Q 5 ASP cc_start: 0.8928 (p0) cc_final: 0.8726 (p0) REVERT: R 18 ASP cc_start: 0.8896 (t70) cc_final: 0.8629 (t70) REVERT: R 22 TYR cc_start: 0.9128 (m-80) cc_final: 0.8624 (m-80) REVERT: T 51 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7448 (mttp) REVERT: U 123 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: V 5 ASP cc_start: 0.8685 (p0) cc_final: 0.8458 (p0) outliers start: 216 outliers final: 136 residues processed: 1040 average time/residue: 0.5539 time to fit residues: 954.2144 Evaluate side-chains 992 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 830 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 320 GLU Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 499 SER Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 484 TYR Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 484 TYR Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 432 LEU Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 215 GLN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 488 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain U residue 123 GLU Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 71 GLN Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 99 SER Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 38 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 399 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 534 optimal weight: 0.7980 chunk 545 optimal weight: 0.6980 chunk 647 optimal weight: 0.6980 chunk 625 optimal weight: 1.9990 chunk 516 optimal weight: 1.9990 chunk 471 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 ASN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN K 215 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094445 restraints weight = 98034.709| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.43 r_work: 0.3092 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 56964 Z= 0.196 Angle : 0.563 11.676 77328 Z= 0.281 Chirality : 0.043 0.227 8256 Planarity : 0.005 0.056 10200 Dihedral : 4.469 59.772 7686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.49 % Allowed : 21.65 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.10), residues: 7032 helix: 1.24 (0.09), residues: 3672 sheet: -1.00 (0.25), residues: 540 loop : -1.16 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 155 HIS 0.003 0.001 HIS F 337 PHE 0.011 0.001 PHE S 4 TYR 0.013 0.001 TYR I 284 ARG 0.004 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 900 time to evaluate : 4.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: L 164 ARG cc_start: 0.8643 (ptp-110) cc_final: 0.8331 (mtm110) REVERT: L 268 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8935 (pp) REVERT: L 386 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8343 (tttm) REVERT: L 424 LYS cc_start: 0.8571 (tptm) cc_final: 0.8029 (tptt) REVERT: L 498 MET cc_start: 0.7984 (mmm) cc_final: 0.7588 (mmt) REVERT: L 515 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7888 (mtpt) REVERT: A 106 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: A 142 LYS cc_start: 0.8535 (tptm) cc_final: 0.8333 (tptm) REVERT: A 424 LYS cc_start: 0.8925 (tptt) cc_final: 0.8604 (tptt) REVERT: A 499 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8997 (p) REVERT: B 106 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: B 515 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7530 (mtpt) REVERT: C 106 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: C 164 ARG cc_start: 0.8640 (ptp-110) cc_final: 0.8323 (mtm110) REVERT: C 268 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8922 (pp) REVERT: C 386 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8335 (tttm) REVERT: C 424 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8497 (tptt) REVERT: D 404 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 424 LYS cc_start: 0.8837 (tptt) cc_final: 0.8574 (tptt) REVERT: D 499 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8747 (p) REVERT: E 106 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: E 515 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7534 (mtpt) REVERT: F 106 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: F 164 ARG cc_start: 0.8655 (ptp-110) cc_final: 0.8340 (mtm110) REVERT: F 268 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8933 (pp) REVERT: F 320 GLU cc_start: 0.8597 (tp30) cc_final: 0.8231 (tp30) REVERT: F 515 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: G 106 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: G 320 GLU cc_start: 0.8418 (tp30) cc_final: 0.8093 (tp30) REVERT: G 324 ASN cc_start: 0.8866 (m-40) cc_final: 0.8419 (m110) REVERT: G 424 LYS cc_start: 0.8908 (tptt) cc_final: 0.8569 (tptt) REVERT: G 499 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8991 (p) REVERT: H 515 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7229 (mtpt) REVERT: I 106 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: I 164 ARG cc_start: 0.8641 (ptp-110) cc_final: 0.8328 (mtm110) REVERT: I 268 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8925 (pp) REVERT: I 335 ASP cc_start: 0.8298 (t0) cc_final: 0.8091 (t0) REVERT: I 386 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8357 (tttm) REVERT: I 424 LYS cc_start: 0.8663 (tptm) cc_final: 0.8050 (tptt) REVERT: I 486 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7098 (ttt90) REVERT: J 106 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: J 424 LYS cc_start: 0.8834 (tptt) cc_final: 0.8572 (tptt) REVERT: J 499 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.9030 (p) REVERT: K 106 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: K 515 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7434 (mtpt) REVERT: M 143 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8629 (mm-30) REVERT: N 8 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8600 (tttm) REVERT: N 15 GLU cc_start: 0.9121 (pm20) cc_final: 0.8886 (pm20) REVERT: N 51 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7321 (pttp) REVERT: N 148 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7037 (ptt-90) REVERT: O 5 ASP cc_start: 0.8857 (p0) cc_final: 0.8486 (p0) REVERT: O 36 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8052 (mm-30) REVERT: P 22 TYR cc_start: 0.9216 (m-80) cc_final: 0.8946 (m-80) REVERT: R 15 GLU cc_start: 0.9150 (pm20) cc_final: 0.8871 (pm20) REVERT: R 18 ASP cc_start: 0.8912 (t70) cc_final: 0.8664 (t70) REVERT: R 22 TYR cc_start: 0.9140 (m-80) cc_final: 0.8895 (m-80) REVERT: S 5 ASP cc_start: 0.8671 (p0) cc_final: 0.8428 (p0) REVERT: T 5 ASP cc_start: 0.8651 (p0) cc_final: 0.8416 (p0) REVERT: T 70 MET cc_start: 0.8457 (ttm) cc_final: 0.8204 (ttm) REVERT: V 15 GLU cc_start: 0.9154 (pm20) cc_final: 0.8921 (pm20) REVERT: V 36 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7925 (mm-30) REVERT: V 133 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8650 (p) outliers start: 204 outliers final: 118 residues processed: 1057 average time/residue: 0.5710 time to fit residues: 999.1142 Evaluate side-chains 983 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 837 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 320 GLU Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 515 LYS Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 106 GLN Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 434 ILE Chi-restraints excluded: chain K residue 488 THR Chi-restraints excluded: chain K residue 515 LYS Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 136 PHE Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 133 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 139 optimal weight: 0.0270 chunk 544 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 562 optimal weight: 0.9980 chunk 424 optimal weight: 0.6980 chunk 376 optimal weight: 2.9990 chunk 456 optimal weight: 0.0980 chunk 201 optimal weight: 4.9990 chunk 277 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 502 ASN C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN ** E 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 GLN ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096349 restraints weight = 97884.005| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.45 r_work: 0.3126 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 56964 Z= 0.160 Angle : 0.545 10.524 77328 Z= 0.271 Chirality : 0.042 0.219 8256 Planarity : 0.005 0.052 10200 Dihedral : 4.338 58.879 7686 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.38 % Favored : 94.61 % Rotamer: Outliers : 3.44 % Allowed : 22.06 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7032 helix: 1.46 (0.09), residues: 3576 sheet: -1.01 (0.25), residues: 540 loop : -1.09 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 155 HIS 0.004 0.001 HIS F 337 PHE 0.010 0.001 PHE M 37 TYR 0.013 0.001 TYR F 284 ARG 0.005 0.000 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 927 time to evaluate : 5.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: L 164 ARG cc_start: 0.8640 (ptp-110) cc_final: 0.8325 (mtm110) REVERT: L 268 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8831 (pp) REVERT: L 381 LEU cc_start: 0.8889 (tp) cc_final: 0.8645 (tp) REVERT: L 386 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8458 (mtpt) REVERT: L 424 LYS cc_start: 0.8660 (tptm) cc_final: 0.8043 (tptt) REVERT: L 498 MET cc_start: 0.7890 (mmm) cc_final: 0.7558 (mmt) REVERT: L 515 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7928 (mtpt) REVERT: A 106 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: A 424 LYS cc_start: 0.8933 (tptt) cc_final: 0.8552 (tptt) REVERT: A 453 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8573 (mmmt) REVERT: A 499 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 498 MET cc_start: 0.7582 (tpp) cc_final: 0.6777 (mmm) REVERT: B 515 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7506 (mtpt) REVERT: C 164 ARG cc_start: 0.8631 (ptp-110) cc_final: 0.8062 (mtm110) REVERT: C 168 ASN cc_start: 0.8169 (m110) cc_final: 0.7556 (m110) REVERT: C 268 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8822 (pp) REVERT: C 381 LEU cc_start: 0.8918 (tp) cc_final: 0.8664 (tp) REVERT: C 386 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8459 (mtpt) REVERT: C 424 LYS cc_start: 0.8827 (tmtt) cc_final: 0.8436 (tptt) REVERT: C 515 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: D 140 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: D 404 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 424 LYS cc_start: 0.8893 (tptt) cc_final: 0.8564 (tptt) REVERT: D 453 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8548 (mmmt) REVERT: D 499 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8713 (p) REVERT: E 106 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: E 515 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7534 (mtpt) REVERT: F 106 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: F 164 ARG cc_start: 0.8642 (ptp-110) cc_final: 0.8059 (mtm110) REVERT: F 168 ASN cc_start: 0.8188 (m110) cc_final: 0.7557 (m110) REVERT: F 268 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8829 (pp) REVERT: F 515 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7917 (mtpt) REVERT: G 106 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.6790 (mp10) REVERT: G 222 MET cc_start: 0.7564 (mtt) cc_final: 0.6902 (ttm) REVERT: G 320 GLU cc_start: 0.8395 (tp30) cc_final: 0.7956 (tp30) REVERT: G 324 ASN cc_start: 0.8825 (m-40) cc_final: 0.8325 (m110) REVERT: G 424 LYS cc_start: 0.8887 (tptt) cc_final: 0.8552 (tptt) REVERT: G 499 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8964 (p) REVERT: H 515 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7215 (mtpt) REVERT: I 106 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: I 164 ARG cc_start: 0.8625 (ptp-110) cc_final: 0.8315 (mtm110) REVERT: I 268 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8817 (pp) REVERT: I 381 LEU cc_start: 0.8930 (tp) cc_final: 0.8689 (tp) REVERT: I 386 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8491 (mtpt) REVERT: I 424 LYS cc_start: 0.8628 (tptm) cc_final: 0.8125 (tptt) REVERT: I 486 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7005 (ttt90) REVERT: J 106 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: J 424 LYS cc_start: 0.8844 (tptt) cc_final: 0.8568 (tptt) REVERT: J 453 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8602 (mmmt) REVERT: J 499 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8996 (p) REVERT: K 515 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7423 (mtpt) REVERT: M 143 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8591 (mm-30) REVERT: N 8 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8673 (tttm) REVERT: N 51 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7267 (pttp) REVERT: N 143 GLU cc_start: 0.8926 (tp30) cc_final: 0.8430 (tp30) REVERT: N 148 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6661 (ptt-90) REVERT: O 5 ASP cc_start: 0.8860 (p0) cc_final: 0.8458 (p0) REVERT: Q 70 MET cc_start: 0.8353 (ttm) cc_final: 0.8101 (ttm) REVERT: R 6 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7600 (mm-30) REVERT: R 15 GLU cc_start: 0.9178 (pm20) cc_final: 0.8970 (pm20) REVERT: R 18 ASP cc_start: 0.8970 (t70) cc_final: 0.8739 (t70) REVERT: S 5 ASP cc_start: 0.8721 (p0) cc_final: 0.8440 (p0) REVERT: T 5 ASP cc_start: 0.8641 (p0) cc_final: 0.8329 (p0) REVERT: V 5 ASP cc_start: 0.8452 (p0) cc_final: 0.8210 (p0) REVERT: V 36 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7864 (mm-30) REVERT: V 133 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8774 (p) outliers start: 201 outliers final: 121 residues processed: 1085 average time/residue: 0.5725 time to fit residues: 1024.9864 Evaluate side-chains 997 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 846 time to evaluate : 4.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 515 LYS Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 106 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 453 LYS Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 453 LYS Chi-restraints excluded: chain K residue 488 THR Chi-restraints excluded: chain K residue 515 LYS Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 136 PHE Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain R residue 102 LYS Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 71 GLN Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 133 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 586 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 527 optimal weight: 0.5980 chunk 628 optimal weight: 9.9990 chunk 402 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 278 optimal weight: 0.4980 chunk 306 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 608 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 324 ASN A 407 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN F 407 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 ASN ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN I 173 ASN I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 ASN J 407 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 GLN ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 GLN ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 122 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095723 restraints weight = 97862.152| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.44 r_work: 0.3113 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56964 Z= 0.183 Angle : 0.547 10.492 77328 Z= 0.272 Chirality : 0.043 0.211 8256 Planarity : 0.005 0.049 10200 Dihedral : 4.298 57.784 7686 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 3.68 % Allowed : 22.07 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7032 helix: 1.51 (0.09), residues: 3576 sheet: -0.98 (0.25), residues: 540 loop : -1.06 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 155 HIS 0.003 0.001 HIS F 337 PHE 0.014 0.001 PHE B 238 TYR 0.014 0.001 TYR H 284 ARG 0.006 0.000 ARG C 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 900 time to evaluate : 4.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: L 164 ARG cc_start: 0.8651 (ptp-110) cc_final: 0.8316 (mtm110) REVERT: L 268 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8868 (pp) REVERT: L 349 GLU cc_start: 0.8623 (pt0) cc_final: 0.7736 (pt0) REVERT: L 381 LEU cc_start: 0.8897 (tp) cc_final: 0.8672 (tp) REVERT: L 386 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8537 (mtpt) REVERT: L 424 LYS cc_start: 0.8653 (tptm) cc_final: 0.8102 (tptt) REVERT: L 498 MET cc_start: 0.7894 (mmm) cc_final: 0.7558 (mmt) REVERT: L 515 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7936 (mtpt) REVERT: A 106 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: A 222 MET cc_start: 0.7505 (mtt) cc_final: 0.6888 (ttm) REVERT: A 424 LYS cc_start: 0.8937 (tptt) cc_final: 0.8548 (tptt) REVERT: A 453 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8595 (mmmt) REVERT: A 499 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 515 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7515 (mtpt) REVERT: C 106 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: C 164 ARG cc_start: 0.8641 (ptp-110) cc_final: 0.8077 (mtm110) REVERT: C 168 ASN cc_start: 0.8091 (m110) cc_final: 0.7451 (m110) REVERT: C 268 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8855 (pp) REVERT: C 349 GLU cc_start: 0.8708 (pt0) cc_final: 0.8486 (pt0) REVERT: C 381 LEU cc_start: 0.8933 (tp) cc_final: 0.8687 (tp) REVERT: C 386 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8506 (mtpt) REVERT: C 424 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8468 (tptt) REVERT: C 515 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: D 106 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: D 140 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: D 222 MET cc_start: 0.7580 (mtt) cc_final: 0.6937 (ttm) REVERT: D 302 MET cc_start: 0.9458 (mmp) cc_final: 0.9234 (mmp) REVERT: D 404 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 424 LYS cc_start: 0.8895 (tptt) cc_final: 0.8554 (tptt) REVERT: D 499 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (p) REVERT: E 106 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: E 386 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8012 (tttm) REVERT: E 515 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7525 (mtpt) REVERT: F 164 ARG cc_start: 0.8660 (ptp-110) cc_final: 0.8057 (mtm110) REVERT: F 168 ASN cc_start: 0.8198 (m110) cc_final: 0.7576 (m110) REVERT: F 268 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8879 (pp) REVERT: F 515 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7900 (mtpt) REVERT: G 106 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: G 222 MET cc_start: 0.7534 (mtt) cc_final: 0.6876 (ttm) REVERT: G 424 LYS cc_start: 0.8894 (tptt) cc_final: 0.8555 (tptt) REVERT: G 453 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8578 (mmmt) REVERT: G 499 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8821 (p) REVERT: H 515 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7227 (mtpt) REVERT: I 164 ARG cc_start: 0.8641 (ptp-110) cc_final: 0.8078 (mtm110) REVERT: I 168 ASN cc_start: 0.8202 (m110) cc_final: 0.7654 (m110) REVERT: I 268 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8858 (pp) REVERT: I 335 ASP cc_start: 0.8170 (t0) cc_final: 0.7788 (t0) REVERT: I 349 GLU cc_start: 0.8690 (pt0) cc_final: 0.8485 (pt0) REVERT: I 381 LEU cc_start: 0.8941 (tp) cc_final: 0.8703 (tp) REVERT: I 386 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8562 (mtpt) REVERT: I 424 LYS cc_start: 0.8658 (tptm) cc_final: 0.8108 (tptt) REVERT: I 486 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7091 (ttt90) REVERT: J 106 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: J 424 LYS cc_start: 0.8903 (tptt) cc_final: 0.8575 (tptt) REVERT: J 453 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8586 (mmmt) REVERT: J 499 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8993 (p) REVERT: K 215 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: K 515 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7429 (mtpt) REVERT: M 71 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: M 143 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8493 (mm-30) REVERT: N 8 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8735 (tttm) REVERT: N 51 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7191 (pttp) REVERT: N 148 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6701 (ptt-90) REVERT: O 5 ASP cc_start: 0.8954 (p0) cc_final: 0.8588 (p0) REVERT: P 22 TYR cc_start: 0.9179 (m-80) cc_final: 0.8970 (m-80) REVERT: Q 5 ASP cc_start: 0.8552 (p0) cc_final: 0.8312 (p0) REVERT: Q 70 MET cc_start: 0.8447 (ttm) cc_final: 0.8210 (ttm) REVERT: R 15 GLU cc_start: 0.9196 (pm20) cc_final: 0.8953 (pm20) REVERT: R 18 ASP cc_start: 0.8945 (t70) cc_final: 0.8738 (t70) REVERT: S 5 ASP cc_start: 0.8779 (p0) cc_final: 0.8471 (p0) REVERT: T 5 ASP cc_start: 0.8635 (p0) cc_final: 0.8434 (p0) REVERT: U 5 ASP cc_start: 0.8525 (p0) cc_final: 0.8313 (p0) REVERT: V 5 ASP cc_start: 0.8425 (p0) cc_final: 0.8136 (p0) REVERT: V 36 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7872 (mm-30) REVERT: V 143 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8595 (mm-30) outliers start: 215 outliers final: 134 residues processed: 1066 average time/residue: 0.5682 time to fit residues: 997.3668 Evaluate side-chains 1013 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 847 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 320 GLU Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 515 LYS Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 453 LYS Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 106 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 453 LYS Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 215 GLN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 453 LYS Chi-restraints excluded: chain K residue 515 LYS Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 136 PHE Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 136 PHE Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 71 GLN Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 71 GLN Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 120 TYR Chi-restraints excluded: chain X residue 133 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 293 optimal weight: 5.9990 chunk 612 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 494 optimal weight: 1.9990 chunk 513 optimal weight: 2.9990 chunk 570 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 673 optimal weight: 0.0010 chunk 310 optimal weight: 3.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN E 295 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 407 GLN ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 ASN I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 GLN T 109 ASN ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093922 restraints weight = 98421.712| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.43 r_work: 0.3083 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 56964 Z= 0.243 Angle : 0.576 15.643 77328 Z= 0.285 Chirality : 0.044 0.219 8256 Planarity : 0.005 0.048 10200 Dihedral : 4.337 57.771 7684 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.75 % Favored : 94.24 % Rotamer: Outliers : 3.61 % Allowed : 22.38 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7032 helix: 1.44 (0.09), residues: 3612 sheet: -1.00 (0.25), residues: 540 loop : -1.09 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 155 HIS 0.004 0.001 HIS Q 63 PHE 0.010 0.001 PHE F 238 TYR 0.015 0.001 TYR H 284 ARG 0.005 0.000 ARG C 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 875 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: L 164 ARG cc_start: 0.8631 (ptp-110) cc_final: 0.8059 (ptt90) REVERT: L 268 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8955 (pp) REVERT: L 349 GLU cc_start: 0.8629 (pt0) cc_final: 0.7761 (pt0) REVERT: L 386 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8551 (mtpt) REVERT: L 424 LYS cc_start: 0.8673 (tptm) cc_final: 0.8049 (tptt) REVERT: L 498 MET cc_start: 0.7939 (mmm) cc_final: 0.7622 (mmt) REVERT: L 515 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7990 (mtpt) REVERT: A 106 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: A 386 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8100 (mtpp) REVERT: A 424 LYS cc_start: 0.8967 (tptt) cc_final: 0.8580 (tptt) REVERT: A 499 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 515 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7531 (mtpt) REVERT: C 106 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: C 164 ARG cc_start: 0.8658 (ptp-110) cc_final: 0.8090 (mtm110) REVERT: C 168 ASN cc_start: 0.8226 (m110) cc_final: 0.7610 (m110) REVERT: C 268 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8947 (pp) REVERT: C 349 GLU cc_start: 0.8689 (pt0) cc_final: 0.8471 (pt0) REVERT: C 381 LEU cc_start: 0.8928 (tp) cc_final: 0.8674 (tp) REVERT: C 386 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8543 (mtpt) REVERT: C 424 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8523 (tptt) REVERT: C 515 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8042 (mtpt) REVERT: D 106 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: D 140 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: D 302 MET cc_start: 0.9454 (mmp) cc_final: 0.9253 (mmp) REVERT: D 404 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7853 (mt-10) REVERT: D 424 LYS cc_start: 0.8923 (tptt) cc_final: 0.8578 (tptt) REVERT: D 453 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8596 (mmmt) REVERT: D 499 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8756 (p) REVERT: E 106 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: E 386 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8272 (tttm) REVERT: E 515 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7547 (mtpt) REVERT: F 164 ARG cc_start: 0.8682 (ptp-110) cc_final: 0.8101 (mtm110) REVERT: F 168 ASN cc_start: 0.8246 (m110) cc_final: 0.7602 (m110) REVERT: F 268 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8954 (pp) REVERT: F 515 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7887 (mtpt) REVERT: G 106 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: G 222 MET cc_start: 0.7533 (mtt) cc_final: 0.6880 (ttm) REVERT: G 424 LYS cc_start: 0.8917 (tptt) cc_final: 0.8575 (tptt) REVERT: G 453 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8617 (mmmt) REVERT: G 499 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8853 (p) REVERT: H 515 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7225 (mtpt) REVERT: I 164 ARG cc_start: 0.8637 (ptp-110) cc_final: 0.7804 (ptt90) REVERT: I 168 ASN cc_start: 0.8255 (m110) cc_final: 0.7649 (m110) REVERT: I 268 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8945 (pp) REVERT: I 349 GLU cc_start: 0.8690 (pt0) cc_final: 0.8486 (pt0) REVERT: I 381 LEU cc_start: 0.8965 (tp) cc_final: 0.8719 (tp) REVERT: I 386 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8563 (mtpt) REVERT: I 424 LYS cc_start: 0.8697 (tptm) cc_final: 0.8141 (tptt) REVERT: I 486 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7126 (ttt90) REVERT: J 106 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: J 424 LYS cc_start: 0.8921 (tptt) cc_final: 0.8572 (tptt) REVERT: J 453 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8554 (mmmt) REVERT: J 499 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.9012 (p) REVERT: K 215 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: K 515 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7424 (mtpt) REVERT: M 143 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8550 (mm-30) REVERT: N 8 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8763 (tttm) REVERT: N 51 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7225 (pttp) REVERT: N 148 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6503 (ptt-90) REVERT: O 5 ASP cc_start: 0.8870 (p0) cc_final: 0.8657 (p0) REVERT: Q 5 ASP cc_start: 0.8619 (p0) cc_final: 0.8340 (p0) REVERT: Q 70 MET cc_start: 0.8528 (ttm) cc_final: 0.8289 (ttm) REVERT: R 15 GLU cc_start: 0.9197 (pm20) cc_final: 0.8907 (pm20) REVERT: S 5 ASP cc_start: 0.8877 (p0) cc_final: 0.8574 (p0) REVERT: U 5 ASP cc_start: 0.8555 (p0) cc_final: 0.8346 (p0) REVERT: V 5 ASP cc_start: 0.8476 (p0) cc_final: 0.8170 (p0) REVERT: V 15 GLU cc_start: 0.9191 (pm20) cc_final: 0.8888 (pm20) REVERT: V 36 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7928 (mm-30) REVERT: V 71 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: X 15 GLU cc_start: 0.9157 (pm20) cc_final: 0.8769 (pm20) outliers start: 211 outliers final: 147 residues processed: 1039 average time/residue: 0.5911 time to fit residues: 1014.9792 Evaluate side-chains 1023 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 844 time to evaluate : 5.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 320 GLU Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 515 LYS Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 453 LYS Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 453 LYS Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 215 GLN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 453 LYS Chi-restraints excluded: chain K residue 515 LYS Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 136 PHE Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 71 GLN Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 99 SER Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 133 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 493 optimal weight: 0.4980 chunk 283 optimal weight: 0.9980 chunk 555 optimal weight: 5.9990 chunk 632 optimal weight: 0.9980 chunk 327 optimal weight: 0.0070 chunk 677 optimal weight: 0.7980 chunk 673 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 458 optimal weight: 0.6980 chunk 509 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 GLN ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.095790 restraints weight = 98439.534| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.46 r_work: 0.3114 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56964 Z= 0.174 Angle : 0.557 14.726 77328 Z= 0.275 Chirality : 0.043 0.211 8256 Planarity : 0.005 0.052 10200 Dihedral : 4.273 56.899 7684 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.45 % Favored : 94.54 % Rotamer: Outliers : 3.52 % Allowed : 22.48 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.10), residues: 7032 helix: 1.49 (0.09), residues: 3612 sheet: -1.00 (0.25), residues: 540 loop : -1.06 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 155 HIS 0.003 0.001 HIS I 337 PHE 0.010 0.001 PHE O 37 TYR 0.014 0.001 TYR L 284 ARG 0.005 0.000 ARG E 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 887 time to evaluate : 4.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7110 (mt0) REVERT: L 164 ARG cc_start: 0.8670 (ptp-110) cc_final: 0.8311 (mtm110) REVERT: L 268 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8857 (pp) REVERT: L 349 GLU cc_start: 0.8656 (pt0) cc_final: 0.7752 (pt0) REVERT: L 386 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8521 (mtpt) REVERT: L 424 LYS cc_start: 0.8654 (tptm) cc_final: 0.8093 (tptt) REVERT: L 498 MET cc_start: 0.7877 (mmm) cc_final: 0.7558 (mmt) REVERT: L 515 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7997 (mtpt) REVERT: A 106 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.6790 (mp10) REVERT: A 222 MET cc_start: 0.7509 (mtt) cc_final: 0.6843 (ttm) REVERT: A 386 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8162 (mtpp) REVERT: A 424 LYS cc_start: 0.8926 (tptt) cc_final: 0.8582 (tptt) REVERT: A 499 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8949 (p) REVERT: B 424 LYS cc_start: 0.8705 (tptt) cc_final: 0.8414 (tptt) REVERT: B 515 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7516 (mtpt) REVERT: C 106 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: C 164 ARG cc_start: 0.8673 (ptp-110) cc_final: 0.8116 (mtm110) REVERT: C 168 ASN cc_start: 0.8094 (m110) cc_final: 0.7511 (m110) REVERT: C 268 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8848 (pp) REVERT: C 349 GLU cc_start: 0.8711 (pt0) cc_final: 0.8485 (pt0) REVERT: C 381 LEU cc_start: 0.8911 (tp) cc_final: 0.8658 (tp) REVERT: C 386 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8547 (mtpt) REVERT: C 424 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8517 (tptt) REVERT: C 515 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8028 (mtpt) REVERT: D 106 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: D 140 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: D 222 MET cc_start: 0.7577 (mtt) cc_final: 0.6942 (ttm) REVERT: D 302 MET cc_start: 0.9450 (mmp) cc_final: 0.9245 (mmp) REVERT: D 386 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8133 (mtpp) REVERT: D 404 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8066 (mt-10) REVERT: D 424 LYS cc_start: 0.8898 (tptt) cc_final: 0.8612 (tptt) REVERT: D 453 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8575 (mmmt) REVERT: D 499 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8705 (p) REVERT: E 106 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: E 386 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8331 (tttm) REVERT: E 515 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7496 (mtpt) REVERT: F 164 ARG cc_start: 0.8695 (ptp-110) cc_final: 0.8126 (mtm110) REVERT: F 168 ASN cc_start: 0.8098 (m110) cc_final: 0.7509 (m110) REVERT: F 268 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8856 (pp) REVERT: F 515 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7861 (mtpt) REVERT: G 106 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: G 222 MET cc_start: 0.7544 (mtt) cc_final: 0.6873 (ttm) REVERT: G 424 LYS cc_start: 0.8893 (tptt) cc_final: 0.8639 (tptt) REVERT: G 453 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8613 (mmmt) REVERT: G 499 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8829 (p) REVERT: H 424 LYS cc_start: 0.8683 (tptt) cc_final: 0.8370 (tptt) REVERT: H 433 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: H 515 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7238 (mtpt) REVERT: I 164 ARG cc_start: 0.8675 (ptp-110) cc_final: 0.8117 (mtm110) REVERT: I 168 ASN cc_start: 0.8182 (m110) cc_final: 0.7616 (m110) REVERT: I 268 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8843 (pp) REVERT: I 349 GLU cc_start: 0.8644 (pt0) cc_final: 0.8244 (pm20) REVERT: I 381 LEU cc_start: 0.8935 (tp) cc_final: 0.8695 (tp) REVERT: I 386 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8590 (mtpt) REVERT: I 424 LYS cc_start: 0.8677 (tptm) cc_final: 0.8120 (tptt) REVERT: I 486 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7072 (ttt90) REVERT: J 106 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: J 424 LYS cc_start: 0.8897 (tptt) cc_final: 0.8610 (tptt) REVERT: J 453 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8547 (mmmt) REVERT: J 499 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8983 (p) REVERT: K 215 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: K 424 LYS cc_start: 0.8681 (tptt) cc_final: 0.8365 (tptt) REVERT: K 515 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7418 (mtpt) REVERT: N 8 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8770 (tttm) REVERT: N 51 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7188 (pttp) REVERT: N 148 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6432 (ptt-90) REVERT: O 36 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8035 (mm-30) REVERT: Q 5 ASP cc_start: 0.8582 (p0) cc_final: 0.8302 (p0) REVERT: Q 70 MET cc_start: 0.8461 (ttm) cc_final: 0.8222 (ttm) REVERT: R 5 ASP cc_start: 0.8714 (p0) cc_final: 0.8493 (p0) REVERT: R 15 GLU cc_start: 0.9234 (pm20) cc_final: 0.8950 (pm20) REVERT: R 51 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6902 (pttt) REVERT: S 5 ASP cc_start: 0.8859 (p0) cc_final: 0.8580 (p0) REVERT: U 5 ASP cc_start: 0.8476 (p0) cc_final: 0.8210 (p0) REVERT: V 5 ASP cc_start: 0.8411 (p0) cc_final: 0.8100 (p0) outliers start: 206 outliers final: 142 residues processed: 1047 average time/residue: 0.5693 time to fit residues: 978.2884 Evaluate side-chains 1019 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 844 time to evaluate : 6.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 320 GLU Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 515 LYS Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 453 LYS Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 453 LYS Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 215 GLN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 453 LYS Chi-restraints excluded: chain K residue 515 LYS Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 136 PHE Chi-restraints excluded: chain R residue 51 LYS Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 71 GLN Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 159 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 579 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 578 optimal weight: 0.8980 chunk 568 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 673 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 HIS C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 GLN ** W 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095672 restraints weight = 98173.726| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.44 r_work: 0.3112 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56964 Z= 0.185 Angle : 0.562 14.509 77328 Z= 0.277 Chirality : 0.043 0.209 8256 Planarity : 0.005 0.052 10200 Dihedral : 4.258 56.227 7684 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.56 % Favored : 94.43 % Rotamer: Outliers : 3.23 % Allowed : 22.91 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7032 helix: 1.49 (0.09), residues: 3612 sheet: -0.97 (0.25), residues: 540 loop : -1.04 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 155 HIS 0.003 0.001 HIS I 337 PHE 0.010 0.001 PHE Q 37 TYR 0.022 0.001 TYR B 284 ARG 0.005 0.000 ARG E 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14064 Ramachandran restraints generated. 7032 Oldfield, 0 Emsley, 7032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 862 time to evaluate : 4.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: L 164 ARG cc_start: 0.8668 (ptp-110) cc_final: 0.8306 (mtm110) REVERT: L 268 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8852 (pp) REVERT: L 349 GLU cc_start: 0.8657 (pt0) cc_final: 0.7742 (pt0) REVERT: L 386 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8529 (mtpt) REVERT: L 424 LYS cc_start: 0.8587 (tptm) cc_final: 0.8046 (tptt) REVERT: L 478 ASP cc_start: 0.8583 (t0) cc_final: 0.8360 (t0) REVERT: L 498 MET cc_start: 0.7873 (mmm) cc_final: 0.7550 (mmt) REVERT: L 515 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7987 (mtpt) REVERT: A 106 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: A 222 MET cc_start: 0.7505 (mtt) cc_final: 0.6854 (ttm) REVERT: A 386 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8067 (mtpp) REVERT: A 424 LYS cc_start: 0.8952 (tptt) cc_final: 0.8645 (tptt) REVERT: A 453 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8555 (mmmt) REVERT: A 499 SER cc_start: 0.9180 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 424 LYS cc_start: 0.8684 (tptt) cc_final: 0.8378 (tptt) REVERT: B 515 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7523 (mtpt) REVERT: C 106 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: C 164 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.8113 (mtm110) REVERT: C 168 ASN cc_start: 0.8080 (m110) cc_final: 0.7506 (m110) REVERT: C 268 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8843 (pp) REVERT: C 309 ILE cc_start: 0.9199 (tt) cc_final: 0.8904 (pt) REVERT: C 349 GLU cc_start: 0.8720 (pt0) cc_final: 0.8278 (pm20) REVERT: C 381 LEU cc_start: 0.8908 (tp) cc_final: 0.8661 (tp) REVERT: C 386 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8538 (mtpt) REVERT: C 424 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8485 (tptt) REVERT: C 515 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8033 (mtpt) REVERT: D 106 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: D 140 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: D 222 MET cc_start: 0.7580 (mtt) cc_final: 0.6944 (ttm) REVERT: D 302 MET cc_start: 0.9462 (mmp) cc_final: 0.9248 (mmp) REVERT: D 386 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8158 (mtpp) REVERT: D 404 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8056 (mt-10) REVERT: D 424 LYS cc_start: 0.8895 (tptt) cc_final: 0.8610 (tptt) REVERT: D 453 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8573 (mmmt) REVERT: D 499 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8730 (p) REVERT: E 106 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: E 386 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8404 (tttm) REVERT: E 515 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7494 (mtpt) REVERT: F 164 ARG cc_start: 0.8700 (ptp-110) cc_final: 0.8132 (mtm110) REVERT: F 168 ASN cc_start: 0.8085 (m110) cc_final: 0.7500 (m110) REVERT: F 268 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8851 (pp) REVERT: F 515 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7871 (mtpt) REVERT: G 106 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: G 222 MET cc_start: 0.7522 (mtt) cc_final: 0.6856 (ttm) REVERT: G 424 LYS cc_start: 0.8887 (tptt) cc_final: 0.8642 (tptt) REVERT: G 453 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8601 (mmmt) REVERT: G 499 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8827 (p) REVERT: H 424 LYS cc_start: 0.8708 (tptt) cc_final: 0.8409 (tptt) REVERT: H 433 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: H 515 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7236 (mtpt) REVERT: I 164 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8112 (mtm110) REVERT: I 168 ASN cc_start: 0.8091 (m110) cc_final: 0.7499 (m110) REVERT: I 268 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8840 (pp) REVERT: I 349 GLU cc_start: 0.8686 (pt0) cc_final: 0.8288 (pm20) REVERT: I 386 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8577 (mtpt) REVERT: I 424 LYS cc_start: 0.8607 (tptm) cc_final: 0.8070 (tptt) REVERT: I 486 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7159 (ttt90) REVERT: J 106 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: J 424 LYS cc_start: 0.8898 (tptt) cc_final: 0.8612 (tptt) REVERT: J 453 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8538 (mmmt) REVERT: J 499 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (p) REVERT: K 215 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: K 424 LYS cc_start: 0.8697 (tptt) cc_final: 0.8393 (tptt) REVERT: K 515 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7372 (mtpt) REVERT: N 8 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8776 (tttm) REVERT: N 145 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8445 (mtt-85) REVERT: N 148 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6395 (ptt-90) REVERT: O 5 ASP cc_start: 0.8546 (p0) cc_final: 0.8318 (p0) REVERT: Q 5 ASP cc_start: 0.8604 (p0) cc_final: 0.8302 (p0) REVERT: Q 70 MET cc_start: 0.8459 (ttm) cc_final: 0.8225 (ttm) REVERT: R 5 ASP cc_start: 0.8716 (p0) cc_final: 0.8476 (p0) REVERT: R 15 GLU cc_start: 0.9247 (pm20) cc_final: 0.8956 (pm20) REVERT: R 51 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7144 (mttp) REVERT: S 5 ASP cc_start: 0.8878 (p0) cc_final: 0.8597 (p0) REVERT: S 8 LYS cc_start: 0.9077 (tttt) cc_final: 0.8785 (tttm) REVERT: S 133 VAL cc_start: 0.8973 (t) cc_final: 0.8729 (p) REVERT: S 143 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8368 (mt-10) REVERT: U 5 ASP cc_start: 0.8469 (p0) cc_final: 0.8170 (p0) REVERT: V 5 ASP cc_start: 0.8421 (p0) cc_final: 0.8101 (p0) REVERT: V 70 MET cc_start: 0.8534 (ttm) cc_final: 0.7821 (mtp) REVERT: V 143 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8556 (mm-30) outliers start: 189 outliers final: 142 residues processed: 1012 average time/residue: 0.5702 time to fit residues: 948.4604 Evaluate side-chains 1014 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 839 time to evaluate : 4.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain L residue 320 GLU Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 515 LYS Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 499 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 409 HIS Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 409 HIS Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LYS Chi-restraints excluded: chain G residue 106 GLN Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 409 HIS Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 453 LYS Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 499 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 321 ASP Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 409 HIS Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 515 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 409 HIS Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 486 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain J residue 106 GLN Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain J residue 409 HIS Chi-restraints excluded: chain J residue 453 LYS Chi-restraints excluded: chain J residue 499 SER Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 215 GLN Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 321 ASP Chi-restraints excluded: chain K residue 353 THR Chi-restraints excluded: chain K residue 359 ASP Chi-restraints excluded: chain K residue 409 HIS Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 453 LYS Chi-restraints excluded: chain K residue 515 LYS Chi-restraints excluded: chain M residue 91 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 136 PHE Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 136 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 136 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 136 PHE Chi-restraints excluded: chain R residue 51 LYS Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 136 PHE Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 136 PHE Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain T residue 136 PHE Chi-restraints excluded: chain U residue 51 LYS Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 51 LYS Chi-restraints excluded: chain V residue 71 GLN Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 136 PHE Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 136 PHE Chi-restraints excluded: chain X residue 85 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain X residue 136 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 163 optimal weight: 0.9980 chunk 601 optimal weight: 0.2980 chunk 383 optimal weight: 3.9990 chunk 623 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 440 optimal weight: 0.9990 chunk 564 optimal weight: 0.7980 chunk 373 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 544 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 407 GLN ** L 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 407 GLN ** G 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN ** I 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095571 restraints weight = 98537.674| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.45 r_work: 0.3110 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56964 Z= 0.190 Angle : 0.562 14.197 77328 Z= 0.277 Chirality : 0.043 0.205 8256 Planarity : 0.005 0.054 10200 Dihedral : 4.257 56.461 7684 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.56 % Favored : 94.43 % Rotamer: Outliers : 3.25 % Allowed : 22.91 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.10), residues: 7032 helix: 1.50 (0.09), residues: 3612 sheet: -0.95 (0.25), residues: 540 loop : -1.03 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 155 HIS 0.004 0.001 HIS F 337 PHE 0.010 0.001 PHE O 37 TYR 0.021 0.001 TYR B 284 ARG 0.005 0.000 ARG E 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27525.16 seconds wall clock time: 473 minutes 43.16 seconds (28423.16 seconds total)