Starting phenix.real_space_refine on Mon Jun 23 09:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7w_47693/06_2025/9e7w_47693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7w_47693/06_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_47693/06_2025/9e7w_47693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7w_47693/06_2025/9e7w_47693.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7w_47693/06_2025/9e7w_47693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7w_47693/06_2025/9e7w_47693.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.30, per 1000 atoms: 0.69 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: 6.16 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.91 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: 9.25 Time building geometry restraints manager: 7.42 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: 403.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 62.380 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 471.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (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 TRP 0.019 0.002 TRP B 528 HIS 0.009 0.001 HIS A 137 PHE 0.026 0.002 PHE E 448 TYR 0.024 0.002 TYR B 342 ARG 0.005 0.001 ARG F 332 Details of bonding type rmsd hydrogen bonds : bond 0.22155 ( 396) hydrogen bonds : angle 8.23485 ( 720) SS BOND : bond 0.00559 ( 9) SS BOND : angle 2.99800 ( 18) covalent geometry : bond 0.00686 (28679) covalent geometry : angle 0.63299 (39238) *********************** 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 : 2.651 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: 0.4207 time to fit residues: 608.9497 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 : 2.721 ------------------------------------------------------------------------------- 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 292 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS B 231 ASN C 95 ASN C 222 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 483 HIS D 242 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.114908 restraints weight = 39574.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118971 restraints weight = 22983.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121707 restraints weight = 15762.802| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28688 Z= 0.247 Angle : 0.590 8.289 39256 Z= 0.313 Chirality : 0.047 0.175 4223 Planarity : 0.005 0.046 5181 Dihedral : 6.363 59.658 3876 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.76 % Allowed : 12.52 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3507 helix: -0.69 (0.45), residues: 96 sheet: -0.64 (0.15), residues: 1008 loop : -0.37 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 279 HIS 0.006 0.001 HIS C 222 PHE 0.024 0.002 PHE A 448 TYR 0.024 0.002 TYR B 342 ARG 0.009 0.001 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 396) hydrogen bonds : angle 6.24004 ( 720) SS BOND : bond 0.00626 ( 9) SS BOND : angle 3.42855 ( 18) covalent geometry : bond 0.00552 (28679) covalent geometry : angle 0.58542 (39238) *********************** 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 1015 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 931 time to evaluate : 2.784 Fit side-chains revert: symmetry clash REVERT: A 44 THR cc_start: 0.7693 (m) cc_final: 0.7369 (p) REVERT: A 49 THR cc_start: 0.7474 (m) cc_final: 0.7135 (p) REVERT: A 60 TYR cc_start: 0.5836 (m-10) cc_final: 0.5473 (m-10) REVERT: A 80 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6936 (mtp180) REVERT: A 109 TRP cc_start: 0.7862 (m100) cc_final: 0.7566 (m100) REVERT: A 135 GLU cc_start: 0.6652 (pt0) cc_final: 0.6154 (pt0) REVERT: A 219 ILE cc_start: 0.8176 (mm) cc_final: 0.7878 (mt) REVERT: A 266 PHE cc_start: 0.7315 (t80) cc_final: 0.6928 (t80) REVERT: A 350 GLN cc_start: 0.7027 (mp10) cc_final: 0.6641 (mp10) REVERT: A 394 THR cc_start: 0.8112 (m) cc_final: 0.7866 (t) REVERT: A 417 ASN cc_start: 0.7523 (t0) cc_final: 0.7126 (t0) REVERT: A 532 LYS cc_start: 0.7313 (ttmm) cc_final: 0.7053 (ttmm) REVERT: A 561 TYR cc_start: 0.7526 (m-80) cc_final: 0.7044 (m-80) REVERT: B 60 TYR cc_start: 0.5551 (m-80) cc_final: 0.5248 (m-10) REVERT: B 80 ARG cc_start: 0.5980 (mmp80) cc_final: 0.5446 (mmp80) REVERT: B 89 LYS cc_start: 0.7418 (tppt) cc_final: 0.7148 (tppt) REVERT: B 99 ASP cc_start: 0.6373 (t0) cc_final: 0.6028 (t0) REVERT: B 223 THR cc_start: 0.7946 (m) cc_final: 0.7497 (p) REVERT: B 310 GLN cc_start: 0.6796 (mt0) cc_final: 0.6527 (mt0) REVERT: B 312 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6913 (mmtt) REVERT: B 314 ARG cc_start: 0.6310 (mtt180) cc_final: 0.6102 (mtp180) REVERT: B 420 PHE cc_start: 0.7488 (t80) cc_final: 0.7249 (t80) REVERT: B 574 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5814 (mm-30) REVERT: C 52 LYS cc_start: 0.7497 (tmtm) cc_final: 0.6887 (tmtm) REVERT: C 125 ASP cc_start: 0.6253 (m-30) cc_final: 0.5966 (m-30) REVERT: C 133 MET cc_start: 0.6943 (mmt) cc_final: 0.6621 (mmt) REVERT: C 135 GLU cc_start: 0.6564 (pt0) cc_final: 0.6043 (pt0) REVERT: C 137 HIS cc_start: 0.7693 (m-70) cc_final: 0.7187 (m90) REVERT: C 144 GLU cc_start: 0.6841 (pt0) cc_final: 0.6475 (pt0) REVERT: C 274 ARG cc_start: 0.6010 (mmm-85) cc_final: 0.5743 (mmm-85) REVERT: C 292 ASN cc_start: 0.7041 (m-40) cc_final: 0.6838 (m-40) REVERT: C 309 GLN cc_start: 0.6731 (tt0) cc_final: 0.6448 (tt0) REVERT: C 346 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6428 (mt-10) REVERT: C 387 LYS cc_start: 0.7299 (tptt) cc_final: 0.6993 (tptt) REVERT: C 414 TRP cc_start: 0.7464 (p90) cc_final: 0.7094 (p90) REVERT: C 439 LYS cc_start: 0.7801 (mmtp) cc_final: 0.7473 (mmtt) REVERT: D 80 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7421 (mtp180) REVERT: D 99 ASP cc_start: 0.6823 (t0) cc_final: 0.6614 (t0) REVERT: D 125 ASP cc_start: 0.6393 (m-30) cc_final: 0.6099 (m-30) REVERT: D 163 LYS cc_start: 0.7144 (ptmt) cc_final: 0.6880 (ptmt) REVERT: D 221 SER cc_start: 0.7954 (p) cc_final: 0.7723 (p) REVERT: D 242 GLN cc_start: 0.7357 (mt0) cc_final: 0.6996 (mt0) REVERT: D 314 ARG cc_start: 0.6205 (mtt-85) cc_final: 0.5989 (mtt-85) REVERT: D 316 VAL cc_start: 0.7900 (t) cc_final: 0.7461 (p) REVERT: D 344 SER cc_start: 0.7562 (OUTLIER) cc_final: 0.7302 (p) REVERT: D 411 GLU cc_start: 0.6627 (mp0) cc_final: 0.6154 (mp0) REVERT: D 414 TRP cc_start: 0.7075 (p90) cc_final: 0.6645 (p90) REVERT: D 530 LYS cc_start: 0.7243 (ttpp) cc_final: 0.7008 (ttpp) REVERT: E 49 THR cc_start: 0.7369 (t) cc_final: 0.7007 (m) REVERT: E 60 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5539 (t80) REVERT: E 80 ARG cc_start: 0.6286 (mtt-85) cc_final: 0.5976 (mtt-85) REVERT: E 115 ASN cc_start: 0.6680 (t0) cc_final: 0.6339 (t0) REVERT: E 192 SER cc_start: 0.6912 (t) cc_final: 0.6645 (t) REVERT: E 198 TYR cc_start: 0.7343 (m-80) cc_final: 0.7073 (m-80) REVERT: E 282 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7308 (m-40) REVERT: E 339 SER cc_start: 0.7341 (m) cc_final: 0.7069 (p) REVERT: E 416 GLN cc_start: 0.7456 (pt0) cc_final: 0.7171 (pt0) REVERT: E 427 ASP cc_start: 0.6937 (m-30) cc_final: 0.6563 (t0) REVERT: E 511 ASP cc_start: 0.6833 (t0) cc_final: 0.6472 (t0) REVERT: F 51 PHE cc_start: 0.7445 (m-80) cc_final: 0.7218 (m-80) REVERT: F 52 LYS cc_start: 0.7299 (tttm) cc_final: 0.6953 (tttm) REVERT: F 59 VAL cc_start: 0.7851 (p) cc_final: 0.7644 (m) REVERT: F 60 TYR cc_start: 0.6113 (m-80) cc_final: 0.5694 (t80) REVERT: F 151 LYS cc_start: 0.7542 (mttm) cc_final: 0.7274 (mttm) REVERT: F 182 THR cc_start: 0.7202 (m) cc_final: 0.6937 (t) REVERT: F 193 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5722 (tt0) REVERT: F 275 LEU cc_start: 0.7687 (mp) cc_final: 0.7461 (mt) REVERT: F 339 SER cc_start: 0.8112 (m) cc_final: 0.7653 (p) REVERT: F 350 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6360 (mt0) REVERT: F 401 ILE cc_start: 0.6700 (mm) cc_final: 0.6479 (mm) REVERT: F 466 ASN cc_start: 0.7133 (m110) cc_final: 0.6817 (m110) REVERT: F 555 VAL cc_start: 0.8402 (p) cc_final: 0.8125 (t) REVERT: F 556 ASP cc_start: 0.6746 (m-30) cc_final: 0.6461 (m-30) REVERT: H 82 MET cc_start: 0.6442 (mtm) cc_final: 0.6224 (mtm) outliers start: 84 outliers final: 39 residues processed: 961 average time/residue: 0.4114 time to fit residues: 618.0738 Evaluate side-chains 949 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 905 time to evaluate : 2.786 ------------------------------------------------------------------------------- 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 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 44 THR Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 230 THR 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 C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 LEU 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 525 SER 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 134 SER Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 539 LEU Chi-restraints excluded: chain E residue 556 ASP 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 302 ASN Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain L residue 30 ILE 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 238 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 345 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 383 GLN A 483 HIS B 95 ASN ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 497 GLN C 222 HIS ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 468 GLN ** F 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 577 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.112775 restraints weight = 39682.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116774 restraints weight = 23326.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.119427 restraints weight = 16199.824| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 28688 Z= 0.332 Angle : 0.619 7.121 39256 Z= 0.329 Chirality : 0.049 0.181 4223 Planarity : 0.006 0.053 5181 Dihedral : 6.030 55.202 3838 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.35 % Allowed : 13.15 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 3507 helix: -0.75 (0.45), residues: 96 sheet: -0.73 (0.15), residues: 1008 loop : -0.45 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 529 HIS 0.011 0.001 HIS C 222 PHE 0.028 0.002 PHE A 448 TYR 0.029 0.002 TYR B 342 ARG 0.007 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 396) hydrogen bonds : angle 6.07256 ( 720) SS BOND : bond 0.00648 ( 9) SS BOND : angle 3.42618 ( 18) covalent geometry : bond 0.00740 (28679) covalent geometry : angle 0.61492 (39238) *********************** 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 1025 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 923 time to evaluate : 4.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7503 (m) cc_final: 0.7142 (p) REVERT: A 60 TYR cc_start: 0.5855 (m-10) cc_final: 0.5537 (m-10) REVERT: A 80 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6867 (mtp180) REVERT: A 109 TRP cc_start: 0.7877 (m100) cc_final: 0.7598 (m100) REVERT: A 135 GLU cc_start: 0.6663 (pt0) cc_final: 0.6224 (pt0) REVERT: A 193 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5556 (tt0) REVERT: A 249 SER cc_start: 0.8177 (m) cc_final: 0.7892 (p) REVERT: A 350 GLN cc_start: 0.7045 (mp10) cc_final: 0.6607 (mp10) REVERT: A 394 THR cc_start: 0.8099 (m) cc_final: 0.7858 (t) REVERT: B 60 TYR cc_start: 0.5540 (m-80) cc_final: 0.5255 (m-10) REVERT: B 80 ARG cc_start: 0.5779 (mmp80) cc_final: 0.5029 (mmp80) REVERT: B 89 LYS cc_start: 0.7465 (tppt) cc_final: 0.7174 (tppt) REVERT: B 99 ASP cc_start: 0.6469 (t0) cc_final: 0.6005 (t0) REVERT: B 223 THR cc_start: 0.7947 (m) cc_final: 0.7487 (p) REVERT: B 310 GLN cc_start: 0.6768 (mt0) cc_final: 0.6560 (mt0) REVERT: B 312 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6897 (mmtt) REVERT: B 559 PHE cc_start: 0.7066 (m-80) cc_final: 0.6822 (m-10) REVERT: B 574 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5858 (mm-30) REVERT: C 52 LYS cc_start: 0.7507 (tmtm) cc_final: 0.6895 (tmtm) REVERT: C 125 ASP cc_start: 0.6271 (m-30) cc_final: 0.5884 (m-30) REVERT: C 133 MET cc_start: 0.6965 (mmt) cc_final: 0.6616 (mmt) REVERT: C 135 GLU cc_start: 0.6598 (pt0) cc_final: 0.6054 (pt0) REVERT: C 137 HIS cc_start: 0.7746 (m-70) cc_final: 0.7234 (m90) REVERT: C 309 GLN cc_start: 0.6747 (tt0) cc_final: 0.6498 (tt0) REVERT: C 414 TRP cc_start: 0.7517 (p90) cc_final: 0.7145 (p90) REVERT: C 439 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7546 (mmtt) REVERT: D 99 ASP cc_start: 0.6899 (t0) cc_final: 0.6574 (t0) REVERT: D 101 THR cc_start: 0.7328 (m) cc_final: 0.7031 (t) REVERT: D 125 ASP cc_start: 0.6374 (m-30) cc_final: 0.6054 (m-30) REVERT: D 163 LYS cc_start: 0.7142 (ptmt) cc_final: 0.6888 (ptmt) REVERT: D 221 SER cc_start: 0.7975 (p) cc_final: 0.7708 (p) REVERT: D 314 ARG cc_start: 0.6185 (mtt-85) cc_final: 0.5882 (mtt-85) REVERT: D 316 VAL cc_start: 0.7877 (t) cc_final: 0.7436 (p) REVERT: D 344 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7370 (p) REVERT: D 411 GLU cc_start: 0.6655 (mp0) cc_final: 0.6105 (mp0) REVERT: D 414 TRP cc_start: 0.7117 (p90) cc_final: 0.6746 (p90) REVERT: E 60 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.5533 (t80) REVERT: E 80 ARG cc_start: 0.6279 (mtt-85) cc_final: 0.5944 (mtt-85) REVERT: E 192 SER cc_start: 0.6914 (t) cc_final: 0.6669 (t) REVERT: E 198 TYR cc_start: 0.7345 (m-80) cc_final: 0.7080 (m-80) REVERT: E 255 LEU cc_start: 0.7127 (mt) cc_final: 0.6765 (mp) REVERT: E 282 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7272 (m-40) REVERT: E 339 SER cc_start: 0.7276 (m) cc_final: 0.7028 (p) REVERT: E 416 GLN cc_start: 0.7440 (pt0) cc_final: 0.7167 (pt0) REVERT: E 427 ASP cc_start: 0.6896 (m-30) cc_final: 0.6492 (t0) REVERT: E 511 ASP cc_start: 0.6861 (t0) cc_final: 0.6485 (t0) REVERT: F 51 PHE cc_start: 0.7425 (m-80) cc_final: 0.7160 (m-80) REVERT: F 52 LYS cc_start: 0.7273 (tttm) cc_final: 0.6923 (tttm) REVERT: F 60 TYR cc_start: 0.6104 (m-80) cc_final: 0.5713 (t80) REVERT: F 151 LYS cc_start: 0.7544 (mttm) cc_final: 0.7276 (mttm) REVERT: F 193 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5722 (tt0) REVERT: F 275 LEU cc_start: 0.7727 (mp) cc_final: 0.7462 (mt) REVERT: F 339 SER cc_start: 0.8110 (m) cc_final: 0.7645 (p) REVERT: F 350 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6384 (mt0) REVERT: F 387 LYS cc_start: 0.6821 (ttpp) cc_final: 0.6551 (ttpp) REVERT: F 390 THR cc_start: 0.7528 (m) cc_final: 0.7191 (p) REVERT: F 401 ILE cc_start: 0.6807 (mm) cc_final: 0.6594 (mm) REVERT: F 466 ASN cc_start: 0.7153 (m110) cc_final: 0.6875 (m110) REVERT: F 555 VAL cc_start: 0.8381 (p) cc_final: 0.8125 (t) REVERT: F 556 ASP cc_start: 0.6741 (m-30) cc_final: 0.6472 (m-30) REVERT: H 82 MET cc_start: 0.6426 (mtm) cc_final: 0.6211 (mtm) outliers start: 102 outliers final: 61 residues processed: 957 average time/residue: 0.6585 time to fit residues: 1002.8863 Evaluate side-chains 981 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 914 time to evaluate : 3.326 ------------------------------------------------------------------------------- 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 96 MET Chi-restraints excluded: chain A residue 144 GLU 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 450 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 MET 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 C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 222 HIS Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 LEU 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 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 192 SER Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 525 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 134 SER Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 282 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 494 CYS Chi-restraints excluded: chain E residue 509 GLN Chi-restraints excluded: chain E residue 539 LEU Chi-restraints excluded: chain E residue 556 ASP Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 172 SER 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 425 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 217 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 328 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 350 GLN B 95 ASN B 167 ASN B 231 ASN C 222 HIS D 383 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN E 95 ASN E 231 ASN F 48 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 558 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 = 0.3590 r_free = 0.3590 target = 0.144463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.119679 restraints weight = 38980.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123911 restraints weight = 21865.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.126724 restraints weight = 14677.068| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28688 Z= 0.121 Angle : 0.508 6.138 39256 Z= 0.264 Chirality : 0.043 0.165 4223 Planarity : 0.005 0.050 5181 Dihedral : 5.409 57.800 3838 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.40 % Allowed : 15.15 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3507 helix: -0.50 (0.46), residues: 96 sheet: -0.59 (0.15), residues: 991 loop : -0.30 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 545 HIS 0.018 0.001 HIS C 222 PHE 0.027 0.001 PHE F 398 TYR 0.017 0.001 TYR A 342 ARG 0.004 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 396) hydrogen bonds : angle 5.63596 ( 720) SS BOND : bond 0.00464 ( 9) SS BOND : angle 2.64289 ( 18) covalent geometry : bond 0.00273 (28679) covalent geometry : angle 0.50506 (39238) *********************** 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 998 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 925 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7686 (m) cc_final: 0.7350 (p) REVERT: A 49 THR cc_start: 0.7468 (m) cc_final: 0.7078 (p) REVERT: A 60 TYR cc_start: 0.5843 (m-10) cc_final: 0.5637 (m-10) REVERT: A 80 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6914 (mtp180) REVERT: A 135 GLU cc_start: 0.6628 (pt0) cc_final: 0.6182 (pt0) REVERT: A 185 PHE cc_start: 0.7146 (t80) cc_final: 0.6931 (t80) REVERT: A 193 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5234 (tt0) REVERT: A 274 ARG cc_start: 0.6255 (mmm-85) cc_final: 0.5936 (mmm-85) REVERT: A 350 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6559 (mp10) REVERT: A 394 THR cc_start: 0.8102 (m) cc_final: 0.7885 (t) REVERT: A 417 ASN cc_start: 0.7536 (t0) cc_final: 0.7138 (t0) REVERT: B 60 TYR cc_start: 0.5525 (m-80) cc_final: 0.5247 (m-10) REVERT: B 80 ARG cc_start: 0.5883 (mmp80) cc_final: 0.5195 (mmp80) REVERT: B 89 LYS cc_start: 0.7500 (tppt) cc_final: 0.7157 (tppt) REVERT: B 99 ASP cc_start: 0.6502 (t0) cc_final: 0.6011 (t0) REVERT: B 312 LYS cc_start: 0.7305 (mmtt) cc_final: 0.6798 (mmtt) REVERT: B 346 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6505 (mt-10) REVERT: B 574 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5795 (mm-30) REVERT: C 52 LYS cc_start: 0.7464 (tmtm) cc_final: 0.6866 (tmtm) REVERT: C 125 ASP cc_start: 0.6219 (m-30) cc_final: 0.5854 (m-30) REVERT: C 133 MET cc_start: 0.6862 (mmt) cc_final: 0.6478 (mmt) REVERT: C 135 GLU cc_start: 0.6647 (pt0) cc_final: 0.6214 (pt0) REVERT: C 137 HIS cc_start: 0.7699 (m-70) cc_final: 0.7201 (m90) REVERT: C 309 GLN cc_start: 0.6738 (tt0) cc_final: 0.6460 (tt0) REVERT: C 346 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6347 (mt-10) REVERT: C 414 TRP cc_start: 0.7527 (p90) cc_final: 0.7125 (p90) REVERT: C 439 LYS cc_start: 0.7722 (mmtp) cc_final: 0.7433 (mmtt) REVERT: D 99 ASP cc_start: 0.6976 (t0) cc_final: 0.6497 (t0) REVERT: D 101 THR cc_start: 0.7371 (m) cc_final: 0.6971 (t) REVERT: D 125 ASP cc_start: 0.6356 (m-30) cc_final: 0.6103 (m-30) REVERT: D 163 LYS cc_start: 0.7113 (ptmt) cc_final: 0.6905 (ptmt) REVERT: D 216 ARG cc_start: 0.7506 (tmt-80) cc_final: 0.7087 (tpt170) REVERT: D 221 SER cc_start: 0.8012 (p) cc_final: 0.7735 (p) REVERT: D 314 ARG cc_start: 0.6267 (mtt-85) cc_final: 0.5939 (mtt-85) REVERT: D 316 VAL cc_start: 0.7897 (t) cc_final: 0.7493 (p) REVERT: D 344 SER cc_start: 0.7504 (t) cc_final: 0.7290 (p) REVERT: D 411 GLU cc_start: 0.6638 (mp0) cc_final: 0.6162 (mp0) REVERT: D 414 TRP cc_start: 0.7105 (p90) cc_final: 0.6626 (p90) REVERT: D 513 ASP cc_start: 0.6388 (m-30) cc_final: 0.6080 (m-30) REVERT: E 68 LEU cc_start: 0.7644 (tp) cc_final: 0.7330 (tt) REVERT: E 80 ARG cc_start: 0.6248 (mtt-85) cc_final: 0.5931 (mtt-85) REVERT: E 99 ASP cc_start: 0.6747 (t0) cc_final: 0.6363 (t70) REVERT: E 192 SER cc_start: 0.6958 (t) cc_final: 0.6716 (t) REVERT: E 198 TYR cc_start: 0.7309 (m-80) cc_final: 0.7045 (m-80) REVERT: E 255 LEU cc_start: 0.7093 (mt) cc_final: 0.6730 (mp) REVERT: E 282 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7188 (m-40) REVERT: E 339 SER cc_start: 0.7293 (m) cc_final: 0.7018 (p) REVERT: E 416 GLN cc_start: 0.7453 (pt0) cc_final: 0.7231 (pt0) REVERT: E 427 ASP cc_start: 0.6851 (m-30) cc_final: 0.6490 (t0) REVERT: E 511 ASP cc_start: 0.6857 (t0) cc_final: 0.6531 (t0) REVERT: F 52 LYS cc_start: 0.7256 (tttm) cc_final: 0.6951 (tttm) REVERT: F 73 MET cc_start: 0.7674 (ptt) cc_final: 0.7441 (ptm) REVERT: F 83 VAL cc_start: 0.7416 (t) cc_final: 0.7190 (t) REVERT: F 151 LYS cc_start: 0.7557 (mttm) cc_final: 0.7280 (mttm) REVERT: F 193 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5713 (tt0) REVERT: F 275 LEU cc_start: 0.7598 (mp) cc_final: 0.7355 (mt) REVERT: F 339 SER cc_start: 0.8177 (m) cc_final: 0.7692 (p) REVERT: F 350 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6325 (mt0) REVERT: F 387 LYS cc_start: 0.6813 (ttpp) cc_final: 0.6531 (ttpp) REVERT: F 390 THR cc_start: 0.7558 (m) cc_final: 0.7255 (p) REVERT: F 401 ILE cc_start: 0.6817 (mm) cc_final: 0.6572 (mm) REVERT: F 466 ASN cc_start: 0.7103 (m110) cc_final: 0.6842 (m110) REVERT: F 555 VAL cc_start: 0.8336 (p) cc_final: 0.8085 (t) REVERT: F 556 ASP cc_start: 0.6693 (m-30) cc_final: 0.6408 (m-30) REVERT: F 561 TYR cc_start: 0.7471 (m-80) cc_final: 0.7119 (m-80) outliers start: 73 outliers final: 39 residues processed: 953 average time/residue: 0.4208 time to fit residues: 625.2836 Evaluate side-chains 933 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 889 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 383 GLN 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 96 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 246 ILE 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 366 THR Chi-restraints excluded: chain C residue 433 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 166 ASN Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain E residue 86 ASN 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 330 ILE 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 193 GLU 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 324 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 249 optimal weight: 50.0000 chunk 244 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN B 167 ASN B 383 GLN C 85 ASN ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN D 242 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 323 ASN F 560 ASN F 577 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111729 restraints weight = 39589.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.115781 restraints weight = 23297.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.118482 restraints weight = 16226.002| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 28688 Z= 0.376 Angle : 0.635 7.832 39256 Z= 0.336 Chirality : 0.050 0.187 4223 Planarity : 0.006 0.059 5181 Dihedral : 5.799 57.892 3825 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.06 % Allowed : 15.91 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3507 helix: -0.65 (0.45), residues: 96 sheet: -0.71 (0.15), residues: 989 loop : -0.49 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 528 HIS 0.007 0.002 HIS B 234 PHE 0.027 0.003 PHE A 448 TYR 0.032 0.002 TYR B 342 ARG 0.011 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 396) hydrogen bonds : angle 5.88581 ( 720) SS BOND : bond 0.00657 ( 9) SS BOND : angle 3.49298 ( 18) covalent geometry : bond 0.00835 (28679) covalent geometry : angle 0.63073 (39238) *********************** 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 1005 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 912 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7478 (m) cc_final: 0.7118 (p) REVERT: A 80 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6945 (mtp180) REVERT: A 109 TRP cc_start: 0.7909 (m100) cc_final: 0.7577 (m100) REVERT: A 135 GLU cc_start: 0.6660 (pt0) cc_final: 0.6224 (pt0) REVERT: A 163 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6401 (ptmt) REVERT: A 193 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5557 (tt0) REVERT: A 329 THR cc_start: 0.7440 (p) cc_final: 0.7152 (t) REVERT: A 344 SER cc_start: 0.7513 (t) cc_final: 0.7054 (p) REVERT: A 350 GLN cc_start: 0.7145 (mp10) cc_final: 0.6713 (mp10) REVERT: A 394 THR cc_start: 0.8088 (m) cc_final: 0.7858 (t) REVERT: A 561 TYR cc_start: 0.7505 (m-80) cc_final: 0.7067 (m-80) REVERT: B 60 TYR cc_start: 0.5584 (m-80) cc_final: 0.5291 (m-10) REVERT: B 80 ARG cc_start: 0.5576 (mtp85) cc_final: 0.4733 (mmp80) REVERT: B 89 LYS cc_start: 0.7422 (tppt) cc_final: 0.7065 (tppt) REVERT: B 95 ASN cc_start: 0.7213 (m-40) cc_final: 0.6952 (m110) REVERT: B 99 ASP cc_start: 0.6587 (t0) cc_final: 0.6056 (t0) REVERT: B 133 MET cc_start: 0.6768 (mmt) cc_final: 0.6523 (mmm) REVERT: B 223 THR cc_start: 0.7907 (m) cc_final: 0.7520 (p) REVERT: B 312 LYS cc_start: 0.7307 (mmtt) cc_final: 0.6814 (mmtt) REVERT: B 457 LEU cc_start: 0.7197 (pt) cc_final: 0.6876 (pp) REVERT: B 509 GLN cc_start: 0.6534 (mt0) cc_final: 0.6253 (mt0) REVERT: B 574 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5782 (mm-30) REVERT: C 52 LYS cc_start: 0.7471 (tmtm) cc_final: 0.6852 (tmtm) REVERT: C 99 ASP cc_start: 0.6999 (t70) cc_final: 0.6563 (t0) REVERT: C 133 MET cc_start: 0.6965 (mmt) cc_final: 0.6613 (mmt) REVERT: C 135 GLU cc_start: 0.6669 (pt0) cc_final: 0.6110 (pt0) REVERT: C 137 HIS cc_start: 0.7736 (m-70) cc_final: 0.7262 (m90) REVERT: C 274 ARG cc_start: 0.6082 (mmm-85) cc_final: 0.5855 (mmm-85) REVERT: C 309 GLN cc_start: 0.6761 (tt0) cc_final: 0.6475 (tt0) REVERT: C 346 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6332 (mt-10) REVERT: C 414 TRP cc_start: 0.7554 (p90) cc_final: 0.7142 (p90) REVERT: D 99 ASP cc_start: 0.6901 (t0) cc_final: 0.6541 (t0) REVERT: D 101 THR cc_start: 0.7306 (m) cc_final: 0.6990 (t) REVERT: D 125 ASP cc_start: 0.6321 (m-30) cc_final: 0.6087 (m-30) REVERT: D 154 SER cc_start: 0.6414 (m) cc_final: 0.5920 (p) REVERT: D 163 LYS cc_start: 0.7192 (ptmt) cc_final: 0.6991 (ptmt) REVERT: D 221 SER cc_start: 0.7958 (p) cc_final: 0.7673 (p) REVERT: D 314 ARG cc_start: 0.6198 (mtt-85) cc_final: 0.5743 (mtt-85) REVERT: D 316 VAL cc_start: 0.7881 (t) cc_final: 0.7429 (p) REVERT: D 411 GLU cc_start: 0.6678 (mp0) cc_final: 0.6120 (mp0) REVERT: D 414 TRP cc_start: 0.7108 (p90) cc_final: 0.6675 (p90) REVERT: D 513 ASP cc_start: 0.6396 (m-30) cc_final: 0.6111 (m-30) REVERT: E 60 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5569 (t80) REVERT: E 80 ARG cc_start: 0.6284 (mtt-85) cc_final: 0.5918 (mtt-85) REVERT: E 192 SER cc_start: 0.6931 (t) cc_final: 0.6691 (t) REVERT: E 198 TYR cc_start: 0.7351 (m-80) cc_final: 0.7096 (m-80) REVERT: E 247 GLU cc_start: 0.6639 (mp0) cc_final: 0.6134 (mp0) REVERT: E 339 SER cc_start: 0.7258 (m) cc_final: 0.7006 (p) REVERT: E 416 GLN cc_start: 0.7382 (pt0) cc_final: 0.7146 (pt0) REVERT: E 427 ASP cc_start: 0.6926 (m-30) cc_final: 0.6512 (t0) REVERT: E 511 ASP cc_start: 0.6871 (t0) cc_final: 0.6488 (t0) REVERT: F 52 LYS cc_start: 0.7276 (tttm) cc_final: 0.6987 (tttm) REVERT: F 60 TYR cc_start: 0.6108 (m-80) cc_final: 0.5706 (t80) REVERT: F 99 ASP cc_start: 0.6750 (t0) cc_final: 0.6417 (t70) REVERT: F 151 LYS cc_start: 0.7550 (mttm) cc_final: 0.7296 (mttm) REVERT: F 193 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5711 (tt0) REVERT: F 275 LEU cc_start: 0.7657 (mp) cc_final: 0.7388 (mt) REVERT: F 339 SER cc_start: 0.8124 (m) cc_final: 0.7648 (p) REVERT: F 350 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6279 (mt0) REVERT: F 401 ILE cc_start: 0.6854 (mm) cc_final: 0.6305 (mt) REVERT: F 466 ASN cc_start: 0.7131 (m110) cc_final: 0.6847 (m110) REVERT: F 555 VAL cc_start: 0.8389 (p) cc_final: 0.8115 (t) REVERT: F 556 ASP cc_start: 0.6728 (m-30) cc_final: 0.6485 (m-30) REVERT: F 571 ILE cc_start: 0.7462 (mt) cc_final: 0.7202 (tt) REVERT: H 82 MET cc_start: 0.6627 (mtm) cc_final: 0.5842 (mtm) outliers start: 93 outliers final: 61 residues processed: 946 average time/residue: 0.4422 time to fit residues: 658.0658 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 : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 144 GLU 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 382 ARG 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 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 265 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 THR 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 433 THR Chi-restraints excluded: chain C residue 454 LEU 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 96 MET Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU 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 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 134 SER Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS Chi-restraints excluded: chain E residue 539 LEU 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 135 GLU 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 494 CYS Chi-restraints excluded: chain F residue 518 MET 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 308 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 238 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN C 47 ASN C 85 ASN C 222 HIS D 127 GLN E 86 ASN E 282 ASN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 323 ASN F 558 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 = 0.3530 r_free = 0.3530 target = 0.140212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.114673 restraints weight = 39633.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118779 restraints weight = 22840.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.121524 restraints weight = 15605.085| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28688 Z= 0.163 Angle : 0.527 7.321 39256 Z= 0.274 Chirality : 0.043 0.170 4223 Planarity : 0.005 0.051 5181 Dihedral : 5.358 59.771 3825 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.93 % Allowed : 16.54 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3507 helix: -0.55 (0.45), residues: 96 sheet: -0.65 (0.15), residues: 991 loop : -0.38 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.004 0.001 HIS F 137 PHE 0.022 0.002 PHE A 448 TYR 0.018 0.001 TYR B 342 ARG 0.007 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 396) hydrogen bonds : angle 5.60747 ( 720) SS BOND : bond 0.00465 ( 9) SS BOND : angle 2.74362 ( 18) covalent geometry : bond 0.00366 (28679) covalent geometry : angle 0.52358 (39238) *********************** 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 997 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 908 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7757 (m) cc_final: 0.7184 (p) REVERT: A 49 THR cc_start: 0.7462 (m) cc_final: 0.7108 (p) REVERT: A 60 TYR cc_start: 0.5889 (m-10) cc_final: 0.5666 (m-10) REVERT: A 80 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6930 (mtp180) REVERT: A 109 TRP cc_start: 0.7879 (m100) cc_final: 0.7586 (m100) REVERT: A 135 GLU cc_start: 0.6653 (pt0) cc_final: 0.6243 (pt0) REVERT: A 163 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6382 (ptmt) REVERT: A 193 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5296 (tt0) REVERT: A 230 THR cc_start: 0.8245 (p) cc_final: 0.7994 (t) REVERT: A 344 SER cc_start: 0.7354 (t) cc_final: 0.6899 (p) REVERT: A 350 GLN cc_start: 0.7091 (mp10) cc_final: 0.6703 (mp10) REVERT: A 394 THR cc_start: 0.8099 (m) cc_final: 0.7896 (t) REVERT: A 417 ASN cc_start: 0.7510 (t0) cc_final: 0.7193 (t0) REVERT: A 561 TYR cc_start: 0.7515 (m-80) cc_final: 0.7073 (m-80) REVERT: B 60 TYR cc_start: 0.5558 (m-80) cc_final: 0.5268 (m-10) REVERT: B 80 ARG cc_start: 0.5686 (mtp85) cc_final: 0.4942 (mmp80) REVERT: B 89 LYS cc_start: 0.7475 (tppt) cc_final: 0.7224 (tppt) REVERT: B 95 ASN cc_start: 0.7125 (m-40) cc_final: 0.6872 (m110) REVERT: B 99 ASP cc_start: 0.6559 (t0) cc_final: 0.5970 (t0) REVERT: B 133 MET cc_start: 0.6686 (mmt) cc_final: 0.6453 (mmm) REVERT: B 312 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6770 (mmtt) REVERT: B 338 TYR cc_start: 0.7021 (p90) cc_final: 0.6777 (p90) REVERT: B 382 ARG cc_start: 0.7289 (mtm-85) cc_final: 0.6717 (mtm-85) REVERT: B 509 GLN cc_start: 0.6544 (mt0) cc_final: 0.6300 (mt0) REVERT: B 574 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5846 (mm-30) REVERT: B 581 ARG cc_start: 0.7516 (ptt-90) cc_final: 0.7163 (ttp80) REVERT: C 52 LYS cc_start: 0.7486 (tmtm) cc_final: 0.6874 (tmtm) REVERT: C 125 ASP cc_start: 0.6162 (m-30) cc_final: 0.5719 (m-30) REVERT: C 133 MET cc_start: 0.6884 (mmt) cc_final: 0.6506 (mmt) REVERT: C 135 GLU cc_start: 0.6646 (pt0) cc_final: 0.6098 (pt0) REVERT: C 137 HIS cc_start: 0.7699 (m-70) cc_final: 0.7233 (m90) REVERT: C 237 ASP cc_start: 0.6513 (m-30) cc_final: 0.6279 (m-30) REVERT: C 274 ARG cc_start: 0.6067 (mmm-85) cc_final: 0.5822 (mmm-85) REVERT: C 309 GLN cc_start: 0.6747 (tt0) cc_final: 0.6470 (tt0) REVERT: C 346 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6376 (mt-10) REVERT: C 350 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.5915 (mt0) REVERT: C 414 TRP cc_start: 0.7520 (p90) cc_final: 0.7093 (p90) REVERT: D 99 ASP cc_start: 0.6941 (t0) cc_final: 0.6542 (t0) REVERT: D 101 THR cc_start: 0.7362 (m) cc_final: 0.7012 (t) REVERT: D 125 ASP cc_start: 0.6268 (m-30) cc_final: 0.6051 (m-30) REVERT: D 154 SER cc_start: 0.6339 (m) cc_final: 0.5882 (p) REVERT: D 221 SER cc_start: 0.7975 (p) cc_final: 0.7685 (p) REVERT: D 314 ARG cc_start: 0.6285 (mtt-85) cc_final: 0.5891 (mtt-85) REVERT: D 316 VAL cc_start: 0.7910 (t) cc_final: 0.7475 (p) REVERT: D 344 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7285 (p) REVERT: D 382 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7147 (mtm-85) REVERT: D 411 GLU cc_start: 0.6678 (mp0) cc_final: 0.6107 (mp0) REVERT: D 414 TRP cc_start: 0.7088 (p90) cc_final: 0.6576 (p90) REVERT: D 513 ASP cc_start: 0.6391 (m-30) cc_final: 0.6100 (m-30) REVERT: E 60 TYR cc_start: 0.5981 (OUTLIER) cc_final: 0.5578 (t80) REVERT: E 68 LEU cc_start: 0.7669 (tp) cc_final: 0.7353 (tt) REVERT: E 80 ARG cc_start: 0.6214 (mtt-85) cc_final: 0.5878 (mtt-85) REVERT: E 99 ASP cc_start: 0.6754 (t0) cc_final: 0.6347 (t70) REVERT: E 192 SER cc_start: 0.6935 (t) cc_final: 0.6713 (t) REVERT: E 198 TYR cc_start: 0.7320 (m-80) cc_final: 0.7057 (m-80) REVERT: E 247 GLU cc_start: 0.6677 (mp0) cc_final: 0.6215 (mp0) REVERT: E 339 SER cc_start: 0.7300 (m) cc_final: 0.7022 (p) REVERT: E 350 GLN cc_start: 0.7072 (mp10) cc_final: 0.6232 (mp10) REVERT: E 416 GLN cc_start: 0.7380 (pt0) cc_final: 0.7157 (pt0) REVERT: E 427 ASP cc_start: 0.6896 (m-30) cc_final: 0.6488 (t0) REVERT: E 511 ASP cc_start: 0.6860 (t0) cc_final: 0.6506 (t0) REVERT: F 52 LYS cc_start: 0.7284 (tttm) cc_final: 0.6980 (tttm) REVERT: F 60 TYR cc_start: 0.6086 (m-80) cc_final: 0.5683 (t80) REVERT: F 73 MET cc_start: 0.7694 (ptt) cc_final: 0.7460 (ptm) REVERT: F 151 LYS cc_start: 0.7554 (mttm) cc_final: 0.7290 (mttm) REVERT: F 193 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5688 (tt0) REVERT: F 215 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: F 275 LEU cc_start: 0.7650 (mp) cc_final: 0.7371 (mt) REVERT: F 339 SER cc_start: 0.8174 (m) cc_final: 0.7701 (p) REVERT: F 350 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6394 (mt0) REVERT: F 387 LYS cc_start: 0.6817 (ttpp) cc_final: 0.6503 (ttpp) REVERT: F 390 THR cc_start: 0.7549 (m) cc_final: 0.7267 (p) REVERT: F 401 ILE cc_start: 0.6887 (mm) cc_final: 0.6299 (mt) REVERT: F 426 ASP cc_start: 0.7466 (t0) cc_final: 0.7118 (t70) REVERT: F 466 ASN cc_start: 0.7093 (m110) cc_final: 0.6868 (m110) REVERT: F 555 VAL cc_start: 0.8343 (p) cc_final: 0.8050 (t) REVERT: F 556 ASP cc_start: 0.6709 (m-30) cc_final: 0.6478 (m-30) REVERT: F 558 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: F 571 ILE cc_start: 0.7441 (mt) cc_final: 0.7160 (tt) REVERT: H 82 MET cc_start: 0.6564 (mtm) cc_final: 0.5812 (mtm) outliers start: 89 outliers final: 57 residues processed: 941 average time/residue: 0.4134 time to fit residues: 602.6594 Evaluate side-chains 965 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 899 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 144 GLU 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 A residue 572 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 249 SER 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 578 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 549 GLN 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 166 ASN Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU 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 518 MET Chi-restraints excluded: chain D residue 519 SER 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 206 THR 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 556 ASP Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 164 VAL 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 249 SER 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 518 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 4 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 271 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 338 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 85 ASN D 127 GLN E 86 ASN E 282 ASN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 560 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.114286 restraints weight = 39410.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.118423 restraints weight = 22721.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.121170 restraints weight = 15558.021| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28688 Z= 0.190 Angle : 0.534 7.492 39256 Z= 0.278 Chirality : 0.044 0.170 4223 Planarity : 0.005 0.050 5181 Dihedral : 5.331 59.915 3825 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.96 % Allowed : 16.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3507 helix: -0.59 (0.45), residues: 96 sheet: -0.58 (0.16), residues: 979 loop : -0.34 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS F 137 PHE 0.021 0.002 PHE A 448 TYR 0.026 0.001 TYR C 561 ARG 0.007 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 396) hydrogen bonds : angle 5.56053 ( 720) SS BOND : bond 0.00527 ( 9) SS BOND : angle 2.80538 ( 18) covalent geometry : bond 0.00425 (28679) covalent geometry : angle 0.53096 (39238) *********************** 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 1005 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 915 time to evaluate : 5.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7652 (m) cc_final: 0.7271 (p) REVERT: A 49 THR cc_start: 0.7448 (m) cc_final: 0.7092 (p) REVERT: A 60 TYR cc_start: 0.5890 (m-10) cc_final: 0.5575 (m-10) REVERT: A 80 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6948 (mtp180) REVERT: A 109 TRP cc_start: 0.7896 (m100) cc_final: 0.7602 (m100) REVERT: A 135 GLU cc_start: 0.6647 (pt0) cc_final: 0.6235 (pt0) REVERT: A 163 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6366 (ptmt) REVERT: A 193 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5324 (tt0) REVERT: A 350 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: A 394 THR cc_start: 0.8099 (m) cc_final: 0.7891 (t) REVERT: A 417 ASN cc_start: 0.7523 (t0) cc_final: 0.7207 (t0) REVERT: A 439 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7220 (mmtm) REVERT: A 468 GLN cc_start: 0.7283 (tt0) cc_final: 0.7081 (tt0) REVERT: A 561 TYR cc_start: 0.7497 (m-80) cc_final: 0.7050 (m-80) REVERT: B 60 TYR cc_start: 0.5561 (m-80) cc_final: 0.5322 (m-80) REVERT: B 80 ARG cc_start: 0.5695 (mtp85) cc_final: 0.3444 (mtp85) REVERT: B 89 LYS cc_start: 0.7487 (tppt) cc_final: 0.7076 (tppt) REVERT: B 95 ASN cc_start: 0.7112 (m-40) cc_final: 0.6864 (m110) REVERT: B 99 ASP cc_start: 0.6594 (t0) cc_final: 0.6025 (t0) REVERT: B 133 MET cc_start: 0.6666 (mmt) cc_final: 0.6419 (mmm) REVERT: B 193 GLU cc_start: 0.5754 (mt-10) cc_final: 0.5515 (mt-10) REVERT: B 206 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6679 (m) REVERT: B 382 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.6718 (mtm-85) REVERT: B 509 GLN cc_start: 0.6572 (mt0) cc_final: 0.6334 (mt0) REVERT: B 574 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5850 (mm-30) REVERT: C 52 LYS cc_start: 0.7491 (tmtm) cc_final: 0.6872 (tmtm) REVERT: C 125 ASP cc_start: 0.6165 (m-30) cc_final: 0.5748 (m-30) REVERT: C 133 MET cc_start: 0.6900 (mmt) cc_final: 0.6530 (mmt) REVERT: C 135 GLU cc_start: 0.6678 (pt0) cc_final: 0.6148 (pt0) REVERT: C 137 HIS cc_start: 0.7707 (m-70) cc_final: 0.7210 (m90) REVERT: C 237 ASP cc_start: 0.6575 (m-30) cc_final: 0.6304 (m-30) REVERT: C 274 ARG cc_start: 0.6089 (mmm-85) cc_final: 0.5842 (mmm-85) REVERT: C 309 GLN cc_start: 0.6746 (tt0) cc_final: 0.6461 (tt0) REVERT: C 346 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6347 (mt-10) REVERT: C 350 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6376 (mt0) REVERT: C 414 TRP cc_start: 0.7521 (p90) cc_final: 0.7085 (p90) REVERT: C 481 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6584 (mtp180) REVERT: D 99 ASP cc_start: 0.6941 (t0) cc_final: 0.6510 (t0) REVERT: D 101 THR cc_start: 0.7351 (m) cc_final: 0.6988 (t) REVERT: D 125 ASP cc_start: 0.6271 (m-30) cc_final: 0.6057 (m-30) REVERT: D 154 SER cc_start: 0.6400 (m) cc_final: 0.5906 (p) REVERT: D 221 SER cc_start: 0.7959 (p) cc_final: 0.7703 (p) REVERT: D 245 THR cc_start: 0.7348 (p) cc_final: 0.7091 (t) REVERT: D 314 ARG cc_start: 0.6209 (mtt-85) cc_final: 0.5777 (mtt-85) REVERT: D 316 VAL cc_start: 0.7903 (t) cc_final: 0.7463 (p) REVERT: D 344 SER cc_start: 0.7478 (OUTLIER) cc_final: 0.7235 (p) REVERT: D 411 GLU cc_start: 0.6689 (mp0) cc_final: 0.6103 (mp0) REVERT: D 414 TRP cc_start: 0.7102 (p90) cc_final: 0.6482 (p90) REVERT: D 513 ASP cc_start: 0.6435 (m-30) cc_final: 0.6133 (m-30) REVERT: E 60 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.5571 (t80) REVERT: E 68 LEU cc_start: 0.7677 (tp) cc_final: 0.7356 (tt) REVERT: E 80 ARG cc_start: 0.6232 (mtt-85) cc_final: 0.5892 (mtt-85) REVERT: E 192 SER cc_start: 0.6945 (t) cc_final: 0.6718 (t) REVERT: E 198 TYR cc_start: 0.7332 (m-80) cc_final: 0.7050 (m-80) REVERT: E 247 GLU cc_start: 0.6678 (mp0) cc_final: 0.6203 (mp0) REVERT: E 283 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7362 (mmm-85) REVERT: E 339 SER cc_start: 0.7299 (m) cc_final: 0.7004 (p) REVERT: E 350 GLN cc_start: 0.7049 (mp10) cc_final: 0.6210 (mp10) REVERT: E 416 GLN cc_start: 0.7389 (pt0) cc_final: 0.7168 (pt0) REVERT: E 427 ASP cc_start: 0.6985 (m-30) cc_final: 0.6576 (t0) REVERT: E 511 ASP cc_start: 0.6858 (t0) cc_final: 0.6503 (t0) REVERT: F 52 LYS cc_start: 0.7272 (tttm) cc_final: 0.6957 (tttm) REVERT: F 60 TYR cc_start: 0.6105 (m-80) cc_final: 0.5694 (t80) REVERT: F 73 MET cc_start: 0.7674 (ptt) cc_final: 0.7436 (ptm) REVERT: F 151 LYS cc_start: 0.7543 (mttm) cc_final: 0.7274 (mttm) REVERT: F 193 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5679 (tt0) REVERT: F 215 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: F 275 LEU cc_start: 0.7652 (mp) cc_final: 0.7371 (mt) REVERT: F 339 SER cc_start: 0.8167 (m) cc_final: 0.7669 (p) REVERT: F 350 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6330 (mt0) REVERT: F 387 LYS cc_start: 0.6796 (ttpp) cc_final: 0.6544 (ttpp) REVERT: F 401 ILE cc_start: 0.6863 (mm) cc_final: 0.6276 (mt) REVERT: F 426 ASP cc_start: 0.7462 (t0) cc_final: 0.7134 (t70) REVERT: F 466 ASN cc_start: 0.7086 (m110) cc_final: 0.6852 (m110) REVERT: F 551 MET cc_start: 0.5996 (ttt) cc_final: 0.5098 (ttt) REVERT: F 555 VAL cc_start: 0.8367 (p) cc_final: 0.8091 (t) REVERT: F 556 ASP cc_start: 0.6725 (m-30) cc_final: 0.6488 (m-30) REVERT: F 571 ILE cc_start: 0.7430 (mt) cc_final: 0.7151 (tt) REVERT: F 574 GLU cc_start: 0.5480 (mm-30) cc_final: 0.5000 (mm-30) REVERT: H 82 MET cc_start: 0.6585 (mtm) cc_final: 0.5814 (mtm) outliers start: 90 outliers final: 68 residues processed: 950 average time/residue: 0.5465 time to fit residues: 806.6747 Evaluate side-chains 989 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 911 time to evaluate : 7.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 GLU 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 350 GLN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 416 GLN 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 96 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 350 GLN 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 454 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 532 LYS Chi-restraints excluded: chain C residue 549 GLN 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 163 LYS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU 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 518 MET Chi-restraints excluded: chain D residue 519 SER 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 206 THR Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 494 CYS 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 163 LYS Chi-restraints excluded: chain F residue 164 VAL 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 249 SER Chi-restraints excluded: chain F residue 274 ARG 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 518 MET Chi-restraints excluded: chain L residue 30 ILE 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 65 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 254 optimal weight: 0.4980 chunk 333 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 305 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 47 ASN C 85 ASN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 323 ASN F 558 GLN F 560 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115394 restraints weight = 39365.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119480 restraints weight = 22579.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.122181 restraints weight = 15415.673| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28688 Z= 0.129 Angle : 0.507 8.101 39256 Z= 0.261 Chirality : 0.042 0.167 4223 Planarity : 0.005 0.051 5181 Dihedral : 5.094 59.491 3825 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.09 % Allowed : 16.70 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3507 helix: 0.80 (0.56), residues: 60 sheet: -0.57 (0.16), residues: 1023 loop : -0.26 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS C 70 PHE 0.021 0.001 PHE F 45 TYR 0.017 0.001 TYR A 342 ARG 0.006 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 396) hydrogen bonds : angle 5.43192 ( 720) SS BOND : bond 0.00418 ( 9) SS BOND : angle 2.48444 ( 18) covalent geometry : bond 0.00290 (28679) covalent geometry : angle 0.50435 (39238) *********************** 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 1011 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 917 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7620 (m) cc_final: 0.7157 (p) REVERT: A 49 THR cc_start: 0.7416 (m) cc_final: 0.7063 (p) REVERT: A 60 TYR cc_start: 0.5913 (m-10) cc_final: 0.5615 (m-10) REVERT: A 80 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6979 (mtp180) REVERT: A 135 GLU cc_start: 0.6625 (pt0) cc_final: 0.6224 (pt0) REVERT: A 163 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6391 (ptmt) REVERT: A 193 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5467 (tt0) REVERT: A 230 THR cc_start: 0.8244 (p) cc_final: 0.7979 (t) REVERT: A 350 GLN cc_start: 0.7092 (mp10) cc_final: 0.6746 (mp10) REVERT: A 394 THR cc_start: 0.8080 (m) cc_final: 0.7859 (t) REVERT: A 411 GLU cc_start: 0.6581 (mp0) cc_final: 0.6061 (mp0) REVERT: A 417 ASN cc_start: 0.7518 (t0) cc_final: 0.7183 (t0) REVERT: A 439 LYS cc_start: 0.7426 (mmtm) cc_final: 0.7077 (mmtm) REVERT: A 561 TYR cc_start: 0.7517 (m-80) cc_final: 0.7067 (m-80) REVERT: B 60 TYR cc_start: 0.5538 (m-80) cc_final: 0.5312 (m-80) REVERT: B 80 ARG cc_start: 0.5712 (mtp85) cc_final: 0.3470 (mtp85) REVERT: B 89 LYS cc_start: 0.7494 (tppt) cc_final: 0.7208 (tppt) REVERT: B 92 VAL cc_start: 0.7933 (t) cc_final: 0.7616 (p) REVERT: B 95 ASN cc_start: 0.7080 (m-40) cc_final: 0.6773 (m110) REVERT: B 99 ASP cc_start: 0.6561 (t0) cc_final: 0.5980 (t0) REVERT: B 206 THR cc_start: 0.6896 (OUTLIER) cc_final: 0.6645 (m) REVERT: B 312 LYS cc_start: 0.7311 (mmtt) cc_final: 0.6992 (mmtt) REVERT: B 509 GLN cc_start: 0.6667 (mt0) cc_final: 0.6446 (mt0) REVERT: B 574 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5733 (mm-30) REVERT: C 52 LYS cc_start: 0.7488 (tmtm) cc_final: 0.6872 (tmtm) REVERT: C 125 ASP cc_start: 0.6103 (m-30) cc_final: 0.5716 (m-30) REVERT: C 133 MET cc_start: 0.6872 (mmt) cc_final: 0.6503 (mmt) REVERT: C 135 GLU cc_start: 0.6674 (pt0) cc_final: 0.6142 (pt0) REVERT: C 137 HIS cc_start: 0.7696 (m-70) cc_final: 0.7223 (m90) REVERT: C 237 ASP cc_start: 0.6537 (m-30) cc_final: 0.6258 (m-30) REVERT: C 274 ARG cc_start: 0.6095 (mmm-85) cc_final: 0.5853 (mmm-85) REVERT: C 309 GLN cc_start: 0.6734 (tt0) cc_final: 0.6459 (tt0) REVERT: C 350 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.5911 (mt0) REVERT: C 414 TRP cc_start: 0.7513 (p90) cc_final: 0.7078 (p90) REVERT: D 99 ASP cc_start: 0.6945 (t0) cc_final: 0.6542 (t0) REVERT: D 101 THR cc_start: 0.7356 (m) cc_final: 0.7021 (t) REVERT: D 154 SER cc_start: 0.6358 (m) cc_final: 0.5910 (p) REVERT: D 221 SER cc_start: 0.8004 (p) cc_final: 0.7730 (p) REVERT: D 245 THR cc_start: 0.7338 (p) cc_final: 0.7086 (t) REVERT: D 314 ARG cc_start: 0.6272 (mtt-85) cc_final: 0.5857 (mtt-85) REVERT: D 316 VAL cc_start: 0.7905 (t) cc_final: 0.7519 (p) REVERT: D 344 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (p) REVERT: D 382 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7055 (mtm-85) REVERT: D 411 GLU cc_start: 0.6680 (mp0) cc_final: 0.6135 (mp0) REVERT: D 414 TRP cc_start: 0.7100 (p90) cc_final: 0.6590 (p90) REVERT: E 60 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5486 (t80) REVERT: E 68 LEU cc_start: 0.7697 (tp) cc_final: 0.7390 (tt) REVERT: E 80 ARG cc_start: 0.6187 (mtt-85) cc_final: 0.5877 (mtt-85) REVERT: E 178 ASP cc_start: 0.6143 (t0) cc_final: 0.5801 (t0) REVERT: E 180 ASN cc_start: 0.7073 (m-40) cc_final: 0.6815 (m-40) REVERT: E 192 SER cc_start: 0.6953 (t) cc_final: 0.6733 (t) REVERT: E 198 TYR cc_start: 0.7325 (m-80) cc_final: 0.7039 (m-80) REVERT: E 247 GLU cc_start: 0.6664 (mp0) cc_final: 0.6206 (mp0) REVERT: E 283 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7390 (mmm-85) REVERT: E 319 MET cc_start: 0.7075 (mtm) cc_final: 0.6788 (mtp) REVERT: E 339 SER cc_start: 0.7318 (m) cc_final: 0.6998 (p) REVERT: E 350 GLN cc_start: 0.7031 (mp10) cc_final: 0.6249 (mp10) REVERT: E 416 GLN cc_start: 0.7390 (pt0) cc_final: 0.7060 (pt0) REVERT: F 52 LYS cc_start: 0.7275 (tttm) cc_final: 0.6972 (tttm) REVERT: F 60 TYR cc_start: 0.6091 (m-80) cc_final: 0.5694 (t80) REVERT: F 73 MET cc_start: 0.7649 (ptt) cc_final: 0.7433 (ptm) REVERT: F 151 LYS cc_start: 0.7522 (mttm) cc_final: 0.7256 (mttm) REVERT: F 193 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5670 (tt0) REVERT: F 215 ASP cc_start: 0.6744 (m-30) cc_final: 0.6496 (m-30) REVERT: F 275 LEU cc_start: 0.7637 (mp) cc_final: 0.7368 (mt) REVERT: F 339 SER cc_start: 0.8181 (m) cc_final: 0.7744 (p) REVERT: F 350 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6268 (mt0) REVERT: F 387 LYS cc_start: 0.6815 (ttpp) cc_final: 0.6551 (ttpp) REVERT: F 390 THR cc_start: 0.7613 (m) cc_final: 0.7357 (p) REVERT: F 401 ILE cc_start: 0.6815 (mm) cc_final: 0.6266 (mt) REVERT: F 466 ASN cc_start: 0.7038 (m110) cc_final: 0.6821 (m110) REVERT: F 511 ASP cc_start: 0.6905 (t0) cc_final: 0.6456 (t0) REVERT: F 555 VAL cc_start: 0.8324 (p) cc_final: 0.7999 (t) REVERT: F 556 ASP cc_start: 0.6709 (m-30) cc_final: 0.6449 (m-30) REVERT: F 558 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7145 (pt0) REVERT: F 561 TYR cc_start: 0.7517 (m-80) cc_final: 0.7169 (m-80) REVERT: F 571 ILE cc_start: 0.7419 (mt) cc_final: 0.7098 (tt) REVERT: H 82 MET cc_start: 0.6535 (mtm) cc_final: 0.5782 (mtm) outliers start: 94 outliers final: 67 residues processed: 956 average time/residue: 0.4320 time to fit residues: 640.7821 Evaluate side-chains 987 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 911 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 427 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 44 THR 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 206 THR Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 GLN 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 96 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 549 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 SER 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 164 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU 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 450 THR Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 519 SER 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 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 539 LEU 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 96 MET Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 274 ARG Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 388 THR Chi-restraints excluded: chain F residue 394 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 518 MET Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 558 GLN Chi-restraints excluded: chain L residue 88 THR 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 166 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 114 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 185 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN B 143 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 85 ASN C 558 GLN D 383 GLN E 86 ASN E 242 GLN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 483 HIS F 560 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.118013 restraints weight = 38779.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122235 restraints weight = 21967.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125007 restraints weight = 14847.081| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28688 Z= 0.279 Angle : 0.586 8.841 39256 Z= 0.307 Chirality : 0.047 0.174 4223 Planarity : 0.005 0.053 5181 Dihedral : 5.447 58.264 3823 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.79 % Allowed : 17.19 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3507 helix: 0.62 (0.56), residues: 60 sheet: -0.61 (0.16), residues: 1008 loop : -0.36 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 528 HIS 0.006 0.001 HIS B 234 PHE 0.024 0.002 PHE A 448 TYR 0.024 0.002 TYR B 342 ARG 0.010 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 396) hydrogen bonds : angle 5.63366 ( 720) SS BOND : bond 0.00605 ( 9) SS BOND : angle 3.14412 ( 18) covalent geometry : bond 0.00625 (28679) covalent geometry : angle 0.58249 (39238) *********************** 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 994 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 909 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7446 (m) cc_final: 0.7094 (p) REVERT: A 60 TYR cc_start: 0.5909 (m-10) cc_final: 0.5592 (m-10) REVERT: A 80 ARG cc_start: 0.7237 (mtt180) cc_final: 0.7020 (mtp180) REVERT: A 109 TRP cc_start: 0.7958 (m100) cc_final: 0.7647 (m100) REVERT: A 135 GLU cc_start: 0.6630 (pt0) cc_final: 0.6212 (pt0) REVERT: A 163 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6389 (ptmt) REVERT: A 193 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5340 (tt0) REVERT: A 230 THR cc_start: 0.8234 (p) cc_final: 0.7967 (t) REVERT: A 350 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6736 (mp10) REVERT: A 394 THR cc_start: 0.8042 (m) cc_final: 0.7827 (t) REVERT: A 411 GLU cc_start: 0.6617 (mp0) cc_final: 0.6100 (mp0) REVERT: A 439 LYS cc_start: 0.7487 (mmtm) cc_final: 0.7275 (mmmm) REVERT: B 60 TYR cc_start: 0.5569 (m-80) cc_final: 0.5354 (m-80) REVERT: B 80 ARG cc_start: 0.5580 (mtp85) cc_final: 0.3352 (mtp85) REVERT: B 89 LYS cc_start: 0.7512 (tppt) cc_final: 0.7103 (tppt) REVERT: B 95 ASN cc_start: 0.7108 (m-40) cc_final: 0.6892 (m110) REVERT: B 99 ASP cc_start: 0.6585 (t0) cc_final: 0.6003 (t0) REVERT: B 133 MET cc_start: 0.6758 (mmt) cc_final: 0.6519 (mmm) REVERT: B 193 GLU cc_start: 0.5790 (mt-10) cc_final: 0.5571 (mt-10) REVERT: B 206 THR cc_start: 0.6926 (OUTLIER) cc_final: 0.6710 (m) REVERT: B 312 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6958 (mmtt) REVERT: B 382 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6691 (mtm-85) REVERT: B 509 GLN cc_start: 0.6689 (mt0) cc_final: 0.6430 (mt0) REVERT: B 574 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5779 (mm-30) REVERT: C 52 LYS cc_start: 0.7448 (tmtm) cc_final: 0.6840 (tmtm) REVERT: C 99 ASP cc_start: 0.7029 (t70) cc_final: 0.6635 (t0) REVERT: C 125 ASP cc_start: 0.6190 (m-30) cc_final: 0.5771 (m-30) REVERT: C 133 MET cc_start: 0.6938 (mmt) cc_final: 0.6579 (mmt) REVERT: C 135 GLU cc_start: 0.6676 (pt0) cc_final: 0.6146 (pt0) REVERT: C 137 HIS cc_start: 0.7725 (m-70) cc_final: 0.7257 (m90) REVERT: C 190 MET cc_start: 0.6448 (mpt) cc_final: 0.6110 (mpt) REVERT: C 237 ASP cc_start: 0.6596 (m-30) cc_final: 0.6317 (m-30) REVERT: C 309 GLN cc_start: 0.6740 (tt0) cc_final: 0.6425 (tt0) REVERT: C 346 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6483 (mt-10) REVERT: C 350 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6449 (mt0) REVERT: C 414 TRP cc_start: 0.7576 (p90) cc_final: 0.7054 (p90) REVERT: C 481 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6603 (mtp180) REVERT: C 501 LYS cc_start: 0.7470 (ttpp) cc_final: 0.7042 (ttpt) REVERT: D 95 ASN cc_start: 0.6821 (m110) cc_final: 0.6568 (m110) REVERT: D 99 ASP cc_start: 0.6943 (t0) cc_final: 0.6544 (t0) REVERT: D 101 THR cc_start: 0.7329 (m) cc_final: 0.6990 (t) REVERT: D 154 SER cc_start: 0.6457 (m) cc_final: 0.5965 (p) REVERT: D 221 SER cc_start: 0.8020 (p) cc_final: 0.7767 (p) REVERT: D 245 THR cc_start: 0.7387 (p) cc_final: 0.7134 (t) REVERT: D 314 ARG cc_start: 0.6206 (mtt-85) cc_final: 0.5834 (mtt-85) REVERT: D 316 VAL cc_start: 0.7916 (t) cc_final: 0.7442 (p) REVERT: D 411 GLU cc_start: 0.6716 (mp0) cc_final: 0.6124 (mp0) REVERT: D 414 TRP cc_start: 0.7128 (p90) cc_final: 0.6663 (p90) REVERT: E 60 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.5551 (t80) REVERT: E 80 ARG cc_start: 0.6238 (mtt-85) cc_final: 0.5898 (mtt-85) REVERT: E 192 SER cc_start: 0.6926 (t) cc_final: 0.6689 (t) REVERT: E 198 TYR cc_start: 0.7357 (m-80) cc_final: 0.7130 (m-80) REVERT: E 247 GLU cc_start: 0.6632 (mp0) cc_final: 0.6143 (mp0) REVERT: E 312 LYS cc_start: 0.7255 (mmtt) cc_final: 0.7008 (mmtt) REVERT: E 339 SER cc_start: 0.7293 (m) cc_final: 0.7009 (p) REVERT: E 416 GLN cc_start: 0.7358 (pt0) cc_final: 0.7155 (pt0) REVERT: E 427 ASP cc_start: 0.6919 (m-30) cc_final: 0.6537 (t0) REVERT: F 52 LYS cc_start: 0.7282 (tttm) cc_final: 0.6976 (tttm) REVERT: F 60 TYR cc_start: 0.6108 (m-80) cc_final: 0.5695 (t80) REVERT: F 73 MET cc_start: 0.7663 (ptt) cc_final: 0.7407 (ptm) REVERT: F 151 LYS cc_start: 0.7535 (mttm) cc_final: 0.7265 (mttm) REVERT: F 193 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5682 (tt0) REVERT: F 215 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6501 (m-30) REVERT: F 275 LEU cc_start: 0.7659 (mp) cc_final: 0.7388 (mt) REVERT: F 339 SER cc_start: 0.8151 (m) cc_final: 0.7692 (p) REVERT: F 350 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6349 (mt0) REVERT: F 387 LYS cc_start: 0.6893 (ttpp) cc_final: 0.6649 (ttpp) REVERT: F 401 ILE cc_start: 0.6829 (mm) cc_final: 0.6296 (mt) REVERT: F 466 ASN cc_start: 0.7077 (m110) cc_final: 0.6823 (m110) REVERT: F 555 VAL cc_start: 0.8345 (p) cc_final: 0.8077 (t) REVERT: F 556 ASP cc_start: 0.6697 (m-30) cc_final: 0.6457 (m-30) REVERT: F 571 ILE cc_start: 0.7415 (mt) cc_final: 0.7134 (tt) REVERT: H 82 MET cc_start: 0.6538 (mtm) cc_final: 0.5799 (mtm) outliers start: 85 outliers final: 67 residues processed: 946 average time/residue: 0.4632 time to fit residues: 678.5515 Evaluate side-chains 973 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 897 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET 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 350 GLN Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 383 GLN 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 96 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 GLN 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 61 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 532 LYS Chi-restraints excluded: chain C residue 549 GLN 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 164 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 519 SER 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 206 THR 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 539 LEU 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 163 LYS Chi-restraints excluded: chain F residue 164 VAL 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 249 SER Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 388 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 518 MET Chi-restraints excluded: chain L residue 88 THR 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 305 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 47 ASN C 85 ASN C 292 ASN C 558 GLN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 558 GLN F 560 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114459 restraints weight = 39667.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.118768 restraints weight = 22508.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121627 restraints weight = 15162.358| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28688 Z= 0.129 Angle : 0.520 9.307 39256 Z= 0.267 Chirality : 0.043 0.183 4223 Planarity : 0.005 0.051 5181 Dihedral : 5.098 58.709 3823 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.40 % Allowed : 18.01 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3507 helix: 0.61 (0.55), residues: 60 sheet: -0.57 (0.16), residues: 1023 loop : -0.27 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 470 HIS 0.004 0.001 HIS E 277 PHE 0.023 0.001 PHE D 448 TYR 0.017 0.001 TYR A 342 ARG 0.007 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 396) hydrogen bonds : angle 5.48086 ( 720) SS BOND : bond 0.00417 ( 9) SS BOND : angle 2.52744 ( 18) covalent geometry : bond 0.00290 (28679) covalent geometry : angle 0.51773 (39238) ********************** 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 969 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 896 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7432 (m) cc_final: 0.7087 (p) REVERT: A 60 TYR cc_start: 0.5822 (m-10) cc_final: 0.5562 (m-10) REVERT: A 135 GLU cc_start: 0.6627 (pt0) cc_final: 0.6181 (pt0) REVERT: A 163 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6383 (ptmt) REVERT: A 193 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5496 (tt0) REVERT: A 230 THR cc_start: 0.8253 (p) cc_final: 0.7978 (t) REVERT: A 350 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6759 (mp10) REVERT: A 394 THR cc_start: 0.8077 (m) cc_final: 0.7865 (t) REVERT: A 411 GLU cc_start: 0.6623 (mp0) cc_final: 0.6161 (mp0) REVERT: A 417 ASN cc_start: 0.7507 (t0) cc_final: 0.7203 (t0) REVERT: A 439 LYS cc_start: 0.7464 (mmtm) cc_final: 0.7263 (mmmm) REVERT: A 561 TYR cc_start: 0.7531 (m-80) cc_final: 0.7078 (m-80) REVERT: B 60 TYR cc_start: 0.5565 (m-80) cc_final: 0.5325 (m-80) REVERT: B 80 ARG cc_start: 0.5676 (mtp85) cc_final: 0.3437 (mtp85) REVERT: B 89 LYS cc_start: 0.7532 (tppt) cc_final: 0.7048 (tppt) REVERT: B 92 VAL cc_start: 0.7937 (t) cc_final: 0.7650 (p) REVERT: B 95 ASN cc_start: 0.7096 (m-40) cc_final: 0.6785 (m110) REVERT: B 99 ASP cc_start: 0.6545 (t0) cc_final: 0.6024 (t0) REVERT: B 206 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6690 (m) REVERT: B 312 LYS cc_start: 0.7320 (mmtt) cc_final: 0.6999 (mmtt) REVERT: B 382 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: B 509 GLN cc_start: 0.6682 (mt0) cc_final: 0.6456 (mt0) REVERT: B 574 GLU cc_start: 0.6158 (mm-30) cc_final: 0.5733 (mm-30) REVERT: C 52 LYS cc_start: 0.7461 (tmtm) cc_final: 0.6833 (tmtm) REVERT: C 125 ASP cc_start: 0.6158 (m-30) cc_final: 0.5751 (m-30) REVERT: C 133 MET cc_start: 0.6844 (mmt) cc_final: 0.6406 (mmt) REVERT: C 135 GLU cc_start: 0.6712 (pt0) cc_final: 0.6338 (pt0) REVERT: C 137 HIS cc_start: 0.7715 (m-70) cc_final: 0.7213 (m90) REVERT: C 190 MET cc_start: 0.6483 (mpt) cc_final: 0.6151 (mpt) REVERT: C 237 ASP cc_start: 0.6568 (m-30) cc_final: 0.6267 (m-30) REVERT: C 309 GLN cc_start: 0.6747 (tt0) cc_final: 0.6438 (tt0) REVERT: C 346 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6415 (mt-10) REVERT: C 350 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6347 (mt0) REVERT: C 414 TRP cc_start: 0.7516 (p90) cc_final: 0.7010 (p90) REVERT: C 481 ARG cc_start: 0.6964 (mtp180) cc_final: 0.6622 (mtp180) REVERT: C 501 LYS cc_start: 0.7461 (ttpp) cc_final: 0.6984 (ttpt) REVERT: D 95 ASN cc_start: 0.6779 (m110) cc_final: 0.6543 (m110) REVERT: D 99 ASP cc_start: 0.6930 (t0) cc_final: 0.6466 (t0) REVERT: D 101 THR cc_start: 0.7321 (m) cc_final: 0.6979 (t) REVERT: D 154 SER cc_start: 0.6404 (m) cc_final: 0.5951 (p) REVERT: D 221 SER cc_start: 0.8025 (p) cc_final: 0.7782 (p) REVERT: D 245 THR cc_start: 0.7363 (p) cc_final: 0.7107 (t) REVERT: D 314 ARG cc_start: 0.6297 (mtt-85) cc_final: 0.5845 (mtt-85) REVERT: D 316 VAL cc_start: 0.7871 (t) cc_final: 0.7451 (p) REVERT: D 344 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.7150 (p) REVERT: D 411 GLU cc_start: 0.6711 (mp0) cc_final: 0.6076 (mp0) REVERT: D 414 TRP cc_start: 0.7083 (p90) cc_final: 0.6556 (p90) REVERT: E 60 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.5565 (t80) REVERT: E 80 ARG cc_start: 0.6271 (mtt-85) cc_final: 0.5940 (mtt-85) REVERT: E 178 ASP cc_start: 0.6084 (t0) cc_final: 0.5673 (t0) REVERT: E 180 ASN cc_start: 0.7087 (m-40) cc_final: 0.6882 (m-40) REVERT: E 192 SER cc_start: 0.6940 (t) cc_final: 0.6706 (t) REVERT: E 198 TYR cc_start: 0.7324 (m-80) cc_final: 0.7042 (m-80) REVERT: E 247 GLU cc_start: 0.6676 (mp0) cc_final: 0.6201 (mp0) REVERT: E 283 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: E 312 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6992 (mmtt) REVERT: E 339 SER cc_start: 0.7304 (m) cc_final: 0.6982 (p) REVERT: E 350 GLN cc_start: 0.7034 (mp10) cc_final: 0.6214 (mp10) REVERT: E 387 LYS cc_start: 0.7246 (tptp) cc_final: 0.7042 (tptp) REVERT: E 416 GLN cc_start: 0.7395 (pt0) cc_final: 0.7067 (pt0) REVERT: E 427 ASP cc_start: 0.6957 (m-30) cc_final: 0.6520 (t0) REVERT: F 52 LYS cc_start: 0.7284 (tttm) cc_final: 0.7011 (tttm) REVERT: F 60 TYR cc_start: 0.6117 (m-80) cc_final: 0.5692 (t80) REVERT: F 73 MET cc_start: 0.7656 (ptt) cc_final: 0.7433 (ptm) REVERT: F 151 LYS cc_start: 0.7522 (mttm) cc_final: 0.7238 (mttm) REVERT: F 193 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5662 (tt0) REVERT: F 215 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6511 (m-30) REVERT: F 275 LEU cc_start: 0.7648 (mp) cc_final: 0.7381 (mt) REVERT: F 339 SER cc_start: 0.8209 (m) cc_final: 0.7665 (p) REVERT: F 350 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6295 (mt0) REVERT: F 387 LYS cc_start: 0.6895 (ttpp) cc_final: 0.6620 (ttpp) REVERT: F 390 THR cc_start: 0.7611 (m) cc_final: 0.7374 (p) REVERT: F 401 ILE cc_start: 0.6796 (mm) cc_final: 0.6244 (mt) REVERT: F 426 ASP cc_start: 0.7430 (t0) cc_final: 0.7106 (t70) REVERT: F 466 ASN cc_start: 0.7062 (m110) cc_final: 0.6850 (m110) REVERT: F 511 ASP cc_start: 0.6899 (t0) cc_final: 0.6451 (t0) REVERT: F 555 VAL cc_start: 0.8298 (p) cc_final: 0.7982 (t) REVERT: F 556 ASP cc_start: 0.6736 (m-30) cc_final: 0.6496 (m-30) REVERT: F 561 TYR cc_start: 0.7521 (m-80) cc_final: 0.7191 (m-80) REVERT: F 571 ILE cc_start: 0.7346 (mt) cc_final: 0.7024 (tt) REVERT: H 82 MET cc_start: 0.6562 (mtm) cc_final: 0.5794 (mtm) outliers start: 73 outliers final: 57 residues processed: 925 average time/residue: 0.5424 time to fit residues: 788.3273 Evaluate side-chains 949 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 882 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 350 GLN Chi-restraints excluded: chain A residue 383 GLN 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 47 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 416 GLN 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 96 MET Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 549 GLN 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 164 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 206 THR 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 539 LEU 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 164 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 388 THR Chi-restraints excluded: chain F residue 394 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 518 MET Chi-restraints excluded: chain L residue 88 THR 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 0 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 146 optimal weight: 0.8980 chunk 288 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 47 ASN C 85 ASN D 242 GLN E 86 ASN E 242 GLN E 310 GLN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS 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 = 0.3529 r_free = 0.3529 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114787 restraints weight = 39839.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.119085 restraints weight = 22296.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121915 restraints weight = 14943.626| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28688 Z= 0.106 Angle : 0.505 9.179 39256 Z= 0.257 Chirality : 0.042 0.167 4223 Planarity : 0.004 0.050 5181 Dihedral : 4.874 57.170 3823 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.40 % Allowed : 18.18 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.74 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3507 helix: 0.61 (0.55), residues: 60 sheet: -0.47 (0.16), residues: 1030 loop : -0.20 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS E 277 PHE 0.022 0.001 PHE F 45 TYR 0.015 0.001 TYR C 561 ARG 0.004 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 396) hydrogen bonds : angle 5.40646 ( 720) SS BOND : bond 0.00335 ( 9) SS BOND : angle 2.20652 ( 18) covalent geometry : bond 0.00241 (28679) covalent geometry : angle 0.50285 (39238) =============================================================================== Job complete usr+sys time: 15549.56 seconds wall clock time: 278 minutes 12.91 seconds (16692.91 seconds total)