Starting phenix.real_space_refine on Sun Sep 13 13:17:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2026/3jd4_6633.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 114 5.16 5 C 15060 2.51 5 N 4194 2.21 5 O 4644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, D, E, F Time building chain proxies: 8.12, per 1000 atoms: 0.34 Number of scatterers: 24054 At special positions: 0 Unit cell: (114.12, 129.421, 165.123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 42 15.00 O 4644 8.00 N 4194 7.00 C 15060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 55 " distance=0.00 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 89 " distance=0.00 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 115 " distance=0.00 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 197 " distance=0.00 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 270 " distance=0.00 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 319 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 874.2 milliseconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 24 sheets defined 56.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.615A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.998A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 118 removed outlier: 4.091A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.526A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.569A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.275A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 229 through 237 removed outlier: 4.201A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 Processing helix chain 'A' and resid 287 through 298 removed outlier: 3.558A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.572A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.859A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 374 through 388 removed outlier: 4.313A pdb=" N VAL A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.731A pdb=" N GLU A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.752A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.645A pdb=" N VAL A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 496 removed outlier: 3.531A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.615A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.998A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 118 removed outlier: 4.091A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.525A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.570A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.274A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.201A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.558A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.573A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.858A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 374 through 388 removed outlier: 4.314A pdb=" N VAL B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.731A pdb=" N GLU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 411 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.752A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.645A pdb=" N VAL B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.531A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.615A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.998A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 118 removed outlier: 4.091A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 155 removed outlier: 3.526A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.570A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.275A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 229 through 237 removed outlier: 4.201A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.558A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.572A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.858A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 374 through 388 removed outlier: 4.314A pdb=" N VAL C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 398 through 421 removed outlier: 3.731A pdb=" N GLU C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 411 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 433 through 439 removed outlier: 3.752A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.645A pdb=" N VAL C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 461 " --> pdb=" O MET C 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 496 removed outlier: 3.532A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 30 removed outlier: 3.614A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 removed outlier: 3.998A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 removed outlier: 4.091A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 155 removed outlier: 3.526A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.569A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.275A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 229 through 237 removed outlier: 4.201A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 Processing helix chain 'D' and resid 287 through 298 removed outlier: 3.557A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.573A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.859A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 374 through 388 removed outlier: 4.313A pdb=" N VAL D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 398 through 421 removed outlier: 3.731A pdb=" N GLU D 402 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D 411 " --> pdb=" O TYR D 407 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 425 Processing helix chain 'D' and resid 433 through 439 removed outlier: 3.752A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.645A pdb=" N VAL D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 461 " --> pdb=" O MET D 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 470 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 496 removed outlier: 3.530A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 removed outlier: 3.614A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 53 removed outlier: 3.998A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 118 removed outlier: 4.092A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 155 removed outlier: 3.525A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.569A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.275A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 228 Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.200A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 Processing helix chain 'E' and resid 287 through 298 removed outlier: 3.558A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.573A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 removed outlier: 3.859A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 374 through 388 removed outlier: 4.313A pdb=" N VAL E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E 383 " --> pdb=" O THR E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 397 No H-bonds generated for 'chain 'E' and resid 395 through 397' Processing helix chain 'E' and resid 398 through 421 removed outlier: 3.730A pdb=" N GLU E 402 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET E 411 " --> pdb=" O TYR E 407 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 433 through 439 removed outlier: 3.753A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.645A pdb=" N VAL E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 461 " --> pdb=" O MET E 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 470 " --> pdb=" O ARG E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 496 removed outlier: 3.530A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 removed outlier: 3.615A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 53 removed outlier: 3.998A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 4.092A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 155 removed outlier: 3.526A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.570A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.275A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 228 Processing helix chain 'F' and resid 229 through 237 removed outlier: 4.201A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 Processing helix chain 'F' and resid 287 through 298 removed outlier: 3.558A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.573A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 removed outlier: 3.859A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 374 through 388 removed outlier: 4.314A pdb=" N VAL F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 383 " --> pdb=" O THR F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 397 No H-bonds generated for 'chain 'F' and resid 395 through 397' Processing helix chain 'F' and resid 398 through 421 removed outlier: 3.731A pdb=" N GLU F 402 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET F 411 " --> pdb=" O TYR F 407 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 433 through 439 removed outlier: 3.752A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.644A pdb=" N VAL F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 461 " --> pdb=" O MET F 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 470 " --> pdb=" O ARG F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 496 removed outlier: 3.531A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 57 through 60 removed outlier: 4.407A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=C, first strand: chain 'A' and resid 246 through 250 removed outlier: 7.824A pdb=" N PHE A 247 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 273 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 249 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER A 279 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 308 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=E, first strand: chain 'B' and resid 57 through 60 removed outlier: 4.408A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=G, first strand: chain 'B' and resid 246 through 250 removed outlier: 7.825A pdb=" N PHE B 247 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 273 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 249 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER B 279 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 308 " --> pdb=" O TRP B 281 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=I, first strand: chain 'C' and resid 57 through 60 removed outlier: 4.407A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=K, first strand: chain 'C' and resid 246 through 250 removed outlier: 7.825A pdb=" N PHE C 247 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 273 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL C 249 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C 279 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 308 " --> pdb=" O TRP C 281 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=M, first strand: chain 'D' and resid 57 through 60 removed outlier: 4.407A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=O, first strand: chain 'D' and resid 246 through 250 removed outlier: 7.824A pdb=" N PHE D 247 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL D 273 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 249 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER D 279 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 308 " --> pdb=" O TRP D 281 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'D' and resid 321 through 322 Processing sheet with id=Q, first strand: chain 'E' and resid 57 through 60 removed outlier: 4.407A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=S, first strand: chain 'E' and resid 246 through 250 removed outlier: 7.825A pdb=" N PHE E 247 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL E 273 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL E 249 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER E 279 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 308 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'E' and resid 321 through 322 Processing sheet with id=U, first strand: chain 'F' and resid 57 through 60 removed outlier: 4.408A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'F' and resid 65 through 66 Processing sheet with id=W, first strand: chain 'F' and resid 246 through 250 removed outlier: 7.824A pdb=" N PHE F 247 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL F 273 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL F 249 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER F 279 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 308 " --> pdb=" O TRP F 281 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'F' and resid 321 through 322 1140 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7511 1.33 - 1.45: 3456 1.45 - 1.57: 13375 1.57 - 1.68: 78 1.68 - 1.80: 192 Bond restraints: 24612 Sorted by residual: bond pdb=" C4A NAI A 601 " pdb=" C5A NAI A 601 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N PRO F 429 " pdb=" CD PRO F 429 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C4A NAI B 602 " pdb=" C5A NAI B 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4A NAI C 602 " pdb=" C5A NAI C 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C4A NAI E 602 " pdb=" C5A NAI E 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 24607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 32776 2.86 - 5.73: 507 5.73 - 8.59: 74 8.59 - 11.46: 15 11.46 - 14.32: 12 Bond angle restraints: 33384 Sorted by residual: angle pdb=" C ILE A 428 " pdb=" N PRO A 429 " pdb=" CA PRO A 429 " ideal model delta sigma weight residual 119.84 114.17 5.67 1.25e+00 6.40e-01 2.06e+01 angle pdb=" C ILE C 428 " pdb=" N PRO C 429 " pdb=" CA PRO C 429 " ideal model delta sigma weight residual 119.84 114.19 5.65 1.25e+00 6.40e-01 2.04e+01 angle pdb=" C ILE E 428 " pdb=" N PRO E 429 " pdb=" CA PRO E 429 " ideal model delta sigma weight residual 119.84 114.20 5.64 1.25e+00 6.40e-01 2.04e+01 angle pdb=" C ILE B 428 " pdb=" N PRO B 429 " pdb=" CA PRO B 429 " ideal model delta sigma weight residual 119.84 114.20 5.64 1.25e+00 6.40e-01 2.03e+01 angle pdb=" C ILE F 428 " pdb=" N PRO F 429 " pdb=" CA PRO F 429 " ideal model delta sigma weight residual 119.84 114.21 5.63 1.25e+00 6.40e-01 2.03e+01 ... (remaining 33379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 14394 33.47 - 66.95: 96 66.95 - 100.42: 6 100.42 - 133.89: 6 133.89 - 167.37: 6 Dihedral angle restraints: 14508 sinusoidal: 6012 harmonic: 8496 Sorted by residual: dihedral pdb=" C8 GTP D 602 " pdb=" C1' GTP D 602 " pdb=" N9 GTP D 602 " pdb=" O4' GTP D 602 " ideal model delta sinusoidal sigma weight residual 104.59 -62.77 167.37 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP F 603 " pdb=" C1' GTP F 603 " pdb=" N9 GTP F 603 " pdb=" O4' GTP F 603 " ideal model delta sinusoidal sigma weight residual 104.59 -62.72 167.32 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP C 603 " pdb=" C1' GTP C 603 " pdb=" N9 GTP C 603 " pdb=" O4' GTP C 603 " ideal model delta sinusoidal sigma weight residual 104.59 -62.72 167.31 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 14505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2508 0.049 - 0.097: 930 0.097 - 0.146: 135 0.146 - 0.195: 31 0.195 - 0.244: 14 Chirality restraints: 3618 Sorted by residual: chirality pdb=" C1B NAI E 602 " pdb=" C2B NAI E 602 " pdb=" N9A NAI E 602 " pdb=" O4B NAI E 602 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1B NAI D 601 " pdb=" C2B NAI D 601 " pdb=" N9A NAI D 601 " pdb=" O4B NAI D 601 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1B NAI B 602 " pdb=" C2B NAI B 602 " pdb=" N9A NAI B 602 " pdb=" O4B NAI B 602 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3615 not shown) Planarity restraints: 4242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 282 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO D 283 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 282 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO F 283 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 283 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 283 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 282 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 283 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.028 5.00e-02 4.00e+02 ... (remaining 4239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1144 2.71 - 3.25: 26307 3.25 - 3.80: 38827 3.80 - 4.35: 52983 4.35 - 4.90: 86076 Nonbonded interactions: 205337 Sorted by model distance: nonbonded pdb=" O HIS D 195 " pdb=" NZ LYS D 201 " model vdw 2.157 3.120 nonbonded pdb=" O HIS C 195 " pdb=" NZ LYS C 201 " model vdw 2.157 3.120 nonbonded pdb=" O HIS A 195 " pdb=" NZ LYS A 201 " model vdw 2.157 3.120 nonbonded pdb=" O HIS B 195 " pdb=" NZ LYS B 201 " model vdw 2.157 3.120 nonbonded pdb=" O HIS E 195 " pdb=" NZ LYS E 201 " model vdw 2.158 3.120 ... (remaining 205332 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' and resid 5 through 601) selection = (chain 'B' and resid 5 through 602) selection = (chain 'C' and resid 5 through 601) selection = (chain 'D' and resid 5 through 601) selection = (chain 'E' and resid 5 through 602) selection = (chain 'F' and resid 5 through 601) } 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.020 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 24612 Z= 0.419 Angle : 0.963 14.319 33390 Z= 0.498 Chirality : 0.052 0.244 3618 Planarity : 0.004 0.051 4242 Dihedral : 10.215 167.367 9084 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.12), residues: 2970 helix: -3.67 (0.08), residues: 1320 sheet: -3.54 (0.22), residues: 312 loop : -2.42 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 86 TYR 0.033 0.003 TYR A 78 PHE 0.034 0.003 PHE C 122 TRP 0.021 0.003 TRP D 178 HIS 0.010 0.002 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00892 / 0.42 (24612) covalent geometry : angle 0.96299 / 0.50 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.28335 / 18.85 ( 1140) hydrogen bonds : angle 10.17480 / 7.16 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8401 (t0) cc_final: 0.7931 (m-30) REVERT: A 33 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7929 (mtmt) REVERT: A 72 TRP cc_start: 0.8355 (m100) cc_final: 0.8147 (m100) REVERT: A 84 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8073 (mm-40) REVERT: A 181 ASP cc_start: 0.8449 (t70) cc_final: 0.7995 (t0) REVERT: A 308 LYS cc_start: 0.7902 (pttt) cc_final: 0.7414 (mttp) REVERT: B 6 ASP cc_start: 0.8395 (t0) cc_final: 0.7865 (m-30) REVERT: B 33 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7871 (mtmt) REVERT: B 72 TRP cc_start: 0.8365 (m100) cc_final: 0.8084 (m100) REVERT: B 84 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8059 (mm-40) REVERT: B 181 ASP cc_start: 0.8531 (t70) cc_final: 0.8037 (t0) REVERT: B 308 LYS cc_start: 0.8002 (pttt) cc_final: 0.7518 (mttp) REVERT: C 6 ASP cc_start: 0.8424 (t0) cc_final: 0.7900 (m-30) REVERT: C 72 TRP cc_start: 0.8371 (m100) cc_final: 0.8043 (m100) REVERT: C 181 ASP cc_start: 0.8463 (t70) cc_final: 0.7995 (t0) REVERT: C 292 GLU cc_start: 0.8434 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 308 LYS cc_start: 0.7915 (pttt) cc_final: 0.7436 (mttp) REVERT: C 372 TYR cc_start: 0.8003 (t80) cc_final: 0.7674 (t80) REVERT: D 6 ASP cc_start: 0.8395 (t0) cc_final: 0.7892 (m-30) REVERT: D 33 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7957 (mtmt) REVERT: D 72 TRP cc_start: 0.8354 (m100) cc_final: 0.8107 (m100) REVERT: D 84 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8086 (mm-40) REVERT: D 181 ASP cc_start: 0.8470 (t70) cc_final: 0.8018 (t0) REVERT: D 308 LYS cc_start: 0.7913 (pttt) cc_final: 0.7442 (mttp) REVERT: E 6 ASP cc_start: 0.8388 (t0) cc_final: 0.7857 (m-30) REVERT: E 33 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7874 (mtmt) REVERT: E 72 TRP cc_start: 0.8356 (m100) cc_final: 0.8077 (m100) REVERT: E 84 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8055 (mm-40) REVERT: E 181 ASP cc_start: 0.8533 (t70) cc_final: 0.8043 (t0) REVERT: E 308 LYS cc_start: 0.8011 (pttt) cc_final: 0.7533 (mttp) REVERT: F 6 ASP cc_start: 0.8424 (t0) cc_final: 0.7897 (m-30) REVERT: F 72 TRP cc_start: 0.8369 (m100) cc_final: 0.8044 (m100) REVERT: F 181 ASP cc_start: 0.8463 (t70) cc_final: 0.7991 (t0) REVERT: F 292 GLU cc_start: 0.8430 (tt0) cc_final: 0.7974 (tm-30) REVERT: F 308 LYS cc_start: 0.7916 (pttt) cc_final: 0.7439 (mttp) REVERT: F 372 TYR cc_start: 0.7999 (t80) cc_final: 0.7670 (t80) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.1984 time to fit residues: 160.1562 Evaluate side-chains 299 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 85 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 85 HIS B 189 HIS B 228 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 189 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS C 494 ASN D 81 GLN D 84 GLN D 85 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 81 GLN E 84 GLN E 85 HIS E 189 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS F 85 HIS F 189 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS F 494 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083099 restraints weight = 44923.416| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.30 r_work: 0.2983 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24612 Z= 0.220 Angle : 0.691 9.987 33390 Z= 0.351 Chirality : 0.047 0.197 3618 Planarity : 0.005 0.043 4242 Dihedral : 12.146 164.751 3480 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.16 % Allowed : 7.79 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2970 helix: -0.98 (0.12), residues: 1386 sheet: -2.75 (0.25), residues: 312 loop : -1.49 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 19 TYR 0.022 0.002 TYR F 78 PHE 0.021 0.002 PHE A 16 TRP 0.009 0.002 TRP B 281 HIS 0.009 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (24612) covalent geometry : angle 0.69098 / 0.35 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05694 / 3.81 ( 1140) hydrogen bonds : angle 5.32560 / 3.77 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8097 (t0) cc_final: 0.7513 (m-30) REVERT: A 33 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7571 (mtmt) REVERT: A 72 TRP cc_start: 0.8502 (m100) cc_final: 0.7221 (m100) REVERT: A 81 GLN cc_start: 0.8508 (mt0) cc_final: 0.8241 (mt0) REVERT: A 84 GLN cc_start: 0.8173 (mm110) cc_final: 0.7879 (mm-40) REVERT: A 181 ASP cc_start: 0.8665 (t70) cc_final: 0.8235 (t0) REVERT: A 308 LYS cc_start: 0.7651 (pttt) cc_final: 0.7011 (mttp) REVERT: A 349 ASN cc_start: 0.9093 (m-40) cc_final: 0.8813 (m110) REVERT: A 495 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 6 ASP cc_start: 0.8120 (t0) cc_final: 0.7497 (m-30) REVERT: B 72 TRP cc_start: 0.8488 (m100) cc_final: 0.7133 (m100) REVERT: B 81 GLN cc_start: 0.8676 (mt0) cc_final: 0.7923 (mt0) REVERT: B 84 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 163 ASP cc_start: 0.8365 (m-30) cc_final: 0.7428 (m-30) REVERT: B 181 ASP cc_start: 0.8720 (t70) cc_final: 0.8307 (t0) REVERT: B 308 LYS cc_start: 0.7882 (pttt) cc_final: 0.7195 (mttp) REVERT: B 349 ASN cc_start: 0.9105 (m-40) cc_final: 0.8678 (m110) REVERT: B 495 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8207 (mt-10) REVERT: C 6 ASP cc_start: 0.8200 (t0) cc_final: 0.7553 (m-30) REVERT: C 72 TRP cc_start: 0.8520 (m100) cc_final: 0.7983 (m100) REVERT: C 81 GLN cc_start: 0.8533 (mt0) cc_final: 0.8227 (mt0) REVERT: C 308 LYS cc_start: 0.7801 (pttt) cc_final: 0.7099 (mttp) REVERT: C 372 TYR cc_start: 0.8630 (t80) cc_final: 0.8239 (t80) REVERT: C 457 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: C 495 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8109 (mt-10) REVERT: D 6 ASP cc_start: 0.8075 (t0) cc_final: 0.7472 (m-30) REVERT: D 33 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7604 (mtmt) REVERT: D 72 TRP cc_start: 0.8489 (m100) cc_final: 0.7208 (m100) REVERT: D 81 GLN cc_start: 0.8502 (mt0) cc_final: 0.8301 (mt0) REVERT: D 181 ASP cc_start: 0.8680 (t70) cc_final: 0.8248 (t0) REVERT: D 308 LYS cc_start: 0.7693 (pttt) cc_final: 0.7047 (mttp) REVERT: D 349 ASN cc_start: 0.9089 (m-40) cc_final: 0.8805 (m110) REVERT: D 495 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7993 (mt-10) REVERT: E 6 ASP cc_start: 0.8121 (t0) cc_final: 0.7497 (m-30) REVERT: E 72 TRP cc_start: 0.8467 (m100) cc_final: 0.7112 (m100) REVERT: E 81 GLN cc_start: 0.8442 (mt0) cc_final: 0.8227 (mt0) REVERT: E 84 GLN cc_start: 0.8042 (mm110) cc_final: 0.7776 (mm-40) REVERT: E 181 ASP cc_start: 0.8709 (t70) cc_final: 0.8309 (t0) REVERT: E 308 LYS cc_start: 0.7879 (pttt) cc_final: 0.7194 (mttp) REVERT: E 349 ASN cc_start: 0.9098 (m-40) cc_final: 0.8679 (m110) REVERT: E 495 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8218 (mt-10) REVERT: F 6 ASP cc_start: 0.8198 (t0) cc_final: 0.7554 (m-30) REVERT: F 72 TRP cc_start: 0.8526 (m100) cc_final: 0.8000 (m100) REVERT: F 81 GLN cc_start: 0.8545 (mt0) cc_final: 0.8245 (mt0) REVERT: F 308 LYS cc_start: 0.7795 (pttt) cc_final: 0.7096 (mttp) REVERT: F 372 TYR cc_start: 0.8630 (t80) cc_final: 0.8244 (t80) REVERT: F 457 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: F 495 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8120 (mt-10) outliers start: 54 outliers final: 43 residues processed: 436 average time/residue: 0.1608 time to fit residues: 111.9521 Evaluate side-chains 334 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 256 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 198 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 266 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 189 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN D 189 HIS ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084777 restraints weight = 44929.060| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.25 r_work: 0.3005 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24612 Z= 0.171 Angle : 0.618 8.621 33390 Z= 0.311 Chirality : 0.046 0.210 3618 Planarity : 0.004 0.040 4242 Dihedral : 11.435 162.239 3480 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.32 % Allowed : 9.27 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2970 helix: 0.30 (0.13), residues: 1422 sheet: -2.22 (0.24), residues: 372 loop : -0.74 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 86 TYR 0.015 0.001 TYR C 78 PHE 0.018 0.002 PHE C 9 TRP 0.014 0.002 TRP E 72 HIS 0.007 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (24612) covalent geometry : angle 0.61853 / 0.31 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04595 / 3.06 ( 1140) hydrogen bonds : angle 4.66683 / 3.30 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 337 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8038 (t0) cc_final: 0.7416 (m-30) REVERT: A 33 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7547 (mtmt) REVERT: A 181 ASP cc_start: 0.8697 (t70) cc_final: 0.8291 (t0) REVERT: A 308 LYS cc_start: 0.7705 (pttt) cc_final: 0.7126 (mttp) REVERT: A 349 ASN cc_start: 0.9109 (m-40) cc_final: 0.8787 (m110) REVERT: B 6 ASP cc_start: 0.8011 (t0) cc_final: 0.7357 (m-30) REVERT: B 14 GLU cc_start: 0.7869 (pt0) cc_final: 0.7354 (pt0) REVERT: B 81 GLN cc_start: 0.8629 (mt0) cc_final: 0.7818 (mt0) REVERT: B 84 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7970 (mp10) REVERT: B 163 ASP cc_start: 0.8294 (m-30) cc_final: 0.7259 (m-30) REVERT: B 181 ASP cc_start: 0.8726 (t70) cc_final: 0.8342 (t0) REVERT: B 308 LYS cc_start: 0.7851 (pttt) cc_final: 0.7243 (mttp) REVERT: C 6 ASP cc_start: 0.7946 (t0) cc_final: 0.7277 (m-30) REVERT: C 72 TRP cc_start: 0.8535 (m100) cc_final: 0.8026 (m100) REVERT: C 81 GLN cc_start: 0.8496 (mt0) cc_final: 0.8207 (mt0) REVERT: C 292 GLU cc_start: 0.8542 (tt0) cc_final: 0.7760 (tm-30) REVERT: C 308 LYS cc_start: 0.7792 (pttt) cc_final: 0.7163 (mttp) REVERT: C 372 TYR cc_start: 0.8595 (t80) cc_final: 0.8226 (t80) REVERT: C 417 LEU cc_start: 0.9257 (mt) cc_final: 0.9026 (mp) REVERT: C 457 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: C 495 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8057 (mt-10) REVERT: D 6 ASP cc_start: 0.8013 (t0) cc_final: 0.7416 (m-30) REVERT: D 33 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7532 (mtmt) REVERT: D 84 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7857 (mm-40) REVERT: D 181 ASP cc_start: 0.8686 (t70) cc_final: 0.8278 (t0) REVERT: D 308 LYS cc_start: 0.7720 (pttt) cc_final: 0.7141 (mttp) REVERT: D 349 ASN cc_start: 0.9093 (m-40) cc_final: 0.8770 (m110) REVERT: E 6 ASP cc_start: 0.8018 (t0) cc_final: 0.7366 (m-30) REVERT: E 14 GLU cc_start: 0.7884 (pt0) cc_final: 0.7370 (pt0) REVERT: E 181 ASP cc_start: 0.8747 (t70) cc_final: 0.8362 (t0) REVERT: E 308 LYS cc_start: 0.7898 (pttt) cc_final: 0.7333 (mttp) REVERT: F 6 ASP cc_start: 0.7962 (t0) cc_final: 0.7288 (m-30) REVERT: F 72 TRP cc_start: 0.8534 (m100) cc_final: 0.8031 (m100) REVERT: F 81 GLN cc_start: 0.8500 (mt0) cc_final: 0.8210 (mt0) REVERT: F 292 GLU cc_start: 0.8531 (tt0) cc_final: 0.7728 (tm-30) REVERT: F 308 LYS cc_start: 0.7780 (pttt) cc_final: 0.7156 (mttp) REVERT: F 372 TYR cc_start: 0.8597 (t80) cc_final: 0.8224 (t80) REVERT: F 457 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7984 (mtm) REVERT: F 495 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8038 (mt-10) outliers start: 83 outliers final: 57 residues processed: 396 average time/residue: 0.1512 time to fit residues: 98.1466 Evaluate side-chains 337 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 278 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 240 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 266 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 HIS B 254 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS E 254 ASN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083107 restraints weight = 44714.927| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.25 r_work: 0.2975 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24612 Z= 0.223 Angle : 0.640 9.231 33390 Z= 0.318 Chirality : 0.047 0.181 3618 Planarity : 0.004 0.039 4242 Dihedral : 11.184 159.680 3480 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.76 % Allowed : 10.39 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.16), residues: 2970 helix: 0.69 (0.14), residues: 1410 sheet: -2.01 (0.24), residues: 372 loop : -0.59 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 396 TYR 0.017 0.002 TYR F 78 PHE 0.019 0.002 PHE D 122 TRP 0.026 0.002 TRP A 72 HIS 0.007 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (24612) covalent geometry : angle 0.64029 / 0.32 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04513 / 3.00 ( 1140) hydrogen bonds : angle 4.50310 / 3.18 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.935 Fit side-chains REVERT: A 33 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7592 (mtmt) REVERT: A 181 ASP cc_start: 0.8743 (t70) cc_final: 0.8314 (t0) REVERT: A 308 LYS cc_start: 0.7737 (pttt) cc_final: 0.7142 (mttp) REVERT: A 417 LEU cc_start: 0.9301 (mt) cc_final: 0.9062 (mp) REVERT: A 495 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 6 ASP cc_start: 0.8083 (t0) cc_final: 0.7463 (m-30) REVERT: B 14 GLU cc_start: 0.7962 (pt0) cc_final: 0.7441 (pt0) REVERT: B 81 GLN cc_start: 0.8689 (mt0) cc_final: 0.7942 (mt0) REVERT: B 163 ASP cc_start: 0.8369 (m-30) cc_final: 0.7399 (m-30) REVERT: B 181 ASP cc_start: 0.8777 (t70) cc_final: 0.8391 (t0) REVERT: B 308 LYS cc_start: 0.7853 (pttt) cc_final: 0.7212 (mttp) REVERT: B 491 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8046 (mtm-85) REVERT: C 6 ASP cc_start: 0.8058 (t0) cc_final: 0.7400 (m-30) REVERT: C 72 TRP cc_start: 0.8504 (m100) cc_final: 0.8044 (m100) REVERT: C 81 GLN cc_start: 0.8588 (mt0) cc_final: 0.8258 (mt0) REVERT: C 291 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 308 LYS cc_start: 0.7811 (pttt) cc_final: 0.7145 (mttp) REVERT: D 33 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7584 (mtmt) REVERT: D 181 ASP cc_start: 0.8742 (t70) cc_final: 0.8310 (t0) REVERT: D 308 LYS cc_start: 0.7759 (pttt) cc_final: 0.7161 (mttp) REVERT: D 417 LEU cc_start: 0.9304 (mt) cc_final: 0.9069 (mp) REVERT: D 495 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8093 (mt-10) REVERT: E 6 ASP cc_start: 0.8054 (t0) cc_final: 0.7449 (m-30) REVERT: E 14 GLU cc_start: 0.7983 (pt0) cc_final: 0.7456 (pt0) REVERT: E 181 ASP cc_start: 0.8793 (t70) cc_final: 0.8399 (t0) REVERT: E 308 LYS cc_start: 0.7857 (pttt) cc_final: 0.7260 (mttp) REVERT: E 491 ARG cc_start: 0.8363 (mtp180) cc_final: 0.8055 (mtm-85) REVERT: F 6 ASP cc_start: 0.8098 (t0) cc_final: 0.7437 (m-30) REVERT: F 14 GLU cc_start: 0.7959 (pt0) cc_final: 0.7434 (pt0) REVERT: F 72 TRP cc_start: 0.8498 (m100) cc_final: 0.8045 (m100) REVERT: F 81 GLN cc_start: 0.8587 (mt0) cc_final: 0.8253 (mt0) REVERT: F 140 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: F 291 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8834 (tt) REVERT: F 308 LYS cc_start: 0.7812 (pttt) cc_final: 0.7145 (mttp) REVERT: F 495 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7983 (mt-10) outliers start: 94 outliers final: 77 residues processed: 357 average time/residue: 0.1647 time to fit residues: 94.7173 Evaluate side-chains 344 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 264 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 89 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 266 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 chunk 280 optimal weight: 8.9990 chunk 274 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088159 restraints weight = 44211.886| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.30 r_work: 0.3070 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24612 Z= 0.105 Angle : 0.549 8.897 33390 Z= 0.273 Chirality : 0.043 0.161 3618 Planarity : 0.004 0.038 4242 Dihedral : 10.419 157.589 3480 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.12 % Allowed : 11.43 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2970 helix: 1.18 (0.14), residues: 1416 sheet: -1.58 (0.25), residues: 402 loop : -0.35 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 261 TYR 0.009 0.001 TYR F 401 PHE 0.017 0.001 PHE D 9 TRP 0.027 0.001 TRP A 72 HIS 0.004 0.001 HIS F 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (24612) covalent geometry : angle 0.54936 / 0.27 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03764 / 2.51 ( 1140) hydrogen bonds : angle 4.13750 / 2.93 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 0.937 Fit side-chains REVERT: A 33 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7476 (mtmt) REVERT: A 150 MET cc_start: 0.8582 (tpp) cc_final: 0.8314 (mpp) REVERT: A 181 ASP cc_start: 0.8670 (t70) cc_final: 0.8463 (t0) REVERT: A 308 LYS cc_start: 0.7641 (pttt) cc_final: 0.7254 (mttp) REVERT: A 349 ASN cc_start: 0.9052 (m-40) cc_final: 0.8751 (m110) REVERT: A 417 LEU cc_start: 0.9309 (mt) cc_final: 0.9081 (mp) REVERT: B 72 TRP cc_start: 0.8466 (m100) cc_final: 0.7960 (m100) REVERT: B 81 GLN cc_start: 0.8566 (mt0) cc_final: 0.7781 (mt0) REVERT: B 150 MET cc_start: 0.8486 (tpp) cc_final: 0.8254 (mpp) REVERT: B 163 ASP cc_start: 0.8283 (m-30) cc_final: 0.7256 (m-30) REVERT: B 181 ASP cc_start: 0.8682 (t70) cc_final: 0.8290 (t0) REVERT: B 308 LYS cc_start: 0.7801 (pttt) cc_final: 0.7394 (mttp) REVERT: B 411 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8593 (tpt) REVERT: B 491 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7917 (mtm-85) REVERT: C 6 ASP cc_start: 0.7885 (t0) cc_final: 0.7307 (m-30) REVERT: C 14 GLU cc_start: 0.7920 (pt0) cc_final: 0.7577 (pt0) REVERT: C 72 TRP cc_start: 0.8444 (m100) cc_final: 0.7997 (m100) REVERT: C 81 GLN cc_start: 0.8443 (mt0) cc_final: 0.8183 (mt0) REVERT: C 84 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7826 (mp10) REVERT: C 308 LYS cc_start: 0.7725 (pttt) cc_final: 0.7308 (mttp) REVERT: C 338 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7827 (mtm-85) REVERT: C 495 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7981 (mt-10) REVERT: D 33 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7460 (mtmt) REVERT: D 84 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7826 (mp10) REVERT: D 150 MET cc_start: 0.8587 (tpp) cc_final: 0.8322 (mpp) REVERT: D 181 ASP cc_start: 0.8672 (t70) cc_final: 0.8463 (t0) REVERT: D 308 LYS cc_start: 0.7637 (pttt) cc_final: 0.7262 (mttp) REVERT: D 349 ASN cc_start: 0.9048 (m-40) cc_final: 0.8751 (m110) REVERT: D 417 LEU cc_start: 0.9300 (mt) cc_final: 0.9075 (mp) REVERT: E 72 TRP cc_start: 0.8458 (m100) cc_final: 0.7958 (m100) REVERT: E 150 MET cc_start: 0.8527 (tpp) cc_final: 0.8310 (mpp) REVERT: E 181 ASP cc_start: 0.8679 (t70) cc_final: 0.8271 (t0) REVERT: E 308 LYS cc_start: 0.7765 (pttt) cc_final: 0.7413 (mttp) REVERT: E 411 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8613 (tpt) REVERT: E 491 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7915 (mtm-85) REVERT: F 6 ASP cc_start: 0.7882 (t0) cc_final: 0.7282 (m-30) REVERT: F 72 TRP cc_start: 0.8444 (m100) cc_final: 0.8008 (m100) REVERT: F 81 GLN cc_start: 0.8438 (mt0) cc_final: 0.8173 (mt0) REVERT: F 84 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7806 (mp10) REVERT: F 308 LYS cc_start: 0.7719 (pttt) cc_final: 0.7302 (mttp) REVERT: F 338 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7812 (mtm-85) REVERT: F 495 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8049 (mt-10) outliers start: 78 outliers final: 44 residues processed: 405 average time/residue: 0.1730 time to fit residues: 110.3326 Evaluate side-chains 327 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 411 MET Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 201 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.085963 restraints weight = 44408.582| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.26 r_work: 0.3033 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24612 Z= 0.143 Angle : 0.574 9.097 33390 Z= 0.283 Chirality : 0.044 0.145 3618 Planarity : 0.004 0.036 4242 Dihedral : 10.177 155.315 3480 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.00 % Allowed : 13.03 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2970 helix: 1.46 (0.14), residues: 1386 sheet: -1.78 (0.25), residues: 372 loop : -0.13 (0.20), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.009 0.001 TYR E 372 PHE 0.013 0.001 PHE D 148 TRP 0.026 0.002 TRP D 72 HIS 0.005 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (24612) covalent geometry : angle 0.57361 / 0.28 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03833 / 2.55 ( 1140) hydrogen bonds : angle 4.10797 / 2.90 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 0.881 Fit side-chains REVERT: A 33 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7542 (mtmt) REVERT: A 308 LYS cc_start: 0.7702 (pttt) cc_final: 0.7259 (mttp) REVERT: A 349 ASN cc_start: 0.9030 (m-40) cc_final: 0.8717 (m110) REVERT: A 372 TYR cc_start: 0.8590 (t80) cc_final: 0.8325 (t80) REVERT: A 417 LEU cc_start: 0.9284 (mt) cc_final: 0.9046 (mp) REVERT: A 495 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 72 TRP cc_start: 0.8477 (m100) cc_final: 0.7974 (m100) REVERT: B 81 GLN cc_start: 0.8610 (mt0) cc_final: 0.7777 (mt0) REVERT: B 163 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 181 ASP cc_start: 0.8715 (t70) cc_final: 0.8264 (t0) REVERT: B 308 LYS cc_start: 0.7785 (pttt) cc_final: 0.7335 (mttp) REVERT: B 411 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8618 (tpt) REVERT: B 491 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7943 (mtm-85) REVERT: C 6 ASP cc_start: 0.7893 (t0) cc_final: 0.7305 (m-30) REVERT: C 72 TRP cc_start: 0.8492 (m100) cc_final: 0.8056 (m100) REVERT: C 81 GLN cc_start: 0.8528 (mt0) cc_final: 0.8256 (mt0) REVERT: C 84 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7885 (mp10) REVERT: C 140 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: C 308 LYS cc_start: 0.7780 (pttt) cc_final: 0.7304 (mttp) REVERT: C 338 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7807 (mtm-85) REVERT: D 33 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7534 (mtmt) REVERT: D 308 LYS cc_start: 0.7683 (pttt) cc_final: 0.7301 (mttp) REVERT: D 349 ASN cc_start: 0.9029 (m-40) cc_final: 0.8722 (m110) REVERT: D 417 LEU cc_start: 0.9280 (mt) cc_final: 0.9044 (mp) REVERT: D 495 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 72 TRP cc_start: 0.8495 (m100) cc_final: 0.7988 (m100) REVERT: E 181 ASP cc_start: 0.8694 (t70) cc_final: 0.8302 (t0) REVERT: E 291 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8735 (tt) REVERT: E 308 LYS cc_start: 0.7813 (pttt) cc_final: 0.7427 (mttp) REVERT: E 411 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8624 (tpt) REVERT: E 491 ARG cc_start: 0.8286 (mtp180) cc_final: 0.7961 (mtm-85) REVERT: F 6 ASP cc_start: 0.7922 (t0) cc_final: 0.7458 (m-30) REVERT: F 72 TRP cc_start: 0.8489 (m100) cc_final: 0.8063 (m100) REVERT: F 81 GLN cc_start: 0.8510 (mt0) cc_final: 0.8237 (mt0) REVERT: F 84 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7878 (mp10) REVERT: F 308 LYS cc_start: 0.7765 (pttt) cc_final: 0.7300 (mttp) REVERT: F 338 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7803 (mtm-85) outliers start: 75 outliers final: 48 residues processed: 328 average time/residue: 0.1575 time to fit residues: 84.3030 Evaluate side-chains 316 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 411 MET Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 263 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 254 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 254 ASN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** 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 = 0.3559 r_free = 0.3559 target = 0.109509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083990 restraints weight = 44613.337| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.26 r_work: 0.2991 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24612 Z= 0.190 Angle : 0.609 9.095 33390 Z= 0.302 Chirality : 0.045 0.135 3618 Planarity : 0.004 0.036 4242 Dihedral : 10.167 153.380 3480 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.00 % Allowed : 13.55 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2970 helix: 1.45 (0.14), residues: 1380 sheet: -1.53 (0.24), residues: 402 loop : -0.12 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 396 TYR 0.013 0.002 TYR C 78 PHE 0.014 0.002 PHE D 122 TRP 0.028 0.002 TRP D 72 HIS 0.006 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (24612) covalent geometry : angle 0.60860 / 0.30 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04062 / 2.71 ( 1140) hydrogen bonds : angle 4.20872 / 2.98 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 0.918 Fit side-chains REVERT: A 33 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7477 (mtmt) REVERT: A 308 LYS cc_start: 0.7702 (pttt) cc_final: 0.7211 (mttp) REVERT: A 349 ASN cc_start: 0.9044 (m-40) cc_final: 0.8762 (m110) REVERT: A 372 TYR cc_start: 0.8622 (t80) cc_final: 0.8356 (t80) REVERT: A 417 LEU cc_start: 0.9289 (mt) cc_final: 0.9042 (mp) REVERT: A 495 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 72 TRP cc_start: 0.8487 (m100) cc_final: 0.7948 (m100) REVERT: B 81 GLN cc_start: 0.8641 (mt0) cc_final: 0.7850 (mt0) REVERT: B 163 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: B 181 ASP cc_start: 0.8730 (t70) cc_final: 0.8325 (t0) REVERT: B 308 LYS cc_start: 0.7790 (pttt) cc_final: 0.7273 (mttp) REVERT: B 491 ARG cc_start: 0.8323 (mtp180) cc_final: 0.7995 (mtm-85) REVERT: C 6 ASP cc_start: 0.7981 (t0) cc_final: 0.7529 (m-30) REVERT: C 72 TRP cc_start: 0.8499 (m100) cc_final: 0.8116 (m100) REVERT: C 81 GLN cc_start: 0.8586 (mt0) cc_final: 0.8281 (mt0) REVERT: C 84 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7939 (mp10) REVERT: C 140 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: C 291 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 308 LYS cc_start: 0.7795 (pttt) cc_final: 0.7268 (mttp) REVERT: C 338 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7792 (mtm-85) REVERT: D 308 LYS cc_start: 0.7706 (pttt) cc_final: 0.7240 (mttp) REVERT: D 417 LEU cc_start: 0.9285 (mt) cc_final: 0.9040 (mp) REVERT: D 495 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8069 (mt-10) REVERT: E 72 TRP cc_start: 0.8477 (m100) cc_final: 0.7927 (m100) REVERT: E 181 ASP cc_start: 0.8728 (t70) cc_final: 0.8321 (t0) REVERT: E 291 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8717 (tt) REVERT: E 308 LYS cc_start: 0.7834 (pttt) cc_final: 0.7366 (mttp) REVERT: E 411 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8620 (tpt) REVERT: E 491 ARG cc_start: 0.8331 (mtp180) cc_final: 0.8001 (mtm-85) REVERT: F 6 ASP cc_start: 0.7990 (t0) cc_final: 0.7590 (m-30) REVERT: F 72 TRP cc_start: 0.8505 (m100) cc_final: 0.8130 (m100) REVERT: F 81 GLN cc_start: 0.8580 (mt0) cc_final: 0.8273 (mt0) REVERT: F 84 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7939 (mp10) REVERT: F 140 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: F 291 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8693 (tt) REVERT: F 308 LYS cc_start: 0.7797 (pttt) cc_final: 0.7264 (mttp) REVERT: F 338 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7787 (mtm-85) outliers start: 75 outliers final: 56 residues processed: 310 average time/residue: 0.1551 time to fit residues: 78.7343 Evaluate side-chains 310 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 411 MET Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 188 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086346 restraints weight = 44451.687| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.27 r_work: 0.3035 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24612 Z= 0.123 Angle : 0.563 9.998 33390 Z= 0.279 Chirality : 0.043 0.138 3618 Planarity : 0.003 0.036 4242 Dihedral : 9.868 151.378 3480 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 14.59 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 2970 helix: 1.64 (0.14), residues: 1380 sheet: -1.36 (0.25), residues: 402 loop : -0.03 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.010 0.001 TYR B 493 PHE 0.012 0.001 PHE D 148 TRP 0.028 0.002 TRP A 72 HIS 0.005 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (24612) covalent geometry : angle 0.56328 / 0.28 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03749 / 2.49 ( 1140) hydrogen bonds : angle 4.11200 / 2.91 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 0.977 Fit side-chains REVERT: A 308 LYS cc_start: 0.7705 (pttt) cc_final: 0.7310 (mttp) REVERT: A 349 ASN cc_start: 0.9023 (m-40) cc_final: 0.8732 (m110) REVERT: A 417 LEU cc_start: 0.9290 (mt) cc_final: 0.9045 (mp) REVERT: A 495 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 72 TRP cc_start: 0.8411 (m100) cc_final: 0.7945 (m100) REVERT: B 81 GLN cc_start: 0.8586 (mt0) cc_final: 0.7763 (mt0) REVERT: B 163 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: B 291 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 308 LYS cc_start: 0.7754 (pttt) cc_final: 0.7307 (mttp) REVERT: B 491 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7969 (mtm-85) REVERT: C 6 ASP cc_start: 0.7953 (t0) cc_final: 0.7539 (m-30) REVERT: C 72 TRP cc_start: 0.8458 (m100) cc_final: 0.7994 (m100) REVERT: C 81 GLN cc_start: 0.8551 (mt0) cc_final: 0.8273 (mt0) REVERT: C 84 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7913 (mp10) REVERT: C 140 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: C 308 LYS cc_start: 0.7762 (pttt) cc_final: 0.7289 (mttp) REVERT: C 338 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7835 (mtm-85) REVERT: C 495 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7875 (mt-10) REVERT: D 291 LEU cc_start: 0.9231 (tp) cc_final: 0.8955 (tt) REVERT: D 308 LYS cc_start: 0.7682 (pttt) cc_final: 0.7310 (mttp) REVERT: D 349 ASN cc_start: 0.9033 (m-40) cc_final: 0.8718 (m110) REVERT: D 417 LEU cc_start: 0.9289 (mt) cc_final: 0.9053 (mp) REVERT: D 495 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8021 (mt-10) REVERT: E 72 TRP cc_start: 0.8398 (m100) cc_final: 0.7921 (m100) REVERT: E 291 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8625 (tt) REVERT: E 308 LYS cc_start: 0.7764 (pttt) cc_final: 0.7375 (mttp) REVERT: E 411 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8590 (tpt) REVERT: E 491 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7951 (mtm-85) REVERT: F 6 ASP cc_start: 0.7947 (t0) cc_final: 0.7528 (m-30) REVERT: F 72 TRP cc_start: 0.8458 (m100) cc_final: 0.8000 (m100) REVERT: F 81 GLN cc_start: 0.8526 (mt0) cc_final: 0.8245 (mt0) REVERT: F 84 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7910 (mp10) REVERT: F 140 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: F 308 LYS cc_start: 0.7757 (pttt) cc_final: 0.7287 (mttp) REVERT: F 338 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7806 (mtm-85) REVERT: F 495 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7888 (mt-10) outliers start: 62 outliers final: 45 residues processed: 317 average time/residue: 0.1628 time to fit residues: 84.1724 Evaluate side-chains 318 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 411 MET Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 262 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 191 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 254 ASN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083205 restraints weight = 44701.623| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.33 r_work: 0.2978 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24612 Z= 0.208 Angle : 0.630 11.118 33390 Z= 0.312 Chirality : 0.046 0.220 3618 Planarity : 0.004 0.037 4242 Dihedral : 9.942 149.960 3480 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.76 % Allowed : 14.23 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2970 helix: 1.52 (0.14), residues: 1416 sheet: -1.33 (0.24), residues: 402 loop : -0.10 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 396 TYR 0.014 0.002 TYR F 78 PHE 0.026 0.002 PHE C 490 TRP 0.029 0.002 TRP A 72 HIS 0.007 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (24612) covalent geometry : angle 0.62982 / 0.31 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04108 / 2.74 ( 1140) hydrogen bonds : angle 4.25310 / 3.00 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 254 time to evaluate : 1.037 Fit side-chains REVERT: A 308 LYS cc_start: 0.7725 (pttt) cc_final: 0.7243 (mttp) REVERT: A 349 ASN cc_start: 0.9057 (m-40) cc_final: 0.8783 (m110) REVERT: A 372 TYR cc_start: 0.8633 (t80) cc_final: 0.8364 (t80) REVERT: A 417 LEU cc_start: 0.9293 (mt) cc_final: 0.9037 (mp) REVERT: A 495 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 72 TRP cc_start: 0.8469 (m100) cc_final: 0.8024 (m100) REVERT: B 81 GLN cc_start: 0.8665 (mt0) cc_final: 0.7936 (mt0) REVERT: B 163 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: B 291 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8649 (tt) REVERT: B 308 LYS cc_start: 0.7802 (pttt) cc_final: 0.7250 (mttp) REVERT: B 491 ARG cc_start: 0.8386 (mtp180) cc_final: 0.8047 (mtm-85) REVERT: C 6 ASP cc_start: 0.8011 (t0) cc_final: 0.7610 (m-30) REVERT: C 72 TRP cc_start: 0.8492 (m100) cc_final: 0.8085 (m100) REVERT: C 81 GLN cc_start: 0.8623 (mt0) cc_final: 0.8284 (mt0) REVERT: C 84 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7971 (mp10) REVERT: C 140 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: C 308 LYS cc_start: 0.7762 (pttt) cc_final: 0.7234 (mttp) REVERT: C 338 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7839 (mtm-85) REVERT: C 495 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7897 (mt-10) REVERT: D 308 LYS cc_start: 0.7735 (pttt) cc_final: 0.7253 (mttp) REVERT: D 417 LEU cc_start: 0.9291 (mt) cc_final: 0.9042 (mp) REVERT: E 72 TRP cc_start: 0.8454 (m100) cc_final: 0.7981 (m100) REVERT: E 291 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8608 (tt) REVERT: E 308 LYS cc_start: 0.7858 (pttt) cc_final: 0.7360 (mttp) REVERT: E 491 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8036 (mtm-85) REVERT: F 6 ASP cc_start: 0.8008 (t0) cc_final: 0.7629 (m-30) REVERT: F 72 TRP cc_start: 0.8500 (m100) cc_final: 0.8098 (m100) REVERT: F 81 GLN cc_start: 0.8613 (mt0) cc_final: 0.8283 (mt0) REVERT: F 84 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7977 (mp10) REVERT: F 140 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: F 308 LYS cc_start: 0.7766 (pttt) cc_final: 0.7234 (mttp) REVERT: F 338 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7813 (mtm-85) REVERT: F 495 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7888 (mt-10) outliers start: 69 outliers final: 57 residues processed: 308 average time/residue: 0.1611 time to fit residues: 81.1985 Evaluate side-chains 311 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 144 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086441 restraints weight = 44456.865| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.33 r_work: 0.3034 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24612 Z= 0.125 Angle : 0.575 11.878 33390 Z= 0.285 Chirality : 0.043 0.167 3618 Planarity : 0.004 0.038 4242 Dihedral : 9.636 148.173 3480 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.28 % Allowed : 15.11 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2970 helix: 1.73 (0.14), residues: 1416 sheet: -1.11 (0.25), residues: 402 loop : -0.07 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 261 TYR 0.008 0.001 TYR B 493 PHE 0.018 0.001 PHE C 490 TRP 0.032 0.002 TRP A 72 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (24612) covalent geometry : angle 0.57503 / 0.28 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03754 / 2.50 ( 1140) hydrogen bonds : angle 4.16101 / 2.94 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8695 (mmm) cc_final: 0.8430 (mmt) REVERT: A 308 LYS cc_start: 0.7704 (pttt) cc_final: 0.7325 (mttp) REVERT: A 349 ASN cc_start: 0.9043 (m-40) cc_final: 0.8761 (m110) REVERT: A 417 LEU cc_start: 0.9276 (mt) cc_final: 0.9033 (mp) REVERT: A 495 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 72 TRP cc_start: 0.8395 (m100) cc_final: 0.7941 (m100) REVERT: B 81 GLN cc_start: 0.8609 (mt0) cc_final: 0.7779 (mt0) REVERT: B 163 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: B 291 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 308 LYS cc_start: 0.7734 (pttt) cc_final: 0.7257 (mttp) REVERT: B 491 ARG cc_start: 0.8346 (mtp180) cc_final: 0.7975 (mtm-85) REVERT: C 72 TRP cc_start: 0.8437 (m100) cc_final: 0.7980 (m100) REVERT: C 81 GLN cc_start: 0.8567 (mt0) cc_final: 0.8212 (mt0) REVERT: C 84 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7928 (mp10) REVERT: C 140 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: C 308 LYS cc_start: 0.7775 (pttt) cc_final: 0.7295 (mttp) REVERT: C 338 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7852 (mtm-85) REVERT: C 495 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 176 MET cc_start: 0.8690 (mmm) cc_final: 0.8421 (mmt) REVERT: D 308 LYS cc_start: 0.7704 (pttt) cc_final: 0.7283 (mttp) REVERT: D 349 ASN cc_start: 0.9031 (m-40) cc_final: 0.8710 (m110) REVERT: D 417 LEU cc_start: 0.9283 (mt) cc_final: 0.9042 (mp) REVERT: E 72 TRP cc_start: 0.8398 (m100) cc_final: 0.7920 (m100) REVERT: E 291 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 308 LYS cc_start: 0.7634 (pttt) cc_final: 0.7336 (mttp) REVERT: E 398 THR cc_start: 0.8566 (p) cc_final: 0.8339 (p) REVERT: E 491 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7977 (mtm-85) REVERT: F 6 ASP cc_start: 0.7928 (t0) cc_final: 0.7541 (m-30) REVERT: F 72 TRP cc_start: 0.8452 (m100) cc_final: 0.8006 (m100) REVERT: F 81 GLN cc_start: 0.8549 (mt0) cc_final: 0.8187 (mt0) REVERT: F 84 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7901 (mp10) REVERT: F 140 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: F 308 LYS cc_start: 0.7758 (pttt) cc_final: 0.7286 (mttp) REVERT: F 338 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7787 (mtm-85) REVERT: F 495 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7769 (mt-10) outliers start: 57 outliers final: 49 residues processed: 319 average time/residue: 0.1592 time to fit residues: 83.4009 Evaluate side-chains 318 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 227 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 276 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085715 restraints weight = 44448.258| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.25 r_work: 0.3030 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24612 Z= 0.142 Angle : 0.587 11.950 33390 Z= 0.291 Chirality : 0.044 0.219 3618 Planarity : 0.004 0.039 4242 Dihedral : 9.552 146.291 3480 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.40 % Allowed : 14.71 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2970 helix: 1.72 (0.14), residues: 1416 sheet: -0.99 (0.25), residues: 402 loop : -0.02 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 19 TYR 0.011 0.001 TYR B 78 PHE 0.024 0.001 PHE F 490 TRP 0.034 0.002 TRP A 72 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (24612) covalent geometry : angle 0.58676 / 0.29 (33384) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03835 / 2.56 ( 1140) hydrogen bonds : angle 4.19914 / 2.96 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5036.25 seconds wall clock time: 88 minutes 0.80 seconds (5280.80 seconds total)