Starting phenix.real_space_refine on Fri Sep 19 05:57:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd4_6633/09_2025/3jd4_6633.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd4_6633/09_2025/3jd4_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_2025/3jd4_6633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2025/3jd4_6633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2025/3jd4_6633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd4_6633/09_2025/3jd4_6633.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-2.0-5805/lib/python3.9/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: 6.37, per 1000 atoms: 0.26 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.80 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: 4.68 Time building geometry restraints manager: 2.87 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: 14791 33.47 - 66.95: 293 66.95 - 100.42: 12 100.42 - 133.89: 6 133.89 - 167.37: 6 Dihedral angle restraints: 15108 sinusoidal: 6612 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 15105 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: 1.080 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: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.290 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 12.302 167.367 9684 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 aren 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 covalent geometry : bond 0.00892 (24612) covalent geometry : angle 0.96299 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.28335 ( 1140) hydrogen bonds : angle 10.17480 ( 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 : 0.968 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: 0.8354 (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: 0.8394 (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: 0.8303 (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: 0.8423 (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: 0.7915 (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: 0.2069 time to fit residues: 165.2453 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 : 0.966 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083296 restraints weight = 44854.200| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.29 r_work: 0.2978 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24612 Z= 0.219 Angle : 0.696 10.077 33390 Z= 0.352 Chirality : 0.048 0.198 3618 Planarity : 0.005 0.043 4242 Dihedral : 14.106 164.705 4080 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.28 % Allowed : 7.59 % Favored : 90.13 % 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 aren not related in a simple way. whole: -2.13 (0.15), residues: 2970 helix: -0.91 (0.12), residues: 1386 sheet: -2.72 (0.25), residues: 312 loop : -1.46 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 19 TYR 0.022 0.002 TYR F 78 PHE 0.022 0.002 PHE A 16 TRP 0.009 0.002 TRP B 281 HIS 0.008 0.002 HIS E 450 Details of bonding type rmsd covalent geometry : bond 0.00502 (24612) covalent geometry : angle 0.69610 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.05428 ( 1140) hydrogen bonds : angle 5.25182 ( 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 441 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 384 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8097 (t0) cc_final: 0.7514 (m-30) REVERT: A 33 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7576 (mtmt) REVERT: A 72 TRP cc_start: 0.8481 (m100) cc_final: 0.7203 (m100) REVERT: A 81 GLN cc_start: 0.8485 (mt0) cc_final: 0.8208 (mt0) REVERT: A 84 GLN cc_start: 0.8167 (mm110) cc_final: 0.7872 (mm-40) REVERT: A 181 ASP cc_start: 0.8660 (t70) cc_final: 0.8235 (t0) REVERT: A 308 LYS cc_start: 0.7637 (pttt) cc_final: 0.7005 (mttp) REVERT: A 495 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 6 ASP cc_start: 0.8124 (t0) cc_final: 0.7492 (m-30) REVERT: B 72 TRP cc_start: 0.8490 (m100) cc_final: 0.7165 (m100) REVERT: B 81 GLN cc_start: 0.8656 (mt0) cc_final: 0.7892 (mt0) REVERT: B 84 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7809 (mm-40) REVERT: B 163 ASP cc_start: 0.8349 (m-30) cc_final: 0.7361 (m-30) REVERT: B 181 ASP cc_start: 0.8718 (t70) cc_final: 0.8308 (t0) REVERT: B 308 LYS cc_start: 0.7870 (pttt) cc_final: 0.7191 (mttp) REVERT: B 384 GLU cc_start: 0.8725 (tt0) cc_final: 0.8398 (tt0) REVERT: B 495 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 6 ASP cc_start: 0.8203 (t0) cc_final: 0.7550 (m-30) REVERT: C 72 TRP cc_start: 0.8529 (m100) cc_final: 0.7996 (m100) REVERT: C 81 GLN cc_start: 0.8527 (mt0) cc_final: 0.8225 (mt0) REVERT: C 308 LYS cc_start: 0.7798 (pttt) cc_final: 0.7101 (mttp) REVERT: C 372 TYR cc_start: 0.8645 (t80) cc_final: 0.8266 (t80) REVERT: C 457 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8308 (mtm) REVERT: C 495 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 6 ASP cc_start: 0.8071 (t0) cc_final: 0.7463 (m-30) REVERT: D 33 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7608 (mtmt) REVERT: D 72 TRP cc_start: 0.8489 (m100) cc_final: 0.7190 (m100) REVERT: D 81 GLN cc_start: 0.8486 (mt0) cc_final: 0.8201 (mt0) REVERT: D 181 ASP cc_start: 0.8679 (t70) cc_final: 0.8250 (t0) REVERT: D 308 LYS cc_start: 0.7690 (pttt) cc_final: 0.7045 (mttp) REVERT: D 495 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7989 (mt-10) REVERT: E 6 ASP cc_start: 0.8120 (t0) cc_final: 0.7492 (m-30) REVERT: E 72 TRP cc_start: 0.8465 (m100) cc_final: 0.7140 (m100) REVERT: E 81 GLN cc_start: 0.8434 (mt0) cc_final: 0.8210 (mt0) REVERT: E 84 GLN cc_start: 0.8037 (mm110) cc_final: 0.7771 (mm-40) REVERT: E 181 ASP cc_start: 0.8711 (t70) cc_final: 0.8308 (t0) REVERT: E 308 LYS cc_start: 0.7868 (pttt) cc_final: 0.7190 (mttp) REVERT: E 384 GLU cc_start: 0.8730 (tt0) cc_final: 0.8404 (tt0) REVERT: E 495 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8217 (mt-10) REVERT: F 6 ASP cc_start: 0.8200 (t0) cc_final: 0.7539 (m-30) REVERT: F 72 TRP cc_start: 0.8534 (m100) cc_final: 0.8008 (m100) REVERT: F 81 GLN cc_start: 0.8532 (mt0) cc_final: 0.8219 (mt0) REVERT: F 308 LYS cc_start: 0.7793 (pttt) cc_final: 0.7099 (mttp) REVERT: F 372 TYR cc_start: 0.8651 (t80) cc_final: 0.8275 (t80) REVERT: F 457 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (mtm) REVERT: F 495 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8119 (mt-10) outliers start: 57 outliers final: 42 residues processed: 431 average time/residue: 0.1711 time to fit residues: 117.0491 Evaluate side-chains 327 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 23 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 277 optimal weight: 0.0030 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 198 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 266 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 189 HIS ** A 330 GLN ** 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** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084374 restraints weight = 44791.801| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.24 r_work: 0.2984 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24612 Z= 0.184 Angle : 0.624 8.715 33390 Z= 0.315 Chirality : 0.047 0.208 3618 Planarity : 0.004 0.040 4242 Dihedral : 13.244 162.391 4080 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.56 % Allowed : 8.99 % Favored : 87.45 % 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 aren not related in a simple way. whole: -0.81 (0.16), residues: 2970 helix: 0.24 (0.13), residues: 1422 sheet: -2.29 (0.23), residues: 372 loop : -0.73 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 86 TYR 0.016 0.002 TYR F 78 PHE 0.017 0.002 PHE C 122 TRP 0.014 0.002 TRP A 72 HIS 0.007 0.002 HIS E 450 Details of bonding type rmsd covalent geometry : bond 0.00423 (24612) covalent geometry : angle 0.62415 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.04680 ( 1140) hydrogen bonds : angle 4.69905 ( 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 402 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 313 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8081 (t0) cc_final: 0.7447 (m-30) REVERT: A 84 GLN cc_start: 0.8096 (mm110) cc_final: 0.7836 (mm-40) REVERT: A 181 ASP cc_start: 0.8705 (t70) cc_final: 0.8295 (t0) REVERT: A 308 LYS cc_start: 0.7715 (pttt) cc_final: 0.7111 (mttp) REVERT: B 6 ASP cc_start: 0.8062 (t0) cc_final: 0.7413 (m-30) REVERT: B 14 GLU cc_start: 0.7880 (pt0) cc_final: 0.7359 (pt0) REVERT: B 72 TRP cc_start: 0.8400 (m100) cc_final: 0.8069 (m100) REVERT: B 81 GLN cc_start: 0.8646 (mt0) cc_final: 0.7869 (mt0) REVERT: B 84 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7959 (mp10) REVERT: B 163 ASP cc_start: 0.8323 (m-30) cc_final: 0.7291 (m-30) REVERT: B 181 ASP cc_start: 0.8733 (t70) cc_final: 0.8338 (t0) REVERT: B 308 LYS cc_start: 0.7887 (pttt) cc_final: 0.7286 (mttp) REVERT: B 384 GLU cc_start: 0.8693 (tt0) cc_final: 0.8455 (tt0) REVERT: C 6 ASP cc_start: 0.8113 (t0) cc_final: 0.7471 (m-30) REVERT: C 72 TRP cc_start: 0.8535 (m100) cc_final: 0.8027 (m100) REVERT: C 81 GLN cc_start: 0.8504 (mt0) cc_final: 0.8216 (mt0) REVERT: C 90 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8343 (tttm) REVERT: C 308 LYS cc_start: 0.7798 (pttt) cc_final: 0.7149 (mttp) REVERT: C 372 TYR cc_start: 0.8607 (t80) cc_final: 0.8247 (t80) REVERT: C 457 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8174 (mtm) REVERT: C 495 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8066 (mt-10) REVERT: D 6 ASP cc_start: 0.8048 (t0) cc_final: 0.7419 (m-30) REVERT: D 33 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7551 (mtmt) REVERT: D 81 GLN cc_start: 0.8503 (mt0) cc_final: 0.8285 (mt0) REVERT: D 181 ASP cc_start: 0.8699 (t70) cc_final: 0.8284 (t0) REVERT: D 289 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8200 (pttt) REVERT: D 308 LYS cc_start: 0.7717 (pttt) cc_final: 0.7124 (mttp) REVERT: E 6 ASP cc_start: 0.8068 (t0) cc_final: 0.7419 (m-30) REVERT: E 14 GLU cc_start: 0.7883 (pt0) cc_final: 0.7363 (pt0) REVERT: E 72 TRP cc_start: 0.8403 (m100) cc_final: 0.8105 (m100) REVERT: E 181 ASP cc_start: 0.8754 (t70) cc_final: 0.8367 (t0) REVERT: E 308 LYS cc_start: 0.7881 (pttt) cc_final: 0.7276 (mttp) REVERT: E 384 GLU cc_start: 0.8708 (tt0) cc_final: 0.8487 (tt0) REVERT: F 6 ASP cc_start: 0.8125 (t0) cc_final: 0.7475 (m-30) REVERT: F 72 TRP cc_start: 0.8544 (m100) cc_final: 0.8033 (m100) REVERT: F 81 GLN cc_start: 0.8512 (mt0) cc_final: 0.8230 (mt0) REVERT: F 90 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8348 (tttm) REVERT: F 158 ILE cc_start: 0.9345 (mt) cc_final: 0.9144 (tt) REVERT: F 308 LYS cc_start: 0.7800 (pttt) cc_final: 0.7144 (mttp) REVERT: F 372 TYR cc_start: 0.8614 (t80) cc_final: 0.8256 (t80) REVERT: F 457 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (mtm) REVERT: F 495 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8065 (mt-10) outliers start: 89 outliers final: 63 residues processed: 379 average time/residue: 0.1574 time to fit residues: 97.6674 Evaluate side-chains 338 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 361 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 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 B residue 448 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 137 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 448 ILE Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 158 ILE 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 90 LYS 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: 7.9990 chunk 265 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 HIS ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083151 restraints weight = 44498.976| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.32 r_work: 0.2966 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24612 Z= 0.211 Angle : 0.624 9.132 33390 Z= 0.312 Chirality : 0.046 0.165 3618 Planarity : 0.004 0.038 4242 Dihedral : 12.922 159.556 4080 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.36 % Allowed : 9.43 % Favored : 86.21 % 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 aren not related in a simple way. whole: -0.29 (0.16), residues: 2970 helix: 0.73 (0.14), residues: 1410 sheet: -1.96 (0.24), residues: 372 loop : -0.58 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 396 TYR 0.017 0.002 TYR C 78 PHE 0.018 0.002 PHE D 122 TRP 0.026 0.002 TRP D 72 HIS 0.007 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00487 (24612) covalent geometry : angle 0.62381 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.04444 ( 1140) hydrogen bonds : angle 4.48518 ( 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 412 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 303 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8226 (mm110) cc_final: 0.7982 (mp10) REVERT: A 181 ASP cc_start: 0.8731 (t70) cc_final: 0.8301 (t0) REVERT: A 308 LYS cc_start: 0.7724 (pttt) cc_final: 0.7117 (mttp) REVERT: B 6 ASP cc_start: 0.8069 (t0) cc_final: 0.7467 (m-30) REVERT: B 14 GLU cc_start: 0.7980 (pt0) cc_final: 0.7452 (pt0) REVERT: B 81 GLN cc_start: 0.8693 (mt0) cc_final: 0.7969 (mt0) REVERT: B 84 GLN cc_start: 0.8232 (mm-40) cc_final: 0.8028 (mp10) REVERT: B 163 ASP cc_start: 0.8381 (m-30) cc_final: 0.7433 (m-30) REVERT: B 181 ASP cc_start: 0.8767 (t70) cc_final: 0.8369 (t0) REVERT: B 308 LYS cc_start: 0.7836 (pttt) cc_final: 0.7250 (mttp) REVERT: B 417 LEU cc_start: 0.9276 (mt) cc_final: 0.9042 (mp) REVERT: B 491 ARG cc_start: 0.8379 (mtp180) cc_final: 0.8066 (mtm-85) REVERT: C 6 ASP cc_start: 0.8133 (t0) cc_final: 0.7649 (m-30) REVERT: C 72 TRP cc_start: 0.8501 (m100) cc_final: 0.8029 (m100) REVERT: C 81 GLN cc_start: 0.8607 (mt0) cc_final: 0.8250 (mt0) REVERT: C 140 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: C 291 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8825 (tt) REVERT: C 308 LYS cc_start: 0.7816 (pttt) cc_final: 0.7157 (mttp) REVERT: C 417 LEU cc_start: 0.9257 (mt) cc_final: 0.9023 (mp) REVERT: D 33 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7589 (mtmt) REVERT: D 81 GLN cc_start: 0.8582 (mt0) cc_final: 0.8343 (mt0) REVERT: D 181 ASP cc_start: 0.8729 (t70) cc_final: 0.8296 (t0) REVERT: D 289 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8221 (pttt) REVERT: D 308 LYS cc_start: 0.7748 (pttt) cc_final: 0.7151 (mttp) REVERT: D 417 LEU cc_start: 0.9297 (mt) cc_final: 0.9049 (mp) REVERT: D 495 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8103 (mt-10) REVERT: E 6 ASP cc_start: 0.8054 (t0) cc_final: 0.7461 (m-30) REVERT: E 14 GLU cc_start: 0.7986 (pt0) cc_final: 0.7539 (pt0) REVERT: E 163 ASP cc_start: 0.8439 (m-30) cc_final: 0.8228 (m-30) REVERT: E 181 ASP cc_start: 0.8776 (t70) cc_final: 0.8384 (t0) REVERT: E 308 LYS cc_start: 0.7841 (pttt) cc_final: 0.7254 (mttp) REVERT: E 417 LEU cc_start: 0.9277 (mt) cc_final: 0.9038 (mp) REVERT: E 491 ARG cc_start: 0.8385 (mtp180) cc_final: 0.8077 (mtm-85) REVERT: F 6 ASP cc_start: 0.8148 (t0) cc_final: 0.7653 (m-30) REVERT: F 72 TRP cc_start: 0.8507 (m100) cc_final: 0.8041 (m100) REVERT: F 81 GLN cc_start: 0.8612 (mt0) cc_final: 0.8277 (mt0) REVERT: F 84 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7867 (mp10) REVERT: F 140 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: F 291 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8845 (tt) REVERT: F 308 LYS cc_start: 0.7795 (pttt) cc_final: 0.7127 (mttp) outliers start: 109 outliers final: 80 residues processed: 381 average time/residue: 0.1688 time to fit residues: 102.9878 Evaluate side-chains 353 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 269 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 411 MET 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 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 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 C residue 448 ILE 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 103 GLU 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 411 MET Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain F residue 24 VAL 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: 6.9990 chunk 293 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN ** F 330 GLN ** 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 = 0.3544 r_free = 0.3544 target = 0.108407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082927 restraints weight = 44439.631| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.25 r_work: 0.2970 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24612 Z= 0.216 Angle : 0.619 9.013 33390 Z= 0.308 Chirality : 0.046 0.162 3618 Planarity : 0.004 0.038 4242 Dihedral : 12.753 157.615 4080 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.20 % Allowed : 10.35 % 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 aren not related in a simple way. whole: -0.12 (0.16), residues: 2970 helix: 0.91 (0.14), residues: 1410 sheet: -1.65 (0.24), residues: 402 loop : -0.57 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.002 TYR F 78 PHE 0.016 0.002 PHE D 122 TRP 0.029 0.002 TRP A 72 HIS 0.007 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00497 (24612) covalent geometry : angle 0.61861 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.04387 ( 1140) hydrogen bonds : angle 4.39986 ( 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 393 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 288 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8285 (mm110) cc_final: 0.8031 (mp10) REVERT: A 181 ASP cc_start: 0.8719 (t70) cc_final: 0.8288 (t0) REVERT: A 291 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8809 (tt) REVERT: A 308 LYS cc_start: 0.7744 (pttt) cc_final: 0.7129 (mttp) REVERT: A 372 TYR cc_start: 0.8616 (t80) cc_final: 0.8369 (t80) REVERT: A 495 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 6 ASP cc_start: 0.8069 (t0) cc_final: 0.7616 (m-30) REVERT: B 14 GLU cc_start: 0.7983 (pt0) cc_final: 0.7451 (pt0) REVERT: B 81 GLN cc_start: 0.8683 (mt0) cc_final: 0.7905 (mt0) REVERT: B 84 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8007 (mp10) REVERT: B 163 ASP cc_start: 0.8299 (m-30) cc_final: 0.7315 (m-30) REVERT: B 181 ASP cc_start: 0.8756 (t70) cc_final: 0.8359 (t0) REVERT: B 308 LYS cc_start: 0.7833 (pttt) cc_final: 0.7281 (mttp) REVERT: B 417 LEU cc_start: 0.9277 (mt) cc_final: 0.9040 (mp) REVERT: B 491 ARG cc_start: 0.8346 (mtp180) cc_final: 0.8020 (mtm-85) REVERT: C 6 ASP cc_start: 0.8098 (t0) cc_final: 0.7676 (m-30) REVERT: C 72 TRP cc_start: 0.8487 (m100) cc_final: 0.8095 (m100) REVERT: C 81 GLN cc_start: 0.8596 (mt0) cc_final: 0.8285 (mt0) REVERT: C 84 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7932 (mp10) REVERT: C 140 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: C 291 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8814 (tt) REVERT: C 308 LYS cc_start: 0.7796 (pttt) cc_final: 0.7143 (mttp) REVERT: C 417 LEU cc_start: 0.9262 (mt) cc_final: 0.9037 (mp) REVERT: D 33 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7496 (mtmt) REVERT: D 81 GLN cc_start: 0.8463 (mt0) cc_final: 0.8233 (mt0) REVERT: D 181 ASP cc_start: 0.8731 (t70) cc_final: 0.8292 (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: 0.9034 (mp) REVERT: E 6 ASP cc_start: 0.8074 (t0) cc_final: 0.7620 (m-30) REVERT: E 14 GLU cc_start: 0.8029 (pt0) cc_final: 0.7565 (pt0) REVERT: E 81 GLN cc_start: 0.8551 (mt0) cc_final: 0.8159 (mt0) REVERT: E 163 ASP cc_start: 0.8376 (m-30) cc_final: 0.7594 (m-30) REVERT: E 181 ASP cc_start: 0.8774 (t70) cc_final: 0.8383 (t0) REVERT: E 308 LYS cc_start: 0.7850 (pttt) cc_final: 0.7283 (mttp) REVERT: E 417 LEU cc_start: 0.9275 (mt) cc_final: 0.9026 (mp) REVERT: E 491 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8036 (mtm-85) REVERT: F 6 ASP cc_start: 0.8100 (t0) cc_final: 0.7689 (m-30) REVERT: F 72 TRP cc_start: 0.8483 (m100) cc_final: 0.8056 (m100) REVERT: F 81 GLN cc_start: 0.8599 (mt0) cc_final: 0.8285 (mt0) REVERT: F 140 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: F 291 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8824 (tt) REVERT: F 308 LYS cc_start: 0.7801 (pttt) cc_final: 0.7147 (mttp) outliers start: 105 outliers final: 79 residues processed: 367 average time/residue: 0.1612 time to fit residues: 94.7418 Evaluate side-chains 349 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 265 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 291 LEU 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 B residue 24 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 239 THR 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 B residue 448 ILE 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 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 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 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 162 VAL 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 E residue 24 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 87 THR 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 24 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 201 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 224 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087026 restraints weight = 44278.394| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.33 r_work: 0.3041 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24612 Z= 0.107 Angle : 0.539 8.632 33390 Z= 0.269 Chirality : 0.043 0.149 3618 Planarity : 0.004 0.039 4242 Dihedral : 12.274 155.464 4080 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.60 % Allowed : 12.55 % Favored : 84.85 % 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 aren not related in a simple way. whole: 0.42 (0.16), residues: 2970 helix: 1.32 (0.14), residues: 1416 sheet: -1.36 (0.25), residues: 390 loop : -0.30 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.010 0.001 TYR C 401 PHE 0.016 0.001 PHE D 9 TRP 0.027 0.002 TRP D 72 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00239 (24612) covalent geometry : angle 0.53892 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03716 ( 1140) hydrogen bonds : angle 4.14461 ( 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 390 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8245 (mm110) cc_final: 0.8016 (mp10) REVERT: A 150 MET cc_start: 0.8557 (tpp) cc_final: 0.8290 (mpp) REVERT: A 181 ASP cc_start: 0.8653 (t70) cc_final: 0.8444 (t0) REVERT: A 308 LYS cc_start: 0.7672 (pttt) cc_final: 0.7268 (mttp) REVERT: A 495 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 14 GLU cc_start: 0.7950 (pt0) cc_final: 0.7579 (pt0) REVERT: B 72 TRP cc_start: 0.8452 (m100) cc_final: 0.7905 (m100) REVERT: B 81 GLN cc_start: 0.8629 (mt0) cc_final: 0.7831 (mt0) REVERT: B 84 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7938 (mp10) REVERT: B 163 ASP cc_start: 0.8300 (m-30) cc_final: 0.7287 (m-30) REVERT: B 181 ASP cc_start: 0.8689 (t70) cc_final: 0.8300 (t0) REVERT: B 291 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8741 (tt) REVERT: B 308 LYS cc_start: 0.7800 (pttt) cc_final: 0.7414 (mttp) REVERT: B 491 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7909 (mtm-85) REVERT: C 72 TRP cc_start: 0.8432 (m100) cc_final: 0.7958 (m100) REVERT: C 81 GLN cc_start: 0.8505 (mt0) cc_final: 0.8238 (mt0) REVERT: C 84 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7868 (mp10) REVERT: C 308 LYS cc_start: 0.7761 (pttt) cc_final: 0.7310 (mttp) REVERT: C 495 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7852 (mt-10) REVERT: D 84 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7816 (mp10) REVERT: D 150 MET cc_start: 0.8571 (tpp) cc_final: 0.8306 (mpp) REVERT: D 181 ASP cc_start: 0.8662 (t70) cc_final: 0.8462 (t0) REVERT: D 242 PHE cc_start: 0.7664 (m-80) cc_final: 0.7454 (m-80) REVERT: D 308 LYS cc_start: 0.7676 (pttt) cc_final: 0.7302 (mttp) REVERT: E 14 GLU cc_start: 0.7998 (pt0) cc_final: 0.7645 (pt0) REVERT: E 72 TRP cc_start: 0.8445 (m100) cc_final: 0.7891 (m100) REVERT: E 81 GLN cc_start: 0.8489 (mt0) cc_final: 0.8061 (mt0) REVERT: E 163 ASP cc_start: 0.8427 (m-30) cc_final: 0.7546 (m-30) REVERT: E 181 ASP cc_start: 0.8706 (t70) cc_final: 0.8307 (t0) REVERT: E 291 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (tt) REVERT: E 308 LYS cc_start: 0.7819 (pttt) cc_final: 0.7425 (mttp) REVERT: E 411 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8585 (tpt) REVERT: E 491 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7930 (mtm-85) REVERT: F 6 ASP cc_start: 0.8006 (t0) cc_final: 0.7622 (m-30) REVERT: F 72 TRP cc_start: 0.8428 (m100) cc_final: 0.7954 (m100) REVERT: F 81 GLN cc_start: 0.8503 (mt0) cc_final: 0.8298 (mt0) REVERT: F 84 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7745 (mp10) REVERT: F 308 LYS cc_start: 0.7755 (pttt) cc_final: 0.7299 (mttp) REVERT: F 417 LEU cc_start: 0.9249 (mt) cc_final: 0.9048 (mp) outliers start: 65 outliers final: 45 residues processed: 371 average time/residue: 0.1556 time to fit residues: 93.2550 Evaluate side-chains 323 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 32 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 322 LEU 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 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 162 VAL 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 32 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 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 411 MET 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 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: 0.5980 chunk 227 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 207 optimal weight: 0.0030 chunk 61 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 34 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 overall best weight: 2.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 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 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 = 0.111388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086011 restraints weight = 44410.936| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.27 r_work: 0.3025 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24612 Z= 0.131 Angle : 0.557 8.899 33390 Z= 0.277 Chirality : 0.043 0.135 3618 Planarity : 0.004 0.039 4242 Dihedral : 11.916 152.842 4080 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.92 % Allowed : 14.03 % Favored : 83.05 % 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 aren not related in a simple way. whole: 0.63 (0.16), residues: 2970 helix: 1.44 (0.14), residues: 1386 sheet: -1.23 (0.25), residues: 390 loop : -0.09 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 261 TYR 0.009 0.001 TYR A 493 PHE 0.013 0.001 PHE D 148 TRP 0.025 0.002 TRP D 72 HIS 0.005 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00302 (24612) covalent geometry : angle 0.55701 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03795 ( 1140) hydrogen bonds : angle 4.13132 ( 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 369 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 296 time to evaluate : 0.835 Fit side-chains REVERT: A 84 GLN cc_start: 0.8233 (mm110) cc_final: 0.7957 (mp10) REVERT: A 308 LYS cc_start: 0.7678 (pttt) cc_final: 0.7289 (mttp) REVERT: A 495 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 72 TRP cc_start: 0.8470 (m100) cc_final: 0.7969 (m100) REVERT: B 81 GLN cc_start: 0.8629 (mt0) cc_final: 0.7795 (mt0) REVERT: B 84 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7946 (mp10) REVERT: B 163 ASP cc_start: 0.8296 (m-30) cc_final: 0.7270 (m-30) REVERT: B 181 ASP cc_start: 0.8713 (t70) cc_final: 0.8312 (t0) REVERT: B 291 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8738 (tt) REVERT: B 308 LYS cc_start: 0.7803 (pttt) cc_final: 0.7420 (mttp) REVERT: B 491 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7929 (mtm-85) REVERT: C 6 ASP cc_start: 0.7958 (t0) cc_final: 0.7547 (m-30) REVERT: C 72 TRP cc_start: 0.8477 (m100) cc_final: 0.8062 (m100) REVERT: C 81 GLN cc_start: 0.8548 (mt0) cc_final: 0.8274 (mt0) REVERT: C 84 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7887 (mp10) REVERT: C 140 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: C 308 LYS cc_start: 0.7766 (pttt) cc_final: 0.7318 (mttp) REVERT: D 84 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7839 (mp10) REVERT: D 308 LYS cc_start: 0.7715 (pttt) cc_final: 0.7321 (mttp) REVERT: D 495 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8049 (mt-10) REVERT: E 72 TRP cc_start: 0.8453 (m100) cc_final: 0.7958 (m100) REVERT: E 81 GLN cc_start: 0.8526 (mt0) cc_final: 0.8032 (mt0) REVERT: E 163 ASP cc_start: 0.8400 (m-30) cc_final: 0.7508 (m-30) REVERT: E 291 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8783 (tt) REVERT: E 294 PHE cc_start: 0.6786 (m-10) cc_final: 0.6339 (m-80) REVERT: E 308 LYS cc_start: 0.7816 (pttt) cc_final: 0.7424 (mttp) REVERT: E 411 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8625 (tpt) REVERT: E 491 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7925 (mtm-85) REVERT: F 6 ASP cc_start: 0.7986 (t0) cc_final: 0.7563 (m-30) REVERT: F 72 TRP cc_start: 0.8475 (m100) cc_final: 0.8064 (m100) REVERT: F 81 GLN cc_start: 0.8537 (mt0) cc_final: 0.8283 (mt0) REVERT: F 84 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7790 (mp10) REVERT: F 140 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: F 308 LYS cc_start: 0.7774 (pttt) cc_final: 0.7311 (mttp) REVERT: F 495 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7894 (mt-10) outliers start: 73 outliers final: 53 residues processed: 346 average time/residue: 0.1544 time to fit residues: 87.1772 Evaluate side-chains 325 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 162 VAL Chi-restraints excluded: chain A residue 239 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 32 LEU 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 291 LEU Chi-restraints excluded: chain B residue 322 LEU 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 162 VAL 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 322 LEU Chi-restraints excluded: chain C residue 413 VAL 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 239 THR 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 32 LEU Chi-restraints excluded: chain E residue 97 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 291 LEU Chi-restraints excluded: chain E residue 322 LEU 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 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET 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 427 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 188 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 242 optimal weight: 0.0770 chunk 177 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 56 ASN ** 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 56 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085994 restraints weight = 44442.746| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.27 r_work: 0.3023 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24612 Z= 0.137 Angle : 0.567 11.731 33390 Z= 0.280 Chirality : 0.044 0.154 3618 Planarity : 0.004 0.040 4242 Dihedral : 11.376 151.030 4080 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.68 % Allowed : 14.43 % 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 aren not related in a simple way. whole: 0.74 (0.16), residues: 2970 helix: 1.56 (0.14), residues: 1386 sheet: -1.20 (0.25), residues: 390 loop : -0.06 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.008 0.001 TYR B 372 PHE 0.012 0.001 PHE B 122 TRP 0.026 0.002 TRP A 72 HIS 0.010 0.001 HIS E 298 Details of bonding type rmsd covalent geometry : bond 0.00316 (24612) covalent geometry : angle 0.56684 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03779 ( 1140) hydrogen bonds : angle 4.14984 ( 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 344 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 0.956 Fit side-chains REVERT: A 84 GLN cc_start: 0.8180 (mm110) cc_final: 0.7960 (mp10) REVERT: A 308 LYS cc_start: 0.7708 (pttt) cc_final: 0.7313 (mttp) REVERT: A 372 TYR cc_start: 0.8592 (t80) cc_final: 0.8306 (t80) REVERT: A 495 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 72 TRP cc_start: 0.8447 (m100) cc_final: 0.7968 (m100) REVERT: B 81 GLN cc_start: 0.8637 (mt0) cc_final: 0.7852 (mt0) REVERT: B 84 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7967 (mp10) REVERT: B 163 ASP cc_start: 0.8303 (m-30) cc_final: 0.7318 (m-30) REVERT: B 181 ASP cc_start: 0.8700 (t70) cc_final: 0.8234 (t0) REVERT: B 291 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 300 THR cc_start: 0.8535 (t) cc_final: 0.8333 (m) REVERT: B 308 LYS cc_start: 0.7804 (pttt) cc_final: 0.7415 (mttp) REVERT: B 491 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7921 (mtm-85) REVERT: C 6 ASP cc_start: 0.7996 (t0) cc_final: 0.7572 (m-30) REVERT: C 72 TRP cc_start: 0.8481 (m100) cc_final: 0.8076 (m100) REVERT: C 81 GLN cc_start: 0.8553 (mt0) cc_final: 0.8264 (mt0) REVERT: C 84 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7887 (mp10) REVERT: C 90 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8426 (tttm) REVERT: C 140 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: C 308 LYS cc_start: 0.7761 (pttt) cc_final: 0.7284 (mttp) REVERT: C 495 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7842 (mt-10) REVERT: D 308 LYS cc_start: 0.7686 (pttt) cc_final: 0.7307 (mttp) REVERT: D 495 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8019 (mt-10) REVERT: E 72 TRP cc_start: 0.8429 (m100) cc_final: 0.7948 (m100) REVERT: E 81 GLN cc_start: 0.8553 (mt0) cc_final: 0.7984 (mt0) REVERT: E 163 ASP cc_start: 0.8363 (m-30) cc_final: 0.7470 (m-30) REVERT: E 291 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8799 (tt) REVERT: E 294 PHE cc_start: 0.6572 (m-10) cc_final: 0.6362 (m-80) REVERT: E 308 LYS cc_start: 0.7800 (pttt) cc_final: 0.7410 (mttp) REVERT: E 411 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8573 (tpt) REVERT: E 491 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7959 (mtm-85) REVERT: F 6 ASP cc_start: 0.7996 (t0) cc_final: 0.7576 (m-30) REVERT: F 72 TRP cc_start: 0.8476 (m100) cc_final: 0.8077 (m100) REVERT: F 81 GLN cc_start: 0.8559 (mt0) cc_final: 0.8307 (mt0) REVERT: F 84 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7826 (mp10) REVERT: F 90 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8423 (tttm) REVERT: F 140 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: F 308 LYS cc_start: 0.7750 (pttt) cc_final: 0.7263 (mttp) REVERT: F 495 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7836 (mt-10) outliers start: 67 outliers final: 53 residues processed: 323 average time/residue: 0.1465 time to fit residues: 77.9300 Evaluate side-chains 326 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 162 VAL 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 322 LEU 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 87 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE 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 322 LEU 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 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 322 LEU 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 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 158 ILE 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 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 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 322 LEU Chi-restraints excluded: chain F residue 413 VAL 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: 8.9990 chunk 131 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 217 optimal weight: 6.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 C 254 ASN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN ** 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 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 = 0.3568 r_free = 0.3568 target = 0.110071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084451 restraints weight = 44454.291| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.26 r_work: 0.2995 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24612 Z= 0.175 Angle : 0.601 12.946 33390 Z= 0.297 Chirality : 0.045 0.156 3618 Planarity : 0.004 0.040 4242 Dihedral : 11.216 149.501 4080 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.72 % Allowed : 14.39 % 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 aren not related in a simple way. whole: 0.72 (0.16), residues: 2970 helix: 1.56 (0.14), residues: 1380 sheet: -1.16 (0.25), residues: 402 loop : -0.09 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.013 0.001 TYR E 493 PHE 0.014 0.001 PHE B 122 TRP 0.029 0.002 TRP D 72 HIS 0.005 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00406 (24612) covalent geometry : angle 0.60103 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03998 ( 1140) hydrogen bonds : angle 4.23931 ( 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 331 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8214 (mm110) cc_final: 0.7996 (mp10) REVERT: A 169 MET cc_start: 0.8907 (ttm) cc_final: 0.8466 (mtm) REVERT: A 308 LYS cc_start: 0.7695 (pttt) cc_final: 0.7269 (mttp) REVERT: A 372 TYR cc_start: 0.8616 (t80) cc_final: 0.8335 (t80) REVERT: A 495 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 72 TRP cc_start: 0.8429 (m100) cc_final: 0.7967 (m100) REVERT: B 81 GLN cc_start: 0.8668 (mt0) cc_final: 0.7938 (mt0) REVERT: B 84 GLN cc_start: 0.8230 (mm-40) cc_final: 0.8003 (mp10) REVERT: B 163 ASP cc_start: 0.8293 (m-30) cc_final: 0.7323 (m-30) REVERT: B 181 ASP cc_start: 0.8696 (t70) cc_final: 0.8288 (t0) REVERT: B 291 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8699 (tt) REVERT: B 300 THR cc_start: 0.8507 (t) cc_final: 0.8283 (m) REVERT: B 308 LYS cc_start: 0.7830 (pttt) cc_final: 0.7387 (mttp) REVERT: B 417 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8970 (mm) REVERT: B 491 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8004 (mtm-85) REVERT: C 6 ASP cc_start: 0.8036 (t0) cc_final: 0.7616 (m-30) REVERT: C 72 TRP cc_start: 0.8489 (m100) cc_final: 0.8089 (m100) REVERT: C 81 GLN cc_start: 0.8600 (mt0) cc_final: 0.8286 (mt0) REVERT: C 84 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7920 (mp10) REVERT: C 90 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8446 (tttm) REVERT: C 140 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 308 LYS cc_start: 0.7812 (pttt) cc_final: 0.7296 (mttp) REVERT: D 308 LYS cc_start: 0.7732 (pttt) cc_final: 0.7273 (mttp) REVERT: D 495 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8032 (mt-10) REVERT: E 72 TRP cc_start: 0.8427 (m100) cc_final: 0.8023 (m100) REVERT: E 81 GLN cc_start: 0.8593 (mt0) cc_final: 0.8011 (mt0) REVERT: E 163 ASP cc_start: 0.8367 (m-30) cc_final: 0.7487 (m-30) REVERT: E 308 LYS cc_start: 0.7857 (pttt) cc_final: 0.7407 (mttp) REVERT: E 417 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8957 (mm) REVERT: E 491 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8020 (mtm-85) REVERT: F 6 ASP cc_start: 0.8053 (t0) cc_final: 0.7626 (m-30) REVERT: F 72 TRP cc_start: 0.8490 (m100) cc_final: 0.8097 (m100) REVERT: F 81 GLN cc_start: 0.8598 (mt0) cc_final: 0.8313 (mt0) REVERT: F 84 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7860 (mp10) REVERT: F 140 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: F 308 LYS cc_start: 0.7803 (pttt) cc_final: 0.7287 (mttp) outliers start: 68 outliers final: 56 residues processed: 317 average time/residue: 0.1478 time to fit residues: 77.5688 Evaluate side-chains 322 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 277 ASP 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 32 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE 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 322 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 417 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 162 VAL 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 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 162 VAL 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 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 158 ILE 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 322 LEU Chi-restraints excluded: chain E residue 417 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 162 VAL 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 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: 6.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 144 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 289 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087226 restraints weight = 44314.995| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.32 r_work: 0.3043 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24612 Z= 0.113 Angle : 0.562 12.706 33390 Z= 0.278 Chirality : 0.043 0.160 3618 Planarity : 0.004 0.044 4242 Dihedral : 10.844 147.291 4080 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.24 % Allowed : 14.99 % Favored : 82.77 % 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 aren not related in a simple way. whole: 0.90 (0.16), residues: 2970 helix: 1.70 (0.14), residues: 1386 sheet: -0.96 (0.25), residues: 390 loop : -0.07 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 19 TYR 0.008 0.001 TYR A 401 PHE 0.015 0.001 PHE C 63 TRP 0.030 0.002 TRP D 72 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00257 (24612) covalent geometry : angle 0.56198 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03695 ( 1140) hydrogen bonds : angle 4.15655 ( 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 352 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.950 Fit side-chains REVERT: A 84 GLN cc_start: 0.8193 (mm110) cc_final: 0.7964 (mp10) REVERT: A 169 MET cc_start: 0.8827 (ttm) cc_final: 0.8374 (mtm) REVERT: A 308 LYS cc_start: 0.7663 (pttt) cc_final: 0.7321 (mttp) REVERT: A 495 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 72 TRP cc_start: 0.8393 (m100) cc_final: 0.7921 (m100) REVERT: B 81 GLN cc_start: 0.8621 (mt0) cc_final: 0.7811 (mt0) REVERT: B 84 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7929 (mp10) REVERT: B 163 ASP cc_start: 0.8305 (m-30) cc_final: 0.7271 (m-30) REVERT: B 181 ASP cc_start: 0.8630 (t70) cc_final: 0.8163 (t0) REVERT: B 291 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 300 THR cc_start: 0.8489 (t) cc_final: 0.8289 (m) REVERT: B 308 LYS cc_start: 0.7763 (pttt) cc_final: 0.7397 (mttp) REVERT: B 491 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7908 (mtm-85) REVERT: C 6 ASP cc_start: 0.7936 (t0) cc_final: 0.7489 (m-30) REVERT: C 72 TRP cc_start: 0.8440 (m100) cc_final: 0.7993 (m100) REVERT: C 81 GLN cc_start: 0.8507 (mt0) cc_final: 0.8230 (mt0) REVERT: C 84 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7877 (mp10) REVERT: C 308 LYS cc_start: 0.7799 (pttt) cc_final: 0.7325 (mttp) REVERT: C 495 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 169 MET cc_start: 0.8798 (ttm) cc_final: 0.8426 (mtm) REVERT: D 308 LYS cc_start: 0.7705 (pttt) cc_final: 0.7299 (mttp) REVERT: D 495 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7971 (mt-10) REVERT: E 72 TRP cc_start: 0.8368 (m100) cc_final: 0.7893 (m100) REVERT: E 81 GLN cc_start: 0.8553 (mt0) cc_final: 0.7941 (mt0) REVERT: E 163 ASP cc_start: 0.8356 (m-30) cc_final: 0.7434 (m-30) REVERT: E 308 LYS cc_start: 0.7789 (pttt) cc_final: 0.7409 (mttp) REVERT: E 417 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8959 (mm) REVERT: E 491 ARG cc_start: 0.8295 (mtp180) cc_final: 0.7947 (mtm-85) REVERT: F 6 ASP cc_start: 0.7950 (t0) cc_final: 0.7501 (m-30) REVERT: F 72 TRP cc_start: 0.8448 (m100) cc_final: 0.8010 (m100) REVERT: F 81 GLN cc_start: 0.8522 (mt0) cc_final: 0.8265 (mt0) REVERT: F 84 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7830 (mp10) REVERT: F 308 LYS cc_start: 0.7774 (pttt) cc_final: 0.7315 (mttp) outliers start: 56 outliers final: 45 residues processed: 335 average time/residue: 0.1524 time to fit residues: 84.3290 Evaluate side-chains 320 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 162 VAL 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 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 THR 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 322 LEU 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 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 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 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 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 417 LEU 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 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 227 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 297 GLN ** 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 254 ASN D 297 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.111257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085637 restraints weight = 44328.470| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.31 r_work: 0.3014 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4407 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= 0.155 Angle : 0.597 12.515 33390 Z= 0.295 Chirality : 0.045 0.231 3618 Planarity : 0.004 0.044 4242 Dihedral : 10.693 145.695 4080 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.24 % Allowed : 15.27 % Favored : 82.49 % 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 aren not related in a simple way. whole: 0.85 (0.16), residues: 2970 helix: 1.64 (0.14), residues: 1416 sheet: -0.90 (0.25), residues: 402 loop : -0.13 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 261 TYR 0.011 0.001 TYR E 78 PHE 0.024 0.002 PHE F 490 TRP 0.032 0.002 TRP D 72 HIS 0.005 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00362 (24612) covalent geometry : angle 0.59728 (33384) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03952 ( 1140) hydrogen bonds : angle 4.20659 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.25 seconds wall clock time: 91 minutes 4.94 seconds (5464.94 seconds total)