Starting phenix.real_space_refine on Mon Aug 25 09:46:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7w_47693/08_2025/9e7w_47693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7w_47693/08_2025/9e7w_47693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7w_47693/08_2025/9e7w_47693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7w_47693/08_2025/9e7w_47693.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7w_47693/08_2025/9e7w_47693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7w_47693/08_2025/9e7w_47693.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 17695 2.51 5 N 4734 2.21 5 O 5330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27857 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4352 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 506} Chain: "B" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4352 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 506} Chain: "C" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4352 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 506} Chain: "D" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4352 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 506} Chain: "E" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4352 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 506} Chain: "F" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4352 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 506} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 786 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 6.98, per 1000 atoms: 0.25 Number of scatterers: 27857 At special positions: 0 Unit cell: (231.012, 142.29, 127.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 5330 8.00 N 4734 7.00 C 17695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.02 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.02 Simple disulfide: pdb=" SG CYS D 490 " - pdb=" SG CYS D 494 " distance=2.03 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.03 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 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: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6504 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 55 sheets defined 13.3% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.795A pdb=" N ASP A 99 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.468A pdb=" N THR A 366 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU A 368 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN A 369 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.140A pdb=" N GLY A 385 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 445 through 448 removed outlier: 3.977A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.599A pdb=" N VAL A 562 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.704A pdb=" N ASP B 99 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.649A pdb=" N TRP B 120 " --> pdb=" O TRP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.565A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 removed outlier: 3.565A pdb=" N LEU B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.643A pdb=" N ARG B 313 " --> pdb=" O GLN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.614A pdb=" N GLN B 370 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.874A pdb=" N VAL B 562 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.511A pdb=" N MET C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.705A pdb=" N VAL C 241 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 363 through 371 removed outlier: 5.665A pdb=" N GLU C 368 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN C 369 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 425 through 427 No H-bonds generated for 'chain 'C' and resid 425 through 427' Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.587A pdb=" N PHE C 448 " --> pdb=" O THR C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 561 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.658A pdb=" N MET D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.523A pdb=" N SER D 249 " --> pdb=" O THR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 309 through 313 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.634A pdb=" N GLN D 370 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'D' and resid 425 through 427 No H-bonds generated for 'chain 'D' and resid 425 through 427' Processing helix chain 'D' and resid 443 through 448 removed outlier: 3.897A pdb=" N ILE D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.518A pdb=" N ASP E 99 " --> pdb=" O MET E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.716A pdb=" N ASP E 240 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 281 through 285 removed outlier: 3.744A pdb=" N LEU E 285 " --> pdb=" O ASN E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 313 removed outlier: 3.704A pdb=" N ARG E 313 " --> pdb=" O GLN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 4.382A pdb=" N THR E 366 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU E 368 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 369 " --> pdb=" O THR E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'E' and resid 425 through 427 No H-bonds generated for 'chain 'E' and resid 425 through 427' Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.848A pdb=" N PHE E 448 " --> pdb=" O THR E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 562 removed outlier: 3.818A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 4.129A pdb=" N VAL F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.750A pdb=" N VAL F 241 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 285 removed outlier: 3.602A pdb=" N LEU F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.732A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'F' and resid 381 through 385 removed outlier: 3.855A pdb=" N GLY F 385 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 443 through 448 Processing helix chain 'F' and resid 557 through 562 removed outlier: 3.695A pdb=" N VAL F 562 " --> pdb=" O PHE F 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.511A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 72 current: chain 'A' and resid 163 through 167 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.149A pdb=" N ASP A 215 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.572A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AB1, first strand: chain 'A' and resid 435 through 436 removed outlier: 5.743A pdb=" N ILE A 442 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 472 removed outlier: 7.680A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 72 current: chain 'B' and resid 163 through 167 Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AB5, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.171A pdb=" N GLY B 235 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 217 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR B 233 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AB7, first strand: chain 'B' and resid 315 through 317 Processing sheet with id=AB8, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.492A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 429 through 430 removed outlier: 3.535A pdb=" N ILE B 415 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 435 through 436 removed outlier: 5.637A pdb=" N ILE B 442 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 470 through 472 removed outlier: 7.386A pdb=" N ASP B 471 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 45 current: chain 'D' and resid 102 through 112 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 72 current: chain 'C' and resid 163 through 167 Processing sheet with id=AC5, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AC6, first strand: chain 'C' and resid 215 through 218 removed outlier: 6.214A pdb=" N ASP C 215 " --> pdb=" O HIS C 234 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 276 through 278 Processing sheet with id=AC8, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.265A pdb=" N GLU C 335 " --> pdb=" O ALA C 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 470 through 472 removed outlier: 7.554A pdb=" N ASP C 471 " --> pdb=" O CYS C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 72 current: chain 'D' and resid 163 through 167 Processing sheet with id=AD2, first strand: chain 'D' and resid 215 through 218 removed outlier: 6.231A pdb=" N ASP D 215 " --> pdb=" O HIS D 234 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 276 through 278 Processing sheet with id=AD4, first strand: chain 'D' and resid 315 through 319 removed outlier: 4.362A pdb=" N MET D 319 " --> pdb=" O ASP E 375 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP E 375 " --> pdb=" O MET D 319 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.658A pdb=" N GLU D 335 " --> pdb=" O ALA D 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 351 through 354 removed outlier: 3.749A pdb=" N SER D 348 " --> pdb=" O GLY D 351 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 396 through 399 removed outlier: 7.551A pdb=" N ASP D 375 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N MET F 319 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 429 through 430 removed outlier: 3.625A pdb=" N SER E 348 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 470 through 472 removed outlier: 6.841A pdb=" N ASP D 471 " --> pdb=" O CYS D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 72 current: chain 'E' and resid 163 through 167 Processing sheet with id=AE2, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AE3, first strand: chain 'E' and resid 215 through 218 removed outlier: 5.990A pdb=" N ASP E 215 " --> pdb=" O HIS E 234 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AE5, first strand: chain 'E' and resid 315 through 319 removed outlier: 4.633A pdb=" N MET E 319 " --> pdb=" O ASP F 375 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASP F 375 " --> pdb=" O MET E 319 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.501A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 429 through 430 removed outlier: 3.674A pdb=" N SER F 348 " --> pdb=" O GLY F 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'F' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 72 current: chain 'F' and resid 163 through 167 Processing sheet with id=AF1, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AF2, first strand: chain 'F' and resid 215 through 218 removed outlier: 6.088A pdb=" N ASP F 215 " --> pdb=" O HIS F 234 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 276 through 278 removed outlier: 6.061A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.525A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 470 through 472 removed outlier: 7.097A pdb=" N ASP F 471 " --> pdb=" O CYS F 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.512A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.591A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 9 through 14 removed outlier: 6.652A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU L 127 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY L 13 " --> pdb=" O LEU L 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'L' and resid 105 through 108 removed outlier: 3.503A pdb=" N ALA L 115 " --> pdb=" O ASP L 108 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9139 1.34 - 1.46: 7025 1.46 - 1.58: 12349 1.58 - 1.70: 0 1.70 - 1.82: 166 Bond restraints: 28679 Sorted by residual: bond pdb=" N GLY C 37 " pdb=" CA GLY C 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.38e+00 bond pdb=" N GLY F 37 " pdb=" CA GLY F 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.37e+00 bond pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.31e+00 bond pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 ... (remaining 28674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 37646 1.41 - 2.83: 1291 2.83 - 4.24: 277 4.24 - 5.65: 18 5.65 - 7.06: 6 Bond angle restraints: 39238 Sorted by residual: angle pdb=" C ALA F 372 " pdb=" CA ALA F 372 " pdb=" CB ALA F 372 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.51e+01 angle pdb=" C ALA E 372 " pdb=" CA ALA E 372 " pdb=" CB ALA E 372 " ideal model delta sigma weight residual 117.23 110.57 6.66 1.36e+00 5.41e-01 2.40e+01 angle pdb=" N ILE D 566 " pdb=" CA ILE D 566 " pdb=" C ILE D 566 " ideal model delta sigma weight residual 111.91 108.70 3.21 8.90e-01 1.26e+00 1.30e+01 angle pdb=" N ILE L 36 " pdb=" CA ILE L 36 " pdb=" C ILE L 36 " ideal model delta sigma weight residual 111.62 108.89 2.73 7.90e-01 1.60e+00 1.19e+01 angle pdb=" N ILE E 566 " pdb=" CA ILE E 566 " pdb=" C ILE E 566 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 ... (remaining 39233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15240 17.93 - 35.87: 1163 35.87 - 53.80: 247 53.80 - 71.74: 79 71.74 - 89.67: 43 Dihedral angle restraints: 16772 sinusoidal: 6596 harmonic: 10176 Sorted by residual: dihedral pdb=" CA CYS C 494 " pdb=" C CYS C 494 " pdb=" N PRO C 495 " pdb=" CA PRO C 495 " ideal model delta harmonic sigma weight residual -180.00 -135.00 -45.00 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA CYS A 494 " pdb=" C CYS A 494 " pdb=" N PRO A 495 " pdb=" CA PRO A 495 " ideal model delta harmonic sigma weight residual -180.00 -139.03 -40.97 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA CYS B 494 " pdb=" C CYS B 494 " pdb=" N PRO B 495 " pdb=" CA PRO B 495 " ideal model delta harmonic sigma weight residual -180.00 -146.82 -33.18 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 16769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2671 0.037 - 0.074: 1092 0.074 - 0.112: 365 0.112 - 0.149: 86 0.149 - 0.186: 9 Chirality restraints: 4223 Sorted by residual: chirality pdb=" CA ILE C 415 " pdb=" N ILE C 415 " pdb=" C ILE C 415 " pdb=" CB ILE C 415 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 4220 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 47 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" CG ASN F 47 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN F 47 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN F 47 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 47 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ASN F 47 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN F 47 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN F 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 159 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO B 160 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.029 5.00e-02 4.00e+02 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 316 2.60 - 3.18: 24666 3.18 - 3.75: 43741 3.75 - 4.33: 65640 4.33 - 4.90: 106583 Nonbonded interactions: 240946 Sorted by model distance: nonbonded pdb=" OE1 GLU E 346 " pdb=" OG1 THR E 355 " model vdw 2.028 3.040 nonbonded pdb=" OD1 ASN D 321 " pdb=" OH TYR E 343 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASN E 321 " pdb=" OH TYR F 343 " model vdw 2.056 3.040 nonbonded pdb=" O LEU E 128 " pdb=" OG1 THR E 132 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASN E 443 " pdb=" OG1 THR E 445 " model vdw 2.077 3.040 ... (remaining 240941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.840 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 : 0.007 0.077 28688 Z= 0.316 Angle : 0.636 7.064 39256 Z= 0.357 Chirality : 0.046 0.186 4223 Planarity : 0.005 0.052 5181 Dihedral : 14.747 89.670 10241 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.25 % Allowed : 13.58 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 1.58 % 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: -0.83 (0.13), residues: 3507 helix: -1.00 (0.46), residues: 96 sheet: -0.59 (0.16), residues: 941 loop : -0.49 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 332 TYR 0.024 0.002 TYR B 342 PHE 0.026 0.002 PHE E 448 TRP 0.019 0.002 TRP B 528 HIS 0.009 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00686 (28679) covalent geometry : angle 0.63299 (39238) SS BOND : bond 0.00559 ( 9) SS BOND : angle 2.99800 ( 18) hydrogen bonds : bond 0.22155 ( 396) hydrogen bonds : angle 8.23485 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 929 time to evaluate : 1.187 Fit side-chains REVERT: A 49 THR cc_start: 0.7410 (m) cc_final: 0.7039 (p) REVERT: A 52 LYS cc_start: 0.7036 (tttm) cc_final: 0.6774 (tttm) REVERT: A 60 TYR cc_start: 0.6327 (m-10) cc_final: 0.5772 (m-10) REVERT: A 109 TRP cc_start: 0.7926 (m100) cc_final: 0.7517 (m100) REVERT: A 119 VAL cc_start: 0.7523 (t) cc_final: 0.7271 (t) REVERT: A 135 GLU cc_start: 0.7149 (pt0) cc_final: 0.6508 (pt0) REVERT: A 150 LEU cc_start: 0.7648 (mp) cc_final: 0.7434 (mp) REVERT: A 261 PHE cc_start: 0.7421 (t80) cc_final: 0.7209 (t80) REVERT: A 266 PHE cc_start: 0.7567 (t80) cc_final: 0.7131 (t80) REVERT: A 394 THR cc_start: 0.8237 (m) cc_final: 0.8008 (t) REVERT: A 417 ASN cc_start: 0.7743 (t0) cc_final: 0.7521 (t0) REVERT: A 532 LYS cc_start: 0.7605 (ttmm) cc_final: 0.7366 (ttmm) REVERT: B 60 TYR cc_start: 0.6480 (m-80) cc_final: 0.5952 (m-10) REVERT: B 80 ARG cc_start: 0.6273 (mmp80) cc_final: 0.5874 (mmp80) REVERT: B 89 LYS cc_start: 0.7600 (tppt) cc_final: 0.7212 (tppt) REVERT: B 151 LYS cc_start: 0.7645 (mttm) cc_final: 0.7415 (mtpt) REVERT: B 223 THR cc_start: 0.8123 (m) cc_final: 0.7695 (p) REVERT: B 310 GLN cc_start: 0.7290 (mt0) cc_final: 0.6863 (mt0) REVERT: B 312 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7177 (mmtt) REVERT: B 314 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6397 (mtp180) REVERT: B 382 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.6967 (mtm-85) REVERT: B 413 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: B 574 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6484 (mm-30) REVERT: B 581 ARG cc_start: 0.7836 (ptt180) cc_final: 0.7467 (ttp80) REVERT: C 52 LYS cc_start: 0.7652 (tmtm) cc_final: 0.7048 (tmtm) REVERT: C 135 GLU cc_start: 0.7034 (pt0) cc_final: 0.6535 (pt0) REVERT: C 137 HIS cc_start: 0.7700 (m-70) cc_final: 0.7308 (m90) REVERT: C 144 GLU cc_start: 0.7227 (pt0) cc_final: 0.6801 (pt0) REVERT: C 211 TYR cc_start: 0.7454 (m-80) cc_final: 0.6986 (m-80) REVERT: C 292 ASN cc_start: 0.7482 (m-40) cc_final: 0.7247 (m-40) REVERT: C 309 GLN cc_start: 0.7288 (tt0) cc_final: 0.6845 (tt0) REVERT: C 324 TYR cc_start: 0.7938 (m-80) cc_final: 0.7692 (m-80) REVERT: C 414 TRP cc_start: 0.7765 (p90) cc_final: 0.7410 (p90) REVERT: C 439 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7692 (mmtt) REVERT: C 530 LYS cc_start: 0.7268 (ttpt) cc_final: 0.7049 (ttpt) REVERT: D 92 VAL cc_start: 0.8046 (t) cc_final: 0.7814 (m) REVERT: D 163 LYS cc_start: 0.7406 (ptmt) cc_final: 0.7107 (ptmt) REVERT: D 174 MET cc_start: 0.6923 (mtp) cc_final: 0.6702 (mtp) REVERT: D 414 TRP cc_start: 0.7204 (p90) cc_final: 0.6773 (p90) REVERT: D 509 GLN cc_start: 0.6983 (mt0) cc_final: 0.6757 (mp10) REVERT: D 582 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7330 (ttpp) REVERT: E 60 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5974 (t80) REVERT: E 80 ARG cc_start: 0.6768 (mtt-85) cc_final: 0.6531 (mtt-85) REVERT: E 125 ASP cc_start: 0.6596 (m-30) cc_final: 0.6300 (m-30) REVERT: E 192 SER cc_start: 0.6972 (t) cc_final: 0.6700 (t) REVERT: E 198 TYR cc_start: 0.7569 (m-80) cc_final: 0.7209 (m-80) REVERT: E 208 TRP cc_start: 0.7706 (t60) cc_final: 0.7305 (t60) REVERT: E 339 SER cc_start: 0.7390 (m) cc_final: 0.7113 (p) REVERT: E 401 ILE cc_start: 0.6572 (mm) cc_final: 0.6335 (mm) REVERT: E 427 ASP cc_start: 0.7557 (m-30) cc_final: 0.7147 (t0) REVERT: E 511 ASP cc_start: 0.6930 (t0) cc_final: 0.6548 (t0) REVERT: F 51 PHE cc_start: 0.7524 (m-80) cc_final: 0.7276 (m-80) REVERT: F 52 LYS cc_start: 0.7542 (tttm) cc_final: 0.7201 (tttm) REVERT: F 59 VAL cc_start: 0.7942 (p) cc_final: 0.7667 (m) REVERT: F 60 TYR cc_start: 0.6658 (m-80) cc_final: 0.6088 (t80) REVERT: F 182 THR cc_start: 0.7291 (m) cc_final: 0.6974 (t) REVERT: F 287 LEU cc_start: 0.7542 (tp) cc_final: 0.7246 (tp) REVERT: F 339 SER cc_start: 0.8172 (m) cc_final: 0.7722 (p) REVERT: F 401 ILE cc_start: 0.6645 (mm) cc_final: 0.6250 (mm) REVERT: F 555 VAL cc_start: 0.8452 (p) cc_final: 0.8186 (t) REVERT: F 556 ASP cc_start: 0.7416 (m-30) cc_final: 0.7189 (m-30) REVERT: F 574 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5857 (mm-30) REVERT: H 82 MET cc_start: 0.6586 (mtm) cc_final: 0.6231 (mtm) outliers start: 38 outliers final: 30 residues processed: 937 average time/residue: 0.2135 time to fit residues: 310.3427 Evaluate side-chains 932 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 900 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain L residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0170 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS B 231 ASN B 242 GLN C 222 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 483 HIS D 242 GLN D 386 GLN D 577 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN E 231 ASN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 323 ASN F 468 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.115451 restraints weight = 39704.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.119624 restraints weight = 22688.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.122400 restraints weight = 15391.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.124267 restraints weight = 11668.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125339 restraints weight = 9660.552| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28688 Z= 0.109 Angle : 0.522 6.562 39256 Z= 0.274 Chirality : 0.043 0.167 4223 Planarity : 0.005 0.046 5181 Dihedral : 5.822 57.167 3876 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.27 % Allowed : 12.69 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.51 (0.13), residues: 3507 helix: -0.62 (0.45), residues: 96 sheet: -0.47 (0.15), residues: 995 loop : -0.20 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 314 TYR 0.018 0.001 TYR A 342 PHE 0.023 0.001 PHE E 448 TRP 0.009 0.001 TRP C 279 HIS 0.008 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00243 (28679) covalent geometry : angle 0.51917 (39238) SS BOND : bond 0.00518 ( 9) SS BOND : angle 2.77436 ( 18) hydrogen bonds : bond 0.03889 ( 396) hydrogen bonds : angle 6.03104 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 921 time to evaluate : 1.177 Fit side-chains REVERT: A 44 THR cc_start: 0.7515 (m) cc_final: 0.7220 (p) REVERT: A 49 THR cc_start: 0.7470 (m) cc_final: 0.7129 (p) REVERT: A 52 LYS cc_start: 0.7049 (tttm) cc_final: 0.6841 (tttm) REVERT: A 60 TYR cc_start: 0.5861 (m-10) cc_final: 0.5572 (m-10) REVERT: A 80 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6889 (mtp180) REVERT: A 109 TRP cc_start: 0.7832 (m100) cc_final: 0.7504 (m100) REVERT: A 135 GLU cc_start: 0.6610 (pt0) cc_final: 0.6184 (pt0) REVERT: A 150 LEU cc_start: 0.7496 (mp) cc_final: 0.7294 (mp) REVERT: A 185 PHE cc_start: 0.7153 (t80) cc_final: 0.6878 (t80) REVERT: A 193 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5303 (tt0) REVERT: A 219 ILE cc_start: 0.8145 (mm) cc_final: 0.7853 (mt) REVERT: A 275 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7267 (mt) REVERT: A 350 GLN cc_start: 0.6963 (mp10) cc_final: 0.6760 (mp10) REVERT: A 394 THR cc_start: 0.8064 (m) cc_final: 0.7841 (t) REVERT: A 417 ASN cc_start: 0.7469 (t0) cc_final: 0.7147 (t0) REVERT: A 530 LYS cc_start: 0.7373 (ttpp) cc_final: 0.7103 (ttpt) REVERT: A 532 LYS cc_start: 0.7273 (ttmm) cc_final: 0.7038 (ttmm) REVERT: A 561 TYR cc_start: 0.7507 (m-80) cc_final: 0.7124 (m-80) REVERT: B 49 THR cc_start: 0.6846 (m) cc_final: 0.6577 (t) REVERT: B 60 TYR cc_start: 0.5481 (m-80) cc_final: 0.5146 (m-10) REVERT: B 80 ARG cc_start: 0.5892 (mmp80) cc_final: 0.5376 (mmp80) REVERT: B 89 LYS cc_start: 0.7438 (tppt) cc_final: 0.7150 (tppt) REVERT: B 99 ASP cc_start: 0.6370 (t0) cc_final: 0.5955 (t0) REVERT: B 151 LYS cc_start: 0.7323 (mttm) cc_final: 0.7087 (mtpt) REVERT: B 312 LYS cc_start: 0.7307 (mmtt) cc_final: 0.6879 (mmtt) REVERT: B 314 ARG cc_start: 0.6325 (mtt180) cc_final: 0.6042 (mtt180) REVERT: B 420 PHE cc_start: 0.7493 (t80) cc_final: 0.7257 (t80) REVERT: B 434 ASP cc_start: 0.7337 (m-30) cc_final: 0.7022 (m-30) REVERT: B 439 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6781 (mmtt) REVERT: B 574 GLU cc_start: 0.6181 (mm-30) cc_final: 0.5806 (mm-30) REVERT: C 52 LYS cc_start: 0.7441 (tmtm) cc_final: 0.6821 (tmtm) REVERT: C 79 TYR cc_start: 0.7777 (m-80) cc_final: 0.7098 (m-80) REVERT: C 92 VAL cc_start: 0.7685 (t) cc_final: 0.7478 (p) REVERT: C 125 ASP cc_start: 0.6198 (m-30) cc_final: 0.5867 (m-30) REVERT: C 133 MET cc_start: 0.6825 (mmt) cc_final: 0.6497 (mmt) REVERT: C 135 GLU cc_start: 0.6582 (pt0) cc_final: 0.6023 (pt0) REVERT: C 137 HIS cc_start: 0.7639 (m-70) cc_final: 0.7131 (m90) REVERT: C 144 GLU cc_start: 0.6882 (pt0) cc_final: 0.6534 (pt0) REVERT: C 211 TYR cc_start: 0.7355 (m-80) cc_final: 0.7153 (m-80) REVERT: C 274 ARG cc_start: 0.6018 (mmm-85) cc_final: 0.5654 (mmm-85) REVERT: C 292 ASN cc_start: 0.7027 (m-40) cc_final: 0.6784 (m-40) REVERT: C 309 GLN cc_start: 0.6723 (tt0) cc_final: 0.6426 (tt0) REVERT: C 324 TYR cc_start: 0.7732 (m-80) cc_final: 0.7490 (m-80) REVERT: C 335 GLU cc_start: 0.5987 (tt0) cc_final: 0.5708 (tt0) REVERT: C 346 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6406 (mt-10) REVERT: C 387 LYS cc_start: 0.7267 (tptt) cc_final: 0.6909 (tptt) REVERT: C 414 TRP cc_start: 0.7434 (p90) cc_final: 0.7035 (p90) REVERT: C 439 LYS cc_start: 0.7709 (mmtp) cc_final: 0.7436 (mmtt) REVERT: C 481 ARG cc_start: 0.6859 (mtm180) cc_final: 0.6633 (mtp180) REVERT: D 51 PHE cc_start: 0.7219 (m-80) cc_final: 0.6888 (m-80) REVERT: D 99 ASP cc_start: 0.6827 (t0) cc_final: 0.6494 (t0) REVERT: D 101 THR cc_start: 0.7413 (m) cc_final: 0.7169 (t) REVERT: D 125 ASP cc_start: 0.6369 (m-30) cc_final: 0.6100 (m-30) REVERT: D 127 GLN cc_start: 0.7224 (tt0) cc_final: 0.6959 (tt0) REVERT: D 163 LYS cc_start: 0.7083 (ptmt) cc_final: 0.6855 (ptmt) REVERT: D 174 MET cc_start: 0.6359 (mtp) cc_final: 0.6141 (mtp) REVERT: D 210 TYR cc_start: 0.8111 (p90) cc_final: 0.7693 (p90) REVERT: D 217 THR cc_start: 0.7433 (m) cc_final: 0.7221 (t) REVERT: D 221 SER cc_start: 0.7957 (p) cc_final: 0.7755 (p) REVERT: D 312 LYS cc_start: 0.6738 (mmtt) cc_final: 0.6507 (mmtt) REVERT: D 316 VAL cc_start: 0.7883 (t) cc_final: 0.7454 (p) REVERT: D 344 SER cc_start: 0.7493 (OUTLIER) cc_final: 0.7235 (p) REVERT: D 411 GLU cc_start: 0.6644 (mp0) cc_final: 0.6183 (mp0) REVERT: D 414 TRP cc_start: 0.7039 (p90) cc_final: 0.6576 (p90) REVERT: D 464 TYR cc_start: 0.7078 (t80) cc_final: 0.6821 (t80) REVERT: D 513 ASP cc_start: 0.6437 (m-30) cc_final: 0.6184 (m-30) REVERT: D 530 LYS cc_start: 0.7303 (ttpp) cc_final: 0.7033 (ttpp) REVERT: D 582 LYS cc_start: 0.7513 (ttpp) cc_final: 0.7085 (ttpp) REVERT: E 60 TYR cc_start: 0.5908 (m-80) cc_final: 0.5687 (m-80) REVERT: E 67 ARG cc_start: 0.7375 (mmt-90) cc_final: 0.7071 (mmt-90) REVERT: E 80 ARG cc_start: 0.6287 (mtt-85) cc_final: 0.5994 (mtt-85) REVERT: E 125 ASP cc_start: 0.6180 (m-30) cc_final: 0.5916 (m-30) REVERT: E 178 ASP cc_start: 0.6202 (t0) cc_final: 0.5856 (t0) REVERT: E 192 SER cc_start: 0.6922 (t) cc_final: 0.6670 (t) REVERT: E 198 TYR cc_start: 0.7314 (m-80) cc_final: 0.7036 (m-80) REVERT: E 255 LEU cc_start: 0.7058 (mt) cc_final: 0.6683 (mp) REVERT: E 303 PHE cc_start: 0.6900 (m-80) cc_final: 0.6623 (m-80) REVERT: E 317 THR cc_start: 0.7773 (p) cc_final: 0.7403 (m) REVERT: E 339 SER cc_start: 0.7354 (m) cc_final: 0.7059 (p) REVERT: E 377 ARG cc_start: 0.7018 (ttt90) cc_final: 0.6808 (ttt90) REVERT: E 394 THR cc_start: 0.7243 (m) cc_final: 0.6759 (t) REVERT: E 416 GLN cc_start: 0.7404 (pt0) cc_final: 0.7094 (pt0) REVERT: E 427 ASP cc_start: 0.6852 (m-30) cc_final: 0.6497 (t0) REVERT: F 51 PHE cc_start: 0.7394 (m-80) cc_final: 0.7123 (m-80) REVERT: F 52 LYS cc_start: 0.7355 (tttm) cc_final: 0.6977 (tttm) REVERT: F 60 TYR cc_start: 0.6100 (m-80) cc_final: 0.5669 (t80) REVERT: F 151 LYS cc_start: 0.7573 (mttm) cc_final: 0.7286 (mttm) REVERT: F 193 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5725 (tt0) REVERT: F 275 LEU cc_start: 0.7642 (mp) cc_final: 0.7407 (mt) REVERT: F 339 SER cc_start: 0.8162 (m) cc_final: 0.7616 (p) REVERT: F 350 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6311 (mt0) REVERT: F 466 ASN cc_start: 0.7122 (m110) cc_final: 0.6792 (m110) REVERT: F 551 MET cc_start: 0.6439 (ttt) cc_final: 0.5292 (ttt) REVERT: F 555 VAL cc_start: 0.8385 (p) cc_final: 0.8090 (t) REVERT: F 556 ASP cc_start: 0.6716 (m-30) cc_final: 0.6422 (m-30) REVERT: F 574 GLU cc_start: 0.5543 (mm-30) cc_final: 0.5254 (mm-30) REVERT: H 82 MET cc_start: 0.6418 (mtm) cc_final: 0.6209 (mtm) outliers start: 69 outliers final: 27 residues processed: 941 average time/residue: 0.2125 time to fit residues: 311.4888 Evaluate side-chains 918 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 886 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 164 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 162 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 186 optimal weight: 6.9990 chunk 251 optimal weight: 0.0040 chunk 147 optimal weight: 1.9990 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 248 ASN B 95 ASN B 242 GLN B 383 GLN C 95 ASN C 222 HIS C 302 ASN E 86 ASN F 47 ASN F 323 ASN F 468 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.121602 restraints weight = 38825.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125914 restraints weight = 21888.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128651 restraints weight = 14533.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130316 restraints weight = 11043.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131728 restraints weight = 9106.688| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28688 Z= 0.093 Angle : 0.486 6.002 39256 Z= 0.252 Chirality : 0.042 0.169 4223 Planarity : 0.004 0.049 5181 Dihedral : 4.931 53.589 3822 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.87 % Allowed : 14.33 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.41 (0.14), residues: 3507 helix: -0.42 (0.46), residues: 96 sheet: -0.50 (0.15), residues: 1051 loop : -0.07 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 274 TYR 0.017 0.001 TYR C 561 PHE 0.022 0.001 PHE F 398 TRP 0.008 0.001 TRP B 528 HIS 0.012 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00209 (28679) covalent geometry : angle 0.48401 (39238) SS BOND : bond 0.00450 ( 9) SS BOND : angle 2.24212 ( 18) hydrogen bonds : bond 0.03332 ( 396) hydrogen bonds : angle 5.61949 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 888 time to evaluate : 1.082 Fit side-chains REVERT: A 44 THR cc_start: 0.7453 (m) cc_final: 0.7204 (p) REVERT: A 49 THR cc_start: 0.7405 (m) cc_final: 0.7073 (p) REVERT: A 60 TYR cc_start: 0.5857 (m-10) cc_final: 0.5624 (m-10) REVERT: A 80 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6953 (mtp180) REVERT: A 135 GLU cc_start: 0.6643 (pt0) cc_final: 0.6201 (pt0) REVERT: A 150 LEU cc_start: 0.7542 (mp) cc_final: 0.7333 (mp) REVERT: A 193 GLU cc_start: 0.5771 (tt0) cc_final: 0.5247 (tt0) REVERT: A 219 ILE cc_start: 0.8175 (mm) cc_final: 0.7886 (mt) REVERT: A 344 SER cc_start: 0.7383 (t) cc_final: 0.6908 (p) REVERT: A 350 GLN cc_start: 0.6930 (mp10) cc_final: 0.6679 (mp10) REVERT: A 394 THR cc_start: 0.8054 (m) cc_final: 0.7787 (t) REVERT: A 401 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7084 (mm) REVERT: A 417 ASN cc_start: 0.7498 (t0) cc_final: 0.7185 (t0) REVERT: A 530 LYS cc_start: 0.7380 (ttpp) cc_final: 0.7156 (ttpt) REVERT: A 532 LYS cc_start: 0.7279 (ttmm) cc_final: 0.6995 (tttm) REVERT: A 561 TYR cc_start: 0.7513 (m-80) cc_final: 0.7089 (m-80) REVERT: B 49 THR cc_start: 0.6845 (m) cc_final: 0.6601 (t) REVERT: B 60 TYR cc_start: 0.5463 (m-80) cc_final: 0.5173 (m-10) REVERT: B 80 ARG cc_start: 0.5954 (mmp80) cc_final: 0.5411 (mmp80) REVERT: B 89 LYS cc_start: 0.7440 (tppt) cc_final: 0.7143 (tppt) REVERT: B 99 ASP cc_start: 0.6377 (t0) cc_final: 0.6002 (t0) REVERT: B 151 LYS cc_start: 0.7413 (mttm) cc_final: 0.7194 (mtpt) REVERT: B 312 LYS cc_start: 0.7310 (mmtt) cc_final: 0.6875 (mmtt) REVERT: B 434 ASP cc_start: 0.7361 (m-30) cc_final: 0.7018 (m-30) REVERT: B 500 VAL cc_start: 0.7933 (m) cc_final: 0.7539 (p) REVERT: B 570 LYS cc_start: 0.7327 (ptmt) cc_final: 0.7124 (ptmt) REVERT: B 574 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5763 (mm-30) REVERT: C 52 LYS cc_start: 0.7439 (tmtm) cc_final: 0.6785 (tmtm) REVERT: C 125 ASP cc_start: 0.6140 (m-30) cc_final: 0.5787 (m-30) REVERT: C 133 MET cc_start: 0.6841 (mmt) cc_final: 0.6506 (mmt) REVERT: C 135 GLU cc_start: 0.6596 (pt0) cc_final: 0.6040 (pt0) REVERT: C 137 HIS cc_start: 0.7612 (m-70) cc_final: 0.7108 (m90) REVERT: C 274 ARG cc_start: 0.6012 (mmm-85) cc_final: 0.5784 (mmm-85) REVERT: C 292 ASN cc_start: 0.6975 (m-40) cc_final: 0.6718 (m-40) REVERT: C 309 GLN cc_start: 0.6698 (tt0) cc_final: 0.6414 (tt0) REVERT: C 324 TYR cc_start: 0.7714 (m-80) cc_final: 0.7485 (m-80) REVERT: C 346 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6301 (mt-10) REVERT: C 387 LYS cc_start: 0.7322 (tptt) cc_final: 0.6969 (tptt) REVERT: C 414 TRP cc_start: 0.7479 (p90) cc_final: 0.7087 (p90) REVERT: C 439 LYS cc_start: 0.7695 (mmtp) cc_final: 0.7453 (mmtt) REVERT: C 481 ARG cc_start: 0.6803 (mtm180) cc_final: 0.6574 (mtp180) REVERT: D 75 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5384 (pp20) REVERT: D 99 ASP cc_start: 0.6861 (t0) cc_final: 0.6457 (t0) REVERT: D 210 TYR cc_start: 0.8134 (p90) cc_final: 0.7759 (p90) REVERT: D 221 SER cc_start: 0.7985 (p) cc_final: 0.7753 (p) REVERT: D 242 GLN cc_start: 0.7345 (mt0) cc_final: 0.7015 (mt0) REVERT: D 312 LYS cc_start: 0.6715 (mmtt) cc_final: 0.6490 (mmtt) REVERT: D 314 ARG cc_start: 0.6235 (mtt-85) cc_final: 0.5975 (mtt-85) REVERT: D 316 VAL cc_start: 0.7913 (t) cc_final: 0.7521 (p) REVERT: D 344 SER cc_start: 0.7374 (OUTLIER) cc_final: 0.7134 (p) REVERT: D 411 GLU cc_start: 0.6597 (mp0) cc_final: 0.6175 (mp0) REVERT: D 414 TRP cc_start: 0.7087 (p90) cc_final: 0.6584 (p90) REVERT: D 464 TYR cc_start: 0.7090 (t80) cc_final: 0.6811 (t80) REVERT: D 582 LYS cc_start: 0.7478 (ttpp) cc_final: 0.7072 (ttpp) REVERT: E 60 TYR cc_start: 0.5932 (m-80) cc_final: 0.5721 (m-80) REVERT: E 80 ARG cc_start: 0.6309 (mtt-85) cc_final: 0.6010 (mtt-85) REVERT: E 99 ASP cc_start: 0.6726 (t0) cc_final: 0.6361 (t70) REVERT: E 178 ASP cc_start: 0.6239 (t0) cc_final: 0.5846 (t0) REVERT: E 181 ASN cc_start: 0.6812 (m-40) cc_final: 0.6507 (m-40) REVERT: E 192 SER cc_start: 0.6975 (t) cc_final: 0.6773 (t) REVERT: E 198 TYR cc_start: 0.7249 (m-80) cc_final: 0.6970 (m-80) REVERT: E 255 LEU cc_start: 0.7047 (mt) cc_final: 0.6673 (mp) REVERT: E 303 PHE cc_start: 0.6894 (m-80) cc_final: 0.6490 (m-80) REVERT: E 317 THR cc_start: 0.7785 (p) cc_final: 0.7451 (m) REVERT: E 339 SER cc_start: 0.7342 (m) cc_final: 0.7071 (p) REVERT: E 350 GLN cc_start: 0.7080 (mp10) cc_final: 0.6163 (mp10) REVERT: E 394 THR cc_start: 0.7225 (m) cc_final: 0.6720 (m) REVERT: E 397 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6972 (mtt90) REVERT: E 416 GLN cc_start: 0.7369 (pt0) cc_final: 0.7020 (pt0) REVERT: E 427 ASP cc_start: 0.6824 (m-30) cc_final: 0.6483 (t0) REVERT: E 532 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7245 (ttmm) REVERT: F 51 PHE cc_start: 0.7324 (m-80) cc_final: 0.7010 (m-80) REVERT: F 52 LYS cc_start: 0.7300 (tttm) cc_final: 0.6967 (tttm) REVERT: F 60 TYR cc_start: 0.6050 (m-80) cc_final: 0.5651 (t80) REVERT: F 73 MET cc_start: 0.7619 (ptt) cc_final: 0.7391 (ptm) REVERT: F 151 LYS cc_start: 0.7569 (mttm) cc_final: 0.7276 (mttm) REVERT: F 193 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5660 (tt0) REVERT: F 275 LEU cc_start: 0.7631 (mp) cc_final: 0.7368 (mt) REVERT: F 310 GLN cc_start: 0.6996 (mt0) cc_final: 0.6743 (mm-40) REVERT: F 313 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6859 (mtt90) REVERT: F 339 SER cc_start: 0.8186 (m) cc_final: 0.7714 (p) REVERT: F 350 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6087 (mp10) REVERT: F 390 THR cc_start: 0.7434 (m) cc_final: 0.7162 (p) REVERT: F 450 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.6933 (p) REVERT: F 466 ASN cc_start: 0.7141 (m110) cc_final: 0.6863 (m110) REVERT: F 511 ASP cc_start: 0.6997 (t0) cc_final: 0.6556 (t0) REVERT: F 551 MET cc_start: 0.6439 (ttt) cc_final: 0.5397 (ttt) REVERT: F 555 VAL cc_start: 0.8373 (p) cc_final: 0.8077 (t) REVERT: F 556 ASP cc_start: 0.6657 (m-30) cc_final: 0.6376 (m-30) REVERT: H 82 MET cc_start: 0.6339 (mtm) cc_final: 0.6132 (mtm) outliers start: 57 outliers final: 26 residues processed: 909 average time/residue: 0.2145 time to fit residues: 302.3726 Evaluate side-chains 902 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 870 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 240 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 276 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 241 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS B 95 ASN B 242 GLN B 280 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS D 127 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 GLN F 323 ASN F 558 GLN F 560 ASN F 577 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.117838 restraints weight = 39025.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121957 restraints weight = 22301.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.124668 restraints weight = 15209.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.126484 restraints weight = 11629.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127538 restraints weight = 9613.113| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28688 Z= 0.179 Angle : 0.516 6.108 39256 Z= 0.269 Chirality : 0.044 0.165 4223 Planarity : 0.004 0.043 5181 Dihedral : 5.076 53.679 3822 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.30 % Allowed : 14.66 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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 (0.14), residues: 3507 helix: -0.39 (0.46), residues: 96 sheet: -0.45 (0.15), residues: 1039 loop : -0.12 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 191 TYR 0.018 0.001 TYR F 305 PHE 0.022 0.002 PHE A 448 TRP 0.012 0.001 TRP B 528 HIS 0.014 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00403 (28679) covalent geometry : angle 0.51290 (39238) SS BOND : bond 0.00493 ( 9) SS BOND : angle 2.73374 ( 18) hydrogen bonds : bond 0.03514 ( 396) hydrogen bonds : angle 5.57640 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 897 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 44 THR cc_start: 0.7541 (m) cc_final: 0.7298 (p) REVERT: A 49 THR cc_start: 0.7423 (m) cc_final: 0.7082 (p) REVERT: A 60 TYR cc_start: 0.5880 (m-10) cc_final: 0.5664 (m-10) REVERT: A 80 ARG cc_start: 0.7172 (mtt180) cc_final: 0.6895 (mtp180) REVERT: A 109 TRP cc_start: 0.7869 (m100) cc_final: 0.7582 (m100) REVERT: A 135 GLU cc_start: 0.6647 (pt0) cc_final: 0.6187 (pt0) REVERT: A 193 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5283 (tt0) REVERT: A 344 SER cc_start: 0.7438 (t) cc_final: 0.6975 (p) REVERT: A 350 GLN cc_start: 0.6963 (mp10) cc_final: 0.6423 (mp10) REVERT: A 394 THR cc_start: 0.8094 (m) cc_final: 0.7880 (t) REVERT: A 401 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7151 (mm) REVERT: A 417 ASN cc_start: 0.7475 (t0) cc_final: 0.7153 (t0) REVERT: A 511 ASP cc_start: 0.7435 (t0) cc_final: 0.7199 (t0) REVERT: A 532 LYS cc_start: 0.7244 (ttmm) cc_final: 0.7010 (tttm) REVERT: A 561 TYR cc_start: 0.7540 (m-80) cc_final: 0.7056 (m-80) REVERT: B 60 TYR cc_start: 0.5509 (m-80) cc_final: 0.5228 (m-10) REVERT: B 80 ARG cc_start: 0.5968 (mmp80) cc_final: 0.5363 (mmp80) REVERT: B 89 LYS cc_start: 0.7418 (tppt) cc_final: 0.7185 (tppt) REVERT: B 99 ASP cc_start: 0.6421 (t0) cc_final: 0.5984 (t0) REVERT: B 151 LYS cc_start: 0.7449 (mttm) cc_final: 0.7235 (mtpt) REVERT: B 312 LYS cc_start: 0.7281 (mmtt) cc_final: 0.6811 (mmtt) REVERT: B 411 GLU cc_start: 0.6414 (mp0) cc_final: 0.6083 (mp0) REVERT: B 457 LEU cc_start: 0.7109 (pt) cc_final: 0.6819 (pp) REVERT: B 570 LYS cc_start: 0.7373 (ptmt) cc_final: 0.7142 (ptmt) REVERT: B 574 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5810 (mm-30) REVERT: C 52 LYS cc_start: 0.7465 (tmtm) cc_final: 0.6812 (tmtm) REVERT: C 95 ASN cc_start: 0.7181 (m110) cc_final: 0.6972 (m-40) REVERT: C 122 ASN cc_start: 0.7349 (p0) cc_final: 0.6796 (p0) REVERT: C 125 ASP cc_start: 0.6230 (m-30) cc_final: 0.5600 (m-30) REVERT: C 133 MET cc_start: 0.6892 (mmt) cc_final: 0.6522 (mmt) REVERT: C 135 GLU cc_start: 0.6610 (pt0) cc_final: 0.6017 (pt0) REVERT: C 137 HIS cc_start: 0.7657 (m-70) cc_final: 0.7163 (m90) REVERT: C 274 ARG cc_start: 0.6064 (mmm-85) cc_final: 0.5855 (mmm-85) REVERT: C 292 ASN cc_start: 0.7036 (m-40) cc_final: 0.6793 (m-40) REVERT: C 309 GLN cc_start: 0.6748 (tt0) cc_final: 0.6442 (tt0) REVERT: C 324 TYR cc_start: 0.7725 (m-80) cc_final: 0.7507 (m-80) REVERT: C 346 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6390 (mt-10) REVERT: C 387 LYS cc_start: 0.7312 (tptt) cc_final: 0.6960 (tptt) REVERT: C 414 TRP cc_start: 0.7525 (p90) cc_final: 0.7166 (p90) REVERT: C 439 LYS cc_start: 0.7741 (mmtp) cc_final: 0.7474 (mmtt) REVERT: D 75 GLU cc_start: 0.5692 (pp20) cc_final: 0.5453 (pp20) REVERT: D 99 ASP cc_start: 0.6920 (t0) cc_final: 0.6520 (t0) REVERT: D 101 THR cc_start: 0.7415 (m) cc_final: 0.7091 (t) REVERT: D 221 SER cc_start: 0.7950 (p) cc_final: 0.7736 (p) REVERT: D 312 LYS cc_start: 0.6726 (mmtt) cc_final: 0.6514 (mmtt) REVERT: D 314 ARG cc_start: 0.6289 (mtt-85) cc_final: 0.5960 (mtt-85) REVERT: D 316 VAL cc_start: 0.7914 (t) cc_final: 0.7460 (p) REVERT: D 344 SER cc_start: 0.7438 (OUTLIER) cc_final: 0.7200 (p) REVERT: D 411 GLU cc_start: 0.6641 (mp0) cc_final: 0.6173 (mp0) REVERT: D 414 TRP cc_start: 0.7092 (p90) cc_final: 0.6556 (p90) REVERT: D 513 ASP cc_start: 0.6431 (m-30) cc_final: 0.6076 (m-30) REVERT: D 582 LYS cc_start: 0.7479 (ttpp) cc_final: 0.7203 (ttpp) REVERT: E 60 TYR cc_start: 0.5930 (m-80) cc_final: 0.5712 (m-80) REVERT: E 80 ARG cc_start: 0.6265 (mtt-85) cc_final: 0.5967 (mtt-85) REVERT: E 178 ASP cc_start: 0.6178 (t0) cc_final: 0.5819 (t0) REVERT: E 198 TYR cc_start: 0.7310 (m-80) cc_final: 0.7021 (m-80) REVERT: E 255 LEU cc_start: 0.7041 (mt) cc_final: 0.6693 (mp) REVERT: E 303 PHE cc_start: 0.6902 (m-80) cc_final: 0.6531 (m-80) REVERT: E 317 THR cc_start: 0.7750 (p) cc_final: 0.7443 (m) REVERT: E 394 THR cc_start: 0.7270 (m) cc_final: 0.6824 (t) REVERT: E 416 GLN cc_start: 0.7391 (pt0) cc_final: 0.7154 (pt0) REVERT: E 427 ASP cc_start: 0.6827 (m-30) cc_final: 0.6471 (t0) REVERT: E 532 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7267 (ttmm) REVERT: F 51 PHE cc_start: 0.7402 (m-80) cc_final: 0.7154 (m-80) REVERT: F 52 LYS cc_start: 0.7307 (tttm) cc_final: 0.6966 (tttm) REVERT: F 60 TYR cc_start: 0.6074 (m-80) cc_final: 0.5734 (t80) REVERT: F 73 MET cc_start: 0.7646 (ptt) cc_final: 0.7412 (ptm) REVERT: F 151 LYS cc_start: 0.7586 (mttm) cc_final: 0.7317 (mttm) REVERT: F 193 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5698 (tt0) REVERT: F 275 LEU cc_start: 0.7742 (mp) cc_final: 0.7496 (mt) REVERT: F 276 THR cc_start: 0.7604 (p) cc_final: 0.7365 (p) REVERT: F 313 ARG cc_start: 0.7241 (mtt180) cc_final: 0.7005 (mtt90) REVERT: F 339 SER cc_start: 0.8177 (m) cc_final: 0.7663 (p) REVERT: F 350 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6271 (mt0) REVERT: F 390 THR cc_start: 0.7447 (m) cc_final: 0.7150 (p) REVERT: F 450 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.6860 (p) REVERT: F 466 ASN cc_start: 0.7051 (m110) cc_final: 0.6793 (m110) REVERT: F 511 ASP cc_start: 0.6986 (t0) cc_final: 0.6530 (t0) REVERT: F 555 VAL cc_start: 0.8358 (p) cc_final: 0.8112 (t) REVERT: F 556 ASP cc_start: 0.6692 (m-30) cc_final: 0.6481 (m-30) REVERT: H 82 MET cc_start: 0.6412 (mtm) cc_final: 0.6211 (mtm) outliers start: 70 outliers final: 45 residues processed: 924 average time/residue: 0.2100 time to fit residues: 301.4125 Evaluate side-chains 931 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 880 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 270 CYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 317 optimal weight: 0.0370 chunk 316 optimal weight: 5.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 95 ASN B 282 ASN B 497 GLN C 222 HIS ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 86 ASN F 302 ASN F 323 ASN F 468 GLN F 560 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.112684 restraints weight = 39574.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116795 restraints weight = 22977.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.119528 restraints weight = 15799.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.121321 restraints weight = 12215.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122488 restraints weight = 10166.184| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 28688 Z= 0.266 Angle : 0.563 6.503 39256 Z= 0.296 Chirality : 0.046 0.170 4223 Planarity : 0.005 0.047 5181 Dihedral : 5.346 54.370 3822 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.86 % Allowed : 14.92 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.53 (0.13), residues: 3507 helix: -0.55 (0.45), residues: 96 sheet: -0.47 (0.15), residues: 998 loop : -0.22 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 581 TYR 0.023 0.002 TYR B 342 PHE 0.025 0.002 PHE A 448 TRP 0.014 0.002 TRP B 528 HIS 0.020 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00592 (28679) covalent geometry : angle 0.55966 (39238) SS BOND : bond 0.00582 ( 9) SS BOND : angle 3.03178 ( 18) hydrogen bonds : bond 0.03839 ( 396) hydrogen bonds : angle 5.64928 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 924 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7619 (m) cc_final: 0.7266 (p) REVERT: A 49 THR cc_start: 0.7463 (m) cc_final: 0.7096 (p) REVERT: A 60 TYR cc_start: 0.5872 (m-10) cc_final: 0.5635 (m-10) REVERT: A 80 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6875 (mtp180) REVERT: A 109 TRP cc_start: 0.7861 (m100) cc_final: 0.7557 (m100) REVERT: A 135 GLU cc_start: 0.6641 (pt0) cc_final: 0.6174 (pt0) REVERT: A 193 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5321 (tt0) REVERT: A 350 GLN cc_start: 0.7001 (mp10) cc_final: 0.6565 (mp10) REVERT: A 394 THR cc_start: 0.8111 (m) cc_final: 0.7906 (t) REVERT: A 511 ASP cc_start: 0.7529 (t0) cc_final: 0.7265 (t0) REVERT: A 532 LYS cc_start: 0.7306 (ttmm) cc_final: 0.7078 (tttm) REVERT: B 60 TYR cc_start: 0.5590 (m-80) cc_final: 0.5292 (m-10) REVERT: B 80 ARG cc_start: 0.5713 (mmp80) cc_final: 0.5004 (mmp80) REVERT: B 89 LYS cc_start: 0.7461 (tppt) cc_final: 0.7193 (tppt) REVERT: B 99 ASP cc_start: 0.6425 (t0) cc_final: 0.5960 (t0) REVERT: B 223 THR cc_start: 0.7927 (m) cc_final: 0.7526 (p) REVERT: B 312 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6820 (mmtt) REVERT: B 457 LEU cc_start: 0.7167 (pt) cc_final: 0.6857 (pp) REVERT: B 570 LYS cc_start: 0.7446 (ptmt) cc_final: 0.7213 (ptmt) REVERT: B 574 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5819 (mm-30) REVERT: C 52 LYS cc_start: 0.7461 (tmtm) cc_final: 0.6805 (tmtm) REVERT: C 122 ASN cc_start: 0.7289 (p0) cc_final: 0.6596 (p0) REVERT: C 125 ASP cc_start: 0.6301 (m-30) cc_final: 0.5613 (m-30) REVERT: C 133 MET cc_start: 0.6943 (mmt) cc_final: 0.6561 (mmt) REVERT: C 135 GLU cc_start: 0.6647 (pt0) cc_final: 0.6054 (pt0) REVERT: C 137 HIS cc_start: 0.7687 (m-70) cc_final: 0.7183 (m90) REVERT: C 292 ASN cc_start: 0.7130 (m-40) cc_final: 0.6882 (m-40) REVERT: C 309 GLN cc_start: 0.6759 (tt0) cc_final: 0.6464 (tt0) REVERT: C 346 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6394 (mt-10) REVERT: C 414 TRP cc_start: 0.7518 (p90) cc_final: 0.7107 (p90) REVERT: C 439 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7549 (mmtt) REVERT: D 51 PHE cc_start: 0.7216 (m-80) cc_final: 0.6966 (m-80) REVERT: D 75 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5420 (pp20) REVERT: D 99 ASP cc_start: 0.6933 (t0) cc_final: 0.6564 (t0) REVERT: D 101 THR cc_start: 0.7369 (m) cc_final: 0.7043 (t) REVERT: D 221 SER cc_start: 0.7936 (p) cc_final: 0.7691 (p) REVERT: D 244 TYR cc_start: 0.7421 (m-80) cc_final: 0.7197 (m-80) REVERT: D 245 THR cc_start: 0.7643 (m) cc_final: 0.7415 (m) REVERT: D 316 VAL cc_start: 0.7890 (t) cc_final: 0.7443 (p) REVERT: D 344 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7263 (p) REVERT: D 411 GLU cc_start: 0.6683 (mp0) cc_final: 0.6165 (mp0) REVERT: D 414 TRP cc_start: 0.7100 (p90) cc_final: 0.6620 (p90) REVERT: D 513 ASP cc_start: 0.6468 (m-30) cc_final: 0.6146 (m-30) REVERT: E 49 THR cc_start: 0.7453 (t) cc_final: 0.7171 (m) REVERT: E 60 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.5534 (t80) REVERT: E 80 ARG cc_start: 0.6208 (mtt-85) cc_final: 0.5877 (mtt-85) REVERT: E 99 ASP cc_start: 0.6758 (t0) cc_final: 0.6347 (t70) REVERT: E 198 TYR cc_start: 0.7328 (m-80) cc_final: 0.7056 (m-80) REVERT: E 255 LEU cc_start: 0.7088 (mt) cc_final: 0.6741 (mp) REVERT: E 282 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7272 (m-40) REVERT: E 416 GLN cc_start: 0.7379 (pt0) cc_final: 0.7149 (pt0) REVERT: E 427 ASP cc_start: 0.6909 (m-30) cc_final: 0.6482 (t0) REVERT: F 51 PHE cc_start: 0.7385 (m-80) cc_final: 0.7161 (m-80) REVERT: F 52 LYS cc_start: 0.7297 (tttm) cc_final: 0.7007 (tttm) REVERT: F 73 MET cc_start: 0.7661 (ptt) cc_final: 0.7421 (ptm) REVERT: F 151 LYS cc_start: 0.7571 (mttm) cc_final: 0.7304 (mttm) REVERT: F 215 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6366 (t0) REVERT: F 275 LEU cc_start: 0.7744 (mp) cc_final: 0.7485 (mt) REVERT: F 276 THR cc_start: 0.7573 (p) cc_final: 0.7323 (p) REVERT: F 318 GLN cc_start: 0.6526 (mt0) cc_final: 0.6266 (mt0) REVERT: F 339 SER cc_start: 0.8137 (m) cc_final: 0.7634 (p) REVERT: F 350 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6363 (mt0) REVERT: F 387 LYS cc_start: 0.6803 (ttpp) cc_final: 0.6497 (ttpp) REVERT: F 390 THR cc_start: 0.7474 (m) cc_final: 0.7175 (p) REVERT: F 401 ILE cc_start: 0.6642 (mm) cc_final: 0.6413 (mm) REVERT: F 466 ASN cc_start: 0.7071 (m110) cc_final: 0.6809 (m110) REVERT: F 555 VAL cc_start: 0.8370 (p) cc_final: 0.8115 (t) REVERT: F 556 ASP cc_start: 0.6732 (m-30) cc_final: 0.6483 (m-30) REVERT: F 571 ILE cc_start: 0.7429 (mt) cc_final: 0.7203 (tt) outliers start: 87 outliers final: 59 residues processed: 954 average time/residue: 0.1962 time to fit residues: 292.2864 Evaluate side-chains 979 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 913 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 558 GLN Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 289 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 321 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 202 optimal weight: 0.0670 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 350 GLN A 383 GLN B 95 ASN B 167 ASN C 95 ASN C 222 HIS C 558 GLN D 95 ASN D 242 GLN D 383 GLN F 323 ASN F 468 GLN F 560 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117087 restraints weight = 39237.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121263 restraints weight = 22576.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124001 restraints weight = 15268.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125690 restraints weight = 11653.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.127033 restraints weight = 9646.693| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28688 Z= 0.102 Angle : 0.488 6.875 39256 Z= 0.251 Chirality : 0.042 0.159 4223 Planarity : 0.004 0.047 5181 Dihedral : 4.921 55.229 3822 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.30 % Allowed : 15.81 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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 (0.14), residues: 3507 helix: -0.45 (0.46), residues: 96 sheet: -0.42 (0.15), residues: 1042 loop : -0.13 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 314 TYR 0.013 0.001 TYR A 342 PHE 0.020 0.001 PHE A 448 TRP 0.010 0.001 TRP A 214 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00225 (28679) covalent geometry : angle 0.48513 (39238) SS BOND : bond 0.00469 ( 9) SS BOND : angle 2.31225 ( 18) hydrogen bonds : bond 0.03094 ( 396) hydrogen bonds : angle 5.41583 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 914 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7511 (m) cc_final: 0.7164 (p) REVERT: A 49 THR cc_start: 0.7443 (m) cc_final: 0.7083 (p) REVERT: A 80 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6936 (mtp180) REVERT: A 135 GLU cc_start: 0.6588 (pt0) cc_final: 0.6184 (pt0) REVERT: A 163 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.6266 (ptmt) REVERT: A 193 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5438 (tt0) REVERT: A 344 SER cc_start: 0.7285 (t) cc_final: 0.6997 (p) REVERT: A 350 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6537 (mp10) REVERT: A 394 THR cc_start: 0.8089 (m) cc_final: 0.7886 (t) REVERT: A 401 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7151 (mm) REVERT: A 417 ASN cc_start: 0.7496 (t0) cc_final: 0.7151 (t0) REVERT: A 439 LYS cc_start: 0.7206 (mmtp) cc_final: 0.6979 (mmtp) REVERT: A 511 ASP cc_start: 0.7462 (t0) cc_final: 0.7174 (t0) REVERT: A 530 LYS cc_start: 0.7461 (ttpp) cc_final: 0.7248 (ttpt) REVERT: A 532 LYS cc_start: 0.7237 (ttmm) cc_final: 0.7010 (tttm) REVERT: A 561 TYR cc_start: 0.7522 (m-80) cc_final: 0.6996 (m-80) REVERT: B 60 TYR cc_start: 0.5497 (m-80) cc_final: 0.5203 (m-10) REVERT: B 80 ARG cc_start: 0.5893 (mmp80) cc_final: 0.5216 (mmp80) REVERT: B 89 LYS cc_start: 0.7429 (tppt) cc_final: 0.7188 (tppt) REVERT: B 95 ASN cc_start: 0.7068 (m-40) cc_final: 0.6758 (m110) REVERT: B 99 ASP cc_start: 0.6438 (t0) cc_final: 0.5895 (t0) REVERT: B 223 THR cc_start: 0.7741 (m) cc_final: 0.7367 (p) REVERT: B 312 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6984 (mmtt) REVERT: B 321 ASN cc_start: 0.6851 (p0) cc_final: 0.6639 (p0) REVERT: B 434 ASP cc_start: 0.7318 (m-30) cc_final: 0.7002 (m-30) REVERT: B 570 LYS cc_start: 0.7346 (ptmt) cc_final: 0.7084 (ptmt) REVERT: B 574 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5716 (mm-30) REVERT: C 52 LYS cc_start: 0.7429 (tmtm) cc_final: 0.6805 (tmtm) REVERT: C 95 ASN cc_start: 0.7207 (m110) cc_final: 0.6922 (m-40) REVERT: C 133 MET cc_start: 0.6823 (mmt) cc_final: 0.6448 (mmt) REVERT: C 135 GLU cc_start: 0.6655 (pt0) cc_final: 0.6131 (pt0) REVERT: C 237 ASP cc_start: 0.6443 (m-30) cc_final: 0.6242 (m-30) REVERT: C 242 GLN cc_start: 0.7306 (mt0) cc_final: 0.7056 (mt0) REVERT: C 292 ASN cc_start: 0.7027 (m-40) cc_final: 0.6767 (m-40) REVERT: C 309 GLN cc_start: 0.6748 (tt0) cc_final: 0.6510 (tt0) REVERT: C 312 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6975 (mmtt) REVERT: C 346 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6312 (mt-10) REVERT: C 414 TRP cc_start: 0.7520 (p90) cc_final: 0.7084 (p90) REVERT: C 481 ARG cc_start: 0.6896 (mtp180) cc_final: 0.6621 (mtp180) REVERT: D 51 PHE cc_start: 0.7198 (m-80) cc_final: 0.6907 (m-80) REVERT: D 75 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5446 (pp20) REVERT: D 99 ASP cc_start: 0.6980 (t0) cc_final: 0.6507 (t0) REVERT: D 101 THR cc_start: 0.7414 (m) cc_final: 0.7060 (t) REVERT: D 221 SER cc_start: 0.7980 (p) cc_final: 0.7766 (p) REVERT: D 244 TYR cc_start: 0.7433 (m-80) cc_final: 0.7216 (m-80) REVERT: D 245 THR cc_start: 0.7556 (m) cc_final: 0.7332 (m) REVERT: D 316 VAL cc_start: 0.7939 (t) cc_final: 0.7552 (p) REVERT: D 344 SER cc_start: 0.7385 (t) cc_final: 0.7165 (p) REVERT: D 411 GLU cc_start: 0.6672 (mp0) cc_final: 0.6162 (mp0) REVERT: D 414 TRP cc_start: 0.7086 (p90) cc_final: 0.6660 (p90) REVERT: D 513 ASP cc_start: 0.6450 (m-30) cc_final: 0.6139 (m-30) REVERT: E 49 THR cc_start: 0.7339 (t) cc_final: 0.7060 (m) REVERT: E 60 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.5717 (m-80) REVERT: E 80 ARG cc_start: 0.6238 (mtt-85) cc_final: 0.5942 (mtt-85) REVERT: E 178 ASP cc_start: 0.6202 (t0) cc_final: 0.5863 (t0) REVERT: E 198 TYR cc_start: 0.7304 (m-80) cc_final: 0.7009 (m-80) REVERT: E 255 LEU cc_start: 0.7070 (mt) cc_final: 0.6720 (mp) REVERT: E 303 PHE cc_start: 0.6867 (m-80) cc_final: 0.6579 (m-80) REVERT: E 350 GLN cc_start: 0.7048 (mp10) cc_final: 0.6284 (mp10) REVERT: E 416 GLN cc_start: 0.7363 (pt0) cc_final: 0.7157 (pt0) REVERT: E 427 ASP cc_start: 0.6836 (m-30) cc_final: 0.6413 (t0) REVERT: E 532 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7291 (ttmm) REVERT: F 52 LYS cc_start: 0.7227 (tttm) cc_final: 0.6952 (tttm) REVERT: F 59 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7553 (m) REVERT: F 60 TYR cc_start: 0.6053 (m-80) cc_final: 0.5647 (t80) REVERT: F 73 MET cc_start: 0.7626 (ptt) cc_final: 0.7425 (ptm) REVERT: F 151 LYS cc_start: 0.7565 (mttm) cc_final: 0.7303 (mttm) REVERT: F 215 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6266 (t0) REVERT: F 275 LEU cc_start: 0.7703 (mp) cc_final: 0.7387 (mt) REVERT: F 339 SER cc_start: 0.8175 (m) cc_final: 0.7661 (p) REVERT: F 350 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6207 (mt0) REVERT: F 387 LYS cc_start: 0.6866 (ttpp) cc_final: 0.6541 (ttpp) REVERT: F 390 THR cc_start: 0.7518 (m) cc_final: 0.7266 (p) REVERT: F 401 ILE cc_start: 0.6524 (mm) cc_final: 0.6267 (mm) REVERT: F 466 ASN cc_start: 0.7006 (m110) cc_final: 0.6771 (m110) REVERT: F 511 ASP cc_start: 0.6996 (t0) cc_final: 0.6556 (t0) REVERT: F 555 VAL cc_start: 0.8308 (p) cc_final: 0.8047 (t) REVERT: F 556 ASP cc_start: 0.6685 (m-30) cc_final: 0.6439 (m-30) REVERT: F 571 ILE cc_start: 0.7400 (mt) cc_final: 0.7177 (tt) REVERT: H 82 MET cc_start: 0.6596 (mtm) cc_final: 0.5886 (mtm) outliers start: 70 outliers final: 43 residues processed: 943 average time/residue: 0.2073 time to fit residues: 303.5207 Evaluate side-chains 940 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 888 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 101 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN B 497 GLN C 47 ASN C 302 ASN C 558 GLN D 242 GLN D 383 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN E 86 ASN ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 323 ASN F 386 GLN F 560 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.112702 restraints weight = 39557.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.116774 restraints weight = 22946.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119525 restraints weight = 15848.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.121210 restraints weight = 12209.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122554 restraints weight = 10223.652| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 28688 Z= 0.268 Angle : 0.569 7.677 39256 Z= 0.297 Chirality : 0.046 0.178 4223 Planarity : 0.005 0.093 5181 Dihedral : 5.275 54.848 3821 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.60 % Allowed : 16.11 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.52 (0.14), residues: 3507 helix: -0.49 (0.46), residues: 96 sheet: -0.44 (0.16), residues: 1008 loop : -0.24 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 67 TYR 0.023 0.002 TYR B 342 PHE 0.025 0.002 PHE A 448 TRP 0.012 0.002 TRP E 529 HIS 0.007 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00600 (28679) covalent geometry : angle 0.56568 (39238) SS BOND : bond 0.00583 ( 9) SS BOND : angle 3.01196 ( 18) hydrogen bonds : bond 0.03710 ( 396) hydrogen bonds : angle 5.54754 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 910 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7638 (m) cc_final: 0.7339 (p) REVERT: A 49 THR cc_start: 0.7455 (m) cc_final: 0.7084 (p) REVERT: A 80 ARG cc_start: 0.7142 (mtt180) cc_final: 0.6920 (mtp180) REVERT: A 109 TRP cc_start: 0.7900 (m100) cc_final: 0.7638 (m100) REVERT: A 135 GLU cc_start: 0.6621 (pt0) cc_final: 0.6180 (pt0) REVERT: A 163 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6355 (ptmt) REVERT: A 193 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5313 (tt0) REVERT: A 350 GLN cc_start: 0.7116 (mp10) cc_final: 0.6883 (mp10) REVERT: A 394 THR cc_start: 0.8096 (m) cc_final: 0.7845 (t) REVERT: A 511 ASP cc_start: 0.7546 (t0) cc_final: 0.7278 (t0) REVERT: B 60 TYR cc_start: 0.5612 (m-80) cc_final: 0.5303 (m-10) REVERT: B 80 ARG cc_start: 0.5682 (mmp80) cc_final: 0.5012 (mmp80) REVERT: B 89 LYS cc_start: 0.7495 (tppt) cc_final: 0.7087 (tppt) REVERT: B 95 ASN cc_start: 0.7117 (m-40) cc_final: 0.6851 (m110) REVERT: B 99 ASP cc_start: 0.6302 (t0) cc_final: 0.5967 (t0) REVERT: B 133 MET cc_start: 0.6772 (mmt) cc_final: 0.6535 (mmm) REVERT: B 223 THR cc_start: 0.7876 (m) cc_final: 0.7487 (p) REVERT: B 231 ASN cc_start: 0.7237 (t0) cc_final: 0.6859 (t0) REVERT: B 312 LYS cc_start: 0.7302 (mmtt) cc_final: 0.6974 (mmtt) REVERT: B 382 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.6723 (mtm-85) REVERT: B 449 ASN cc_start: 0.7683 (t0) cc_final: 0.7463 (t0) REVERT: B 509 GLN cc_start: 0.6549 (mt0) cc_final: 0.6268 (mt0) REVERT: B 570 LYS cc_start: 0.7433 (ptmt) cc_final: 0.7190 (ptmt) REVERT: B 574 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5821 (mm-30) REVERT: C 52 LYS cc_start: 0.7456 (tmtm) cc_final: 0.6814 (tmtm) REVERT: C 125 ASP cc_start: 0.6225 (m-30) cc_final: 0.5787 (m-30) REVERT: C 133 MET cc_start: 0.6921 (mmt) cc_final: 0.6576 (mmt) REVERT: C 135 GLU cc_start: 0.6634 (pt0) cc_final: 0.6166 (pt0) REVERT: C 137 HIS cc_start: 0.7703 (m-70) cc_final: 0.7218 (m90) REVERT: C 237 ASP cc_start: 0.6519 (m-30) cc_final: 0.6288 (m-30) REVERT: C 292 ASN cc_start: 0.7121 (m-40) cc_final: 0.6869 (m-40) REVERT: C 309 GLN cc_start: 0.6789 (tt0) cc_final: 0.6508 (tt0) REVERT: C 312 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6806 (mmtt) REVERT: C 346 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6312 (mt-10) REVERT: C 414 TRP cc_start: 0.7505 (p90) cc_final: 0.7093 (p90) REVERT: D 51 PHE cc_start: 0.7193 (m-80) cc_final: 0.6823 (m-80) REVERT: D 75 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5412 (pp20) REVERT: D 99 ASP cc_start: 0.6890 (t0) cc_final: 0.6500 (t0) REVERT: D 101 THR cc_start: 0.7345 (m) cc_final: 0.7030 (t) REVERT: D 125 ASP cc_start: 0.6378 (m-30) cc_final: 0.6076 (m-30) REVERT: D 221 SER cc_start: 0.7971 (p) cc_final: 0.7717 (p) REVERT: D 316 VAL cc_start: 0.7903 (t) cc_final: 0.7445 (p) REVERT: D 344 SER cc_start: 0.7503 (OUTLIER) cc_final: 0.7240 (p) REVERT: D 411 GLU cc_start: 0.6680 (mp0) cc_final: 0.6066 (mp0) REVERT: D 414 TRP cc_start: 0.7132 (p90) cc_final: 0.6580 (p90) REVERT: D 513 ASP cc_start: 0.6470 (m-30) cc_final: 0.6191 (m-30) REVERT: E 49 THR cc_start: 0.7430 (t) cc_final: 0.7140 (m) REVERT: E 60 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5525 (t80) REVERT: E 80 ARG cc_start: 0.6242 (mtt-85) cc_final: 0.5906 (mtt-85) REVERT: E 198 TYR cc_start: 0.7328 (m-80) cc_final: 0.7068 (m-80) REVERT: E 350 GLN cc_start: 0.6975 (mp10) cc_final: 0.6178 (mp10) REVERT: E 416 GLN cc_start: 0.7370 (pt0) cc_final: 0.7164 (pt0) REVERT: E 427 ASP cc_start: 0.6972 (m-30) cc_final: 0.6578 (t0) REVERT: F 51 PHE cc_start: 0.7543 (m-10) cc_final: 0.7282 (m-80) REVERT: F 52 LYS cc_start: 0.7300 (tttm) cc_final: 0.6995 (tttm) REVERT: F 60 TYR cc_start: 0.6076 (m-80) cc_final: 0.5723 (t80) REVERT: F 73 MET cc_start: 0.7649 (ptt) cc_final: 0.7420 (ptm) REVERT: F 215 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6320 (t0) REVERT: F 275 LEU cc_start: 0.7653 (mp) cc_final: 0.7378 (mt) REVERT: F 310 GLN cc_start: 0.6810 (mt0) cc_final: 0.6521 (mm-40) REVERT: F 339 SER cc_start: 0.8118 (m) cc_final: 0.7607 (p) REVERT: F 350 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6328 (mt0) REVERT: F 387 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6500 (ttpp) REVERT: F 390 THR cc_start: 0.7507 (m) cc_final: 0.7216 (p) REVERT: F 466 ASN cc_start: 0.7041 (m110) cc_final: 0.6785 (m110) REVERT: F 555 VAL cc_start: 0.8358 (p) cc_final: 0.8077 (t) REVERT: F 556 ASP cc_start: 0.6705 (m-30) cc_final: 0.6501 (m-30) REVERT: F 571 ILE cc_start: 0.7400 (mt) cc_final: 0.7164 (tt) REVERT: H 82 MET cc_start: 0.6639 (mtm) cc_final: 0.5864 (mtm) outliers start: 79 outliers final: 54 residues processed: 940 average time/residue: 0.1856 time to fit residues: 272.4926 Evaluate side-chains 952 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 891 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 532 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 333 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN D 242 GLN D 383 GLN E 86 ASN ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 560 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114822 restraints weight = 39762.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118975 restraints weight = 22998.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121747 restraints weight = 15677.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123517 restraints weight = 11960.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124861 restraints weight = 9859.602| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28688 Z= 0.119 Angle : 0.495 7.999 39256 Z= 0.255 Chirality : 0.042 0.174 4223 Planarity : 0.004 0.049 5181 Dihedral : 4.921 56.205 3821 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.14 % Allowed : 17.29 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.45 (0.14), residues: 3507 helix: -0.48 (0.46), residues: 96 sheet: -0.43 (0.15), residues: 1042 loop : -0.16 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 216 TYR 0.015 0.001 TYR A 244 PHE 0.026 0.001 PHE E 45 TRP 0.011 0.001 TRP B 414 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00269 (28679) covalent geometry : angle 0.49285 (39238) SS BOND : bond 0.00362 ( 9) SS BOND : angle 2.35721 ( 18) hydrogen bonds : bond 0.03093 ( 396) hydrogen bonds : angle 5.38195 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 906 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7606 (m) cc_final: 0.7326 (p) REVERT: A 49 THR cc_start: 0.7416 (m) cc_final: 0.7052 (p) REVERT: A 60 TYR cc_start: 0.5843 (m-10) cc_final: 0.5608 (m-10) REVERT: A 80 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6968 (mtp180) REVERT: A 135 GLU cc_start: 0.6606 (pt0) cc_final: 0.6185 (pt0) REVERT: A 163 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6344 (ptmt) REVERT: A 193 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5478 (tt0) REVERT: A 230 THR cc_start: 0.8245 (p) cc_final: 0.7942 (t) REVERT: A 401 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7180 (mm) REVERT: A 417 ASN cc_start: 0.7507 (t0) cc_final: 0.7173 (t0) REVERT: A 530 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7113 (ttpp) REVERT: B 60 TYR cc_start: 0.5560 (m-80) cc_final: 0.5274 (m-10) REVERT: B 80 ARG cc_start: 0.5872 (mmp80) cc_final: 0.5160 (mmp80) REVERT: B 89 LYS cc_start: 0.7496 (tppt) cc_final: 0.7207 (tppt) REVERT: B 95 ASN cc_start: 0.7083 (m-40) cc_final: 0.6722 (m-40) REVERT: B 99 ASP cc_start: 0.6446 (t0) cc_final: 0.5932 (t0) REVERT: B 312 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6984 (mmtt) REVERT: B 570 LYS cc_start: 0.7361 (ptmt) cc_final: 0.7080 (ptmt) REVERT: B 574 GLU cc_start: 0.6213 (mm-30) cc_final: 0.5807 (mm-30) REVERT: B 583 LEU cc_start: 0.8138 (tp) cc_final: 0.7887 (tt) REVERT: C 52 LYS cc_start: 0.7420 (tmtm) cc_final: 0.6815 (tmtm) REVERT: C 125 ASP cc_start: 0.6136 (m-30) cc_final: 0.5716 (m-30) REVERT: C 133 MET cc_start: 0.6854 (mmt) cc_final: 0.6504 (mmt) REVERT: C 135 GLU cc_start: 0.6624 (pt0) cc_final: 0.6200 (pt0) REVERT: C 137 HIS cc_start: 0.7646 (m-70) cc_final: 0.7187 (m90) REVERT: C 237 ASP cc_start: 0.6489 (m-30) cc_final: 0.6248 (m-30) REVERT: C 292 ASN cc_start: 0.7066 (m-40) cc_final: 0.6789 (m-40) REVERT: C 309 GLN cc_start: 0.6772 (tt0) cc_final: 0.6521 (tt0) REVERT: C 312 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6871 (mmtt) REVERT: C 411 GLU cc_start: 0.6547 (mp0) cc_final: 0.6019 (mp0) REVERT: C 414 TRP cc_start: 0.7474 (p90) cc_final: 0.7037 (p90) REVERT: C 481 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6685 (mtp180) REVERT: C 558 GLN cc_start: 0.7102 (tt0) cc_final: 0.6884 (pt0) REVERT: D 51 PHE cc_start: 0.7184 (m-80) cc_final: 0.6778 (m-80) REVERT: D 75 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5375 (pp20) REVERT: D 99 ASP cc_start: 0.6944 (t0) cc_final: 0.6501 (t0) REVERT: D 101 THR cc_start: 0.7370 (m) cc_final: 0.7024 (t) REVERT: D 125 ASP cc_start: 0.6370 (m-30) cc_final: 0.6041 (m-30) REVERT: D 221 SER cc_start: 0.7972 (p) cc_final: 0.7679 (p) REVERT: D 316 VAL cc_start: 0.7899 (t) cc_final: 0.7544 (p) REVERT: D 344 SER cc_start: 0.7419 (t) cc_final: 0.7160 (p) REVERT: D 382 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.7104 (mtm-85) REVERT: D 411 GLU cc_start: 0.6675 (mp0) cc_final: 0.6085 (mp0) REVERT: D 414 TRP cc_start: 0.7098 (p90) cc_final: 0.6639 (p90) REVERT: E 49 THR cc_start: 0.7343 (t) cc_final: 0.7057 (m) REVERT: E 60 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5702 (m-80) REVERT: E 80 ARG cc_start: 0.6292 (mtt-85) cc_final: 0.5955 (mtt-85) REVERT: E 198 TYR cc_start: 0.7312 (m-80) cc_final: 0.6993 (m-80) REVERT: E 255 LEU cc_start: 0.7074 (mt) cc_final: 0.6708 (mp) REVERT: E 350 GLN cc_start: 0.7018 (mp10) cc_final: 0.6234 (mp10) REVERT: E 416 GLN cc_start: 0.7364 (pt0) cc_final: 0.7154 (pt0) REVERT: E 427 ASP cc_start: 0.6975 (m-30) cc_final: 0.6579 (t0) REVERT: F 51 PHE cc_start: 0.7526 (m-10) cc_final: 0.7296 (m-80) REVERT: F 52 LYS cc_start: 0.7270 (tttm) cc_final: 0.6934 (tttm) REVERT: F 60 TYR cc_start: 0.6080 (m-80) cc_final: 0.5724 (t80) REVERT: F 151 LYS cc_start: 0.7512 (mttm) cc_final: 0.7303 (mttm) REVERT: F 275 LEU cc_start: 0.7642 (mp) cc_final: 0.7376 (mt) REVERT: F 310 GLN cc_start: 0.6788 (mt0) cc_final: 0.6510 (mm-40) REVERT: F 339 SER cc_start: 0.8163 (m) cc_final: 0.7624 (p) REVERT: F 350 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6352 (mt0) REVERT: F 387 LYS cc_start: 0.6887 (ttpp) cc_final: 0.6530 (ttpp) REVERT: F 390 THR cc_start: 0.7548 (m) cc_final: 0.7334 (p) REVERT: F 511 ASP cc_start: 0.6977 (t0) cc_final: 0.6527 (t0) REVERT: F 532 LYS cc_start: 0.7497 (ttmm) cc_final: 0.7252 (ttpp) REVERT: F 555 VAL cc_start: 0.8262 (p) cc_final: 0.8011 (t) REVERT: F 556 ASP cc_start: 0.6717 (m-30) cc_final: 0.6483 (m-30) REVERT: F 571 ILE cc_start: 0.7414 (mt) cc_final: 0.7163 (tt) REVERT: F 581 ARG cc_start: 0.7664 (ptt-90) cc_final: 0.7362 (ptt-90) REVERT: H 82 MET cc_start: 0.6599 (mtm) cc_final: 0.5846 (mtm) outliers start: 65 outliers final: 46 residues processed: 932 average time/residue: 0.1992 time to fit residues: 288.5505 Evaluate side-chains 955 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 903 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 163 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 237 optimal weight: 0.0770 chunk 321 optimal weight: 0.7980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 383 GLN B 383 GLN B 449 ASN C 47 ASN C 416 GLN D 242 GLN E 86 ASN E 127 GLN ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 468 GLN F 560 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.119906 restraints weight = 38704.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.124168 restraints weight = 21908.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.126904 restraints weight = 14709.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128691 restraints weight = 11155.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129989 restraints weight = 9142.847| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28688 Z= 0.161 Angle : 0.518 8.746 39256 Z= 0.267 Chirality : 0.043 0.170 4223 Planarity : 0.005 0.047 5181 Dihedral : 4.989 55.855 3821 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.01 % Allowed : 17.42 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.45 (0.14), residues: 3507 helix: -0.44 (0.46), residues: 96 sheet: -0.43 (0.15), residues: 1042 loop : -0.16 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 382 TYR 0.022 0.001 TYR A 244 PHE 0.026 0.002 PHE E 353 TRP 0.016 0.001 TRP C 214 HIS 0.006 0.001 HIS C 70 Details of bonding type rmsd covalent geometry : bond 0.00364 (28679) covalent geometry : angle 0.51525 (39238) SS BOND : bond 0.00459 ( 9) SS BOND : angle 2.60199 ( 18) hydrogen bonds : bond 0.03254 ( 396) hydrogen bonds : angle 5.38090 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 891 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7638 (m) cc_final: 0.7266 (p) REVERT: A 49 THR cc_start: 0.7424 (m) cc_final: 0.7060 (p) REVERT: A 60 TYR cc_start: 0.5846 (m-10) cc_final: 0.5578 (m-10) REVERT: A 80 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6974 (mtp180) REVERT: A 109 TRP cc_start: 0.7912 (m100) cc_final: 0.7626 (m100) REVERT: A 135 GLU cc_start: 0.6597 (pt0) cc_final: 0.6191 (pt0) REVERT: A 163 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6355 (ptmt) REVERT: A 193 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5444 (tt0) REVERT: A 230 THR cc_start: 0.8260 (p) cc_final: 0.7951 (t) REVERT: A 350 GLN cc_start: 0.6996 (mp10) cc_final: 0.6733 (mp10) REVERT: A 401 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7185 (mm) REVERT: A 417 ASN cc_start: 0.7477 (t0) cc_final: 0.7106 (t0) REVERT: A 530 LYS cc_start: 0.7507 (ttpp) cc_final: 0.7205 (ttpt) REVERT: B 60 TYR cc_start: 0.5557 (m-80) cc_final: 0.5278 (m-10) REVERT: B 80 ARG cc_start: 0.5725 (mmp80) cc_final: 0.5027 (mmp80) REVERT: B 89 LYS cc_start: 0.7510 (tppt) cc_final: 0.7067 (tppt) REVERT: B 99 ASP cc_start: 0.6481 (t0) cc_final: 0.6007 (t0) REVERT: B 312 LYS cc_start: 0.7289 (mmtt) cc_final: 0.7013 (mmtt) REVERT: B 322 THR cc_start: 0.6904 (t) cc_final: 0.6534 (p) REVERT: B 353 PHE cc_start: 0.7428 (p90) cc_final: 0.7095 (p90) REVERT: B 509 GLN cc_start: 0.6544 (mt0) cc_final: 0.6269 (mt0) REVERT: B 570 LYS cc_start: 0.7360 (ptmt) cc_final: 0.7096 (ptmt) REVERT: B 574 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5781 (mm-30) REVERT: C 52 LYS cc_start: 0.7425 (tmtm) cc_final: 0.6841 (tmtm) REVERT: C 125 ASP cc_start: 0.6142 (m-30) cc_final: 0.5724 (m-30) REVERT: C 133 MET cc_start: 0.6888 (mmt) cc_final: 0.6547 (mmt) REVERT: C 135 GLU cc_start: 0.6642 (pt0) cc_final: 0.6182 (pt0) REVERT: C 137 HIS cc_start: 0.7633 (m-70) cc_final: 0.7197 (m90) REVERT: C 237 ASP cc_start: 0.6508 (m-30) cc_final: 0.6257 (m-30) REVERT: C 292 ASN cc_start: 0.7048 (m-40) cc_final: 0.6783 (m-40) REVERT: C 309 GLN cc_start: 0.6788 (tt0) cc_final: 0.6443 (tt0) REVERT: C 414 TRP cc_start: 0.7576 (p90) cc_final: 0.7111 (p90) REVERT: C 526 ASP cc_start: 0.6239 (m-30) cc_final: 0.6014 (m-30) REVERT: D 51 PHE cc_start: 0.7188 (m-80) cc_final: 0.6839 (m-80) REVERT: D 75 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5364 (pp20) REVERT: D 99 ASP cc_start: 0.6876 (t0) cc_final: 0.6457 (t0) REVERT: D 101 THR cc_start: 0.7382 (m) cc_final: 0.7064 (t) REVERT: D 125 ASP cc_start: 0.6368 (m-30) cc_final: 0.6119 (m-30) REVERT: D 221 SER cc_start: 0.7952 (p) cc_final: 0.7654 (p) REVERT: D 242 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: D 316 VAL cc_start: 0.7908 (t) cc_final: 0.7543 (p) REVERT: D 344 SER cc_start: 0.7403 (t) cc_final: 0.7138 (p) REVERT: D 350 GLN cc_start: 0.7211 (mp10) cc_final: 0.6627 (mp10) REVERT: D 382 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.7095 (mtm-85) REVERT: D 411 GLU cc_start: 0.6669 (mp0) cc_final: 0.6112 (mp0) REVERT: D 414 TRP cc_start: 0.7117 (p90) cc_final: 0.6677 (p90) REVERT: E 49 THR cc_start: 0.7382 (t) cc_final: 0.7087 (m) REVERT: E 60 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.5709 (m-80) REVERT: E 80 ARG cc_start: 0.6237 (mtt-85) cc_final: 0.5910 (mtt-85) REVERT: E 198 TYR cc_start: 0.7318 (m-80) cc_final: 0.7037 (m-80) REVERT: E 255 LEU cc_start: 0.7118 (mt) cc_final: 0.6747 (mp) REVERT: E 317 THR cc_start: 0.7663 (p) cc_final: 0.7451 (m) REVERT: E 350 GLN cc_start: 0.6999 (mp10) cc_final: 0.6216 (mp10) REVERT: E 427 ASP cc_start: 0.6876 (m-30) cc_final: 0.6501 (t0) REVERT: F 51 PHE cc_start: 0.7519 (m-10) cc_final: 0.7304 (m-80) REVERT: F 52 LYS cc_start: 0.7264 (tttm) cc_final: 0.6954 (tttm) REVERT: F 60 TYR cc_start: 0.6047 (m-80) cc_final: 0.5717 (t80) REVERT: F 151 LYS cc_start: 0.7530 (mttm) cc_final: 0.7325 (mttm) REVERT: F 275 LEU cc_start: 0.7664 (mp) cc_final: 0.7369 (mt) REVERT: F 310 GLN cc_start: 0.6773 (mt0) cc_final: 0.6489 (mm-40) REVERT: F 339 SER cc_start: 0.8153 (m) cc_final: 0.7636 (p) REVERT: F 350 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6321 (mt0) REVERT: F 387 LYS cc_start: 0.6872 (ttpp) cc_final: 0.6534 (ttpp) REVERT: F 390 THR cc_start: 0.7585 (m) cc_final: 0.7336 (p) REVERT: F 511 ASP cc_start: 0.6957 (t0) cc_final: 0.6518 (t0) REVERT: F 532 LYS cc_start: 0.7536 (ttmm) cc_final: 0.7298 (ttpp) REVERT: F 555 VAL cc_start: 0.8277 (p) cc_final: 0.8029 (t) REVERT: F 556 ASP cc_start: 0.6683 (m-30) cc_final: 0.6442 (m-30) REVERT: F 571 ILE cc_start: 0.7407 (mt) cc_final: 0.7173 (tt) REVERT: H 82 MET cc_start: 0.6537 (mtm) cc_final: 0.5851 (mtm) outliers start: 61 outliers final: 48 residues processed: 915 average time/residue: 0.1948 time to fit residues: 277.7228 Evaluate side-chains 938 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 883 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 230 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 312 optimal weight: 0.4980 chunk 232 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 47 ASN C 558 GLN D 242 GLN D 383 GLN E 86 ASN F 47 ASN F 48 GLN F 323 ASN F 560 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.114851 restraints weight = 39640.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.118961 restraints weight = 22642.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121746 restraints weight = 15428.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.123564 restraints weight = 11776.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124617 restraints weight = 9724.055| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28688 Z= 0.155 Angle : 0.519 9.059 39256 Z= 0.267 Chirality : 0.043 0.169 4223 Planarity : 0.005 0.049 5181 Dihedral : 4.979 56.042 3821 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.10 % Allowed : 17.29 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.45 (0.14), residues: 3507 helix: -0.47 (0.46), residues: 96 sheet: -0.42 (0.15), residues: 1052 loop : -0.16 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 382 TYR 0.019 0.001 TYR A 244 PHE 0.023 0.002 PHE C 398 TRP 0.017 0.001 TRP E 279 HIS 0.006 0.001 HIS C 70 Details of bonding type rmsd covalent geometry : bond 0.00351 (28679) covalent geometry : angle 0.51652 (39238) SS BOND : bond 0.00465 ( 9) SS BOND : angle 2.57112 ( 18) hydrogen bonds : bond 0.03250 ( 396) hydrogen bonds : angle 5.37292 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 884 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7638 (m) cc_final: 0.7249 (p) REVERT: A 49 THR cc_start: 0.7421 (m) cc_final: 0.7035 (p) REVERT: A 60 TYR cc_start: 0.5762 (m-10) cc_final: 0.5518 (m-10) REVERT: A 80 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6975 (mtp180) REVERT: A 135 GLU cc_start: 0.6613 (pt0) cc_final: 0.6178 (pt0) REVERT: A 193 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5457 (tt0) REVERT: A 230 THR cc_start: 0.8267 (p) cc_final: 0.7958 (t) REVERT: A 350 GLN cc_start: 0.7002 (mp10) cc_final: 0.6752 (mp10) REVERT: A 401 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7192 (mm) REVERT: A 417 ASN cc_start: 0.7474 (t0) cc_final: 0.7129 (t0) REVERT: A 530 LYS cc_start: 0.7500 (ttpp) cc_final: 0.7180 (ttpt) REVERT: B 60 TYR cc_start: 0.5581 (m-80) cc_final: 0.5278 (m-10) REVERT: B 80 ARG cc_start: 0.5706 (mmp80) cc_final: 0.4988 (mmp80) REVERT: B 89 LYS cc_start: 0.7541 (tppt) cc_final: 0.7063 (tppt) REVERT: B 96 MET cc_start: 0.7547 (ptp) cc_final: 0.7282 (ptp) REVERT: B 99 ASP cc_start: 0.6495 (t0) cc_final: 0.5980 (t0) REVERT: B 174 MET cc_start: 0.6948 (mtm) cc_final: 0.6737 (mtm) REVERT: B 206 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6673 (m) REVERT: B 219 ILE cc_start: 0.7685 (mt) cc_final: 0.7450 (mt) REVERT: B 312 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6976 (mmtt) REVERT: B 322 THR cc_start: 0.6891 (t) cc_final: 0.6539 (p) REVERT: B 353 PHE cc_start: 0.7419 (p90) cc_final: 0.7073 (p90) REVERT: B 570 LYS cc_start: 0.7378 (ptmt) cc_final: 0.7093 (ptmt) REVERT: B 574 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5829 (mm-30) REVERT: B 583 LEU cc_start: 0.8127 (tp) cc_final: 0.7877 (tt) REVERT: C 52 LYS cc_start: 0.7413 (tmtm) cc_final: 0.6816 (tmtm) REVERT: C 125 ASP cc_start: 0.6161 (m-30) cc_final: 0.5741 (m-30) REVERT: C 133 MET cc_start: 0.6871 (mmt) cc_final: 0.6520 (mmt) REVERT: C 135 GLU cc_start: 0.6659 (pt0) cc_final: 0.6213 (pt0) REVERT: C 137 HIS cc_start: 0.7631 (m-70) cc_final: 0.7190 (m90) REVERT: C 237 ASP cc_start: 0.6538 (m-30) cc_final: 0.6274 (m-30) REVERT: C 292 ASN cc_start: 0.7063 (m-40) cc_final: 0.6791 (m-40) REVERT: C 309 GLN cc_start: 0.6800 (tt0) cc_final: 0.6524 (tt0) REVERT: C 312 LYS cc_start: 0.7300 (mmtt) cc_final: 0.6836 (mmtt) REVERT: C 414 TRP cc_start: 0.7525 (p90) cc_final: 0.7097 (p90) REVERT: C 526 ASP cc_start: 0.6266 (m-30) cc_final: 0.6032 (m-30) REVERT: C 538 LYS cc_start: 0.7700 (tttt) cc_final: 0.7401 (tttt) REVERT: D 51 PHE cc_start: 0.7183 (m-80) cc_final: 0.6826 (m-80) REVERT: D 75 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5362 (pp20) REVERT: D 95 ASN cc_start: 0.6702 (m110) cc_final: 0.6486 (m-40) REVERT: D 99 ASP cc_start: 0.6872 (t0) cc_final: 0.6420 (t0) REVERT: D 101 THR cc_start: 0.7369 (m) cc_final: 0.7054 (t) REVERT: D 221 SER cc_start: 0.7945 (p) cc_final: 0.7644 (p) REVERT: D 242 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: D 316 VAL cc_start: 0.7892 (t) cc_final: 0.7523 (p) REVERT: D 344 SER cc_start: 0.7407 (t) cc_final: 0.7126 (p) REVERT: D 350 GLN cc_start: 0.7222 (mp10) cc_final: 0.6644 (mp10) REVERT: D 382 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7088 (mtm-85) REVERT: D 411 GLU cc_start: 0.6668 (mp0) cc_final: 0.6075 (mp0) REVERT: D 414 TRP cc_start: 0.7105 (p90) cc_final: 0.6663 (p90) REVERT: E 49 THR cc_start: 0.7393 (t) cc_final: 0.7106 (m) REVERT: E 60 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5698 (m-80) REVERT: E 80 ARG cc_start: 0.6252 (mtt-85) cc_final: 0.5909 (mtt-85) REVERT: E 198 TYR cc_start: 0.7312 (m-80) cc_final: 0.7021 (m-80) REVERT: E 247 GLU cc_start: 0.6696 (mp0) cc_final: 0.6226 (mp0) REVERT: E 350 GLN cc_start: 0.6984 (mp10) cc_final: 0.6211 (mp10) REVERT: E 380 PHE cc_start: 0.6567 (p90) cc_final: 0.6354 (p90) REVERT: E 427 ASP cc_start: 0.6923 (m-30) cc_final: 0.6499 (t0) REVERT: F 51 PHE cc_start: 0.7499 (m-10) cc_final: 0.7299 (m-80) REVERT: F 52 LYS cc_start: 0.7274 (tttm) cc_final: 0.6986 (tttm) REVERT: F 60 TYR cc_start: 0.6090 (m-80) cc_final: 0.5735 (t80) REVERT: F 151 LYS cc_start: 0.7521 (mttm) cc_final: 0.7313 (mttm) REVERT: F 213 GLN cc_start: 0.6913 (tm-30) cc_final: 0.6646 (tm-30) REVERT: F 275 LEU cc_start: 0.7660 (mp) cc_final: 0.7375 (mt) REVERT: F 310 GLN cc_start: 0.6782 (mt0) cc_final: 0.6489 (mm-40) REVERT: F 339 SER cc_start: 0.8154 (m) cc_final: 0.7611 (p) REVERT: F 350 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6315 (mt0) REVERT: F 387 LYS cc_start: 0.6870 (ttpp) cc_final: 0.6594 (ttpp) REVERT: F 390 THR cc_start: 0.7581 (m) cc_final: 0.7348 (p) REVERT: F 401 ILE cc_start: 0.6466 (mm) cc_final: 0.6229 (mm) REVERT: F 511 ASP cc_start: 0.6953 (t0) cc_final: 0.6485 (t0) REVERT: F 532 LYS cc_start: 0.7534 (ttmm) cc_final: 0.7279 (ttpp) REVERT: F 555 VAL cc_start: 0.8258 (p) cc_final: 0.7985 (t) REVERT: F 556 ASP cc_start: 0.6707 (m-30) cc_final: 0.6464 (m-30) REVERT: F 571 ILE cc_start: 0.7392 (mt) cc_final: 0.7151 (tt) REVERT: F 581 ARG cc_start: 0.7678 (ptt-90) cc_final: 0.7458 (ptt-90) REVERT: H 82 MET cc_start: 0.6582 (mtm) cc_final: 0.5845 (mtm) outliers start: 64 outliers final: 54 residues processed: 911 average time/residue: 0.2106 time to fit residues: 297.8097 Evaluate side-chains 938 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 877 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 176 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 254 optimal weight: 0.0370 chunk 335 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 338 optimal weight: 0.1980 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 47 ASN D 242 GLN D 383 GLN D 577 GLN E 86 ASN F 560 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.140050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.114170 restraints weight = 39852.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118292 restraints weight = 22826.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.121063 restraints weight = 15557.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.122846 restraints weight = 11911.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.124162 restraints weight = 9848.233| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28688 Z= 0.244 Angle : 0.562 8.688 39256 Z= 0.291 Chirality : 0.045 0.172 4223 Planarity : 0.005 0.065 5181 Dihedral : 5.171 56.065 3821 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.14 % Allowed : 17.16 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -0.54 (0.14), residues: 3507 helix: -0.52 (0.46), residues: 96 sheet: -0.46 (0.15), residues: 1050 loop : -0.24 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 382 TYR 0.022 0.002 TYR A 244 PHE 0.028 0.002 PHE E 45 TRP 0.019 0.002 TRP C 214 HIS 0.007 0.001 HIS C 70 Details of bonding type rmsd covalent geometry : bond 0.00546 (28679) covalent geometry : angle 0.55876 (39238) SS BOND : bond 0.00578 ( 9) SS BOND : angle 2.88409 ( 18) hydrogen bonds : bond 0.03569 ( 396) hydrogen bonds : angle 5.46063 ( 720) =============================================================================== Job complete usr+sys time: 6832.93 seconds wall clock time: 118 minutes 33.98 seconds (7113.98 seconds total)