Starting phenix.real_space_refine on Thu Mar 5 22:07:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uts_26788/03_2026/7uts_26788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uts_26788/03_2026/7uts_26788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uts_26788/03_2026/7uts_26788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uts_26788/03_2026/7uts_26788.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uts_26788/03_2026/7uts_26788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uts_26788/03_2026/7uts_26788.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.045 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 95 5.16 5 C 16442 2.51 5 N 4406 2.21 5 O 4861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25804 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "L" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 466 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'CIS': 1, 'TRANS': 91} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 92} Unresolved non-hydrogen planarities: 92 Chain: "H" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 551 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4191 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 3971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3971 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 457} Chain breaks: 6 Chain: "E" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2786 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 318} Chain breaks: 15 Chain: "I" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4108 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 474} Chain breaks: 4 Chain: "F" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4185 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 484} Chain breaks: 2 Chain: "C" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 985 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain breaks: 7 Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 323 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain breaks: 5 Time building chain proxies: 5.67, per 1000 atoms: 0.22 Number of scatterers: 25804 At special positions: 0 Unit cell: (188.1, 161.7, 124.3, 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 95 16.00 O 4861 8.00 N 4406 7.00 C 16442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.04 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.03 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.04 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.03 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: 1.81 Conformation dependent library (CDL) restraints added in 768.0 milliseconds 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6206 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 53 sheets defined 13.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'G' and resid 86 through 92 removed outlier: 4.315A pdb=" N VAL G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.607A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.837A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 281 through 285 removed outlier: 3.539A pdb=" N LEU G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 removed outlier: 3.664A pdb=" N GLY G 385 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 443 through 447 Processing helix chain 'G' and resid 557 through 561 Processing helix chain 'L' and resid 1 through 5 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.578A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.642A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.754A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 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 443 through 448 removed outlier: 4.143A pdb=" N ILE A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.151A pdb=" N VAL B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.757A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.661A pdb=" N ASP B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) 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 561 removed outlier: 3.868A pdb=" N ASN B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 removed outlier: 4.141A pdb=" N ASP E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS E 89 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 4.423A pdb=" N ALA E 97 " --> pdb=" O GLY E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.649A pdb=" N THR E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 326 through 330 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 409 through 413 removed outlier: 4.306A pdb=" N ASP E 413 " --> pdb=" O PRO E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 562 removed outlier: 3.679A pdb=" N ASN E 560 " --> pdb=" O ASN E 557 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E 561 " --> pdb=" O GLN E 558 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 557 through 562' Processing helix chain 'I' and resid 86 through 92 removed outlier: 3.511A pdb=" N VAL I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 removed outlier: 4.663A pdb=" N ALA I 97 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 99 " --> pdb=" O MET I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.528A pdb=" N VAL I 119 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.894A pdb=" N LEU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 409 through 413 removed outlier: 4.019A pdb=" N ASP I 413 " --> pdb=" O PRO I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 443 through 447 Processing helix chain 'I' and resid 557 through 562 removed outlier: 3.774A pdb=" N VAL I 562 " --> pdb=" O PHE I 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.936A 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 245 through 250 Processing helix chain 'F' and resid 281 through 285 removed outlier: 3.513A pdb=" N LEU F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.739A pdb=" N ASP F 413 " --> pdb=" O PRO F 410 " (cutoff:3.500A) 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 447 Processing helix chain 'F' and resid 557 through 562 removed outlier: 3.902A pdb=" N VAL F 562 " --> pdb=" O PHE F 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing sheet with id=AA1, first strand: chain 'G' and resid 50 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 72 current: chain 'G' and resid 164 through 167 Processing sheet with id=AA2, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AA3, first strand: chain 'G' and resid 206 through 207 removed outlier: 4.541A pdb=" N LEU G 498 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 217 through 218 removed outlier: 4.000A pdb=" N THR G 217 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 277 Processing sheet with id=AA6, first strand: chain 'G' and resid 315 through 317 Processing sheet with id=AA7, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.783A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 351 through 354 removed outlier: 3.568A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 396 through 399 Processing sheet with id=AB1, first strand: chain 'G' and resid 429 through 430 Processing sheet with id=AB2, first strand: chain 'G' and resid 470 through 472 removed outlier: 6.809A pdb=" N ASP G 471 " --> pdb=" O CYS G 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.475A pdb=" N UNK H 85 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AB6, 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 164 through 167 Processing sheet with id=AB7, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AB8, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AB9, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AC1, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.831A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AC3, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AC4, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.357A pdb=" N TYR A 464 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 574 " --> pdb=" O TYR A 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 470 through 472 removed outlier: 6.797A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 45 current: chain 'C' and resid 105 through 111 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, 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 164 through 167 Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AC9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AD1, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AD2, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.498A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 345 through 348 Processing sheet with id=AD4, first strand: chain 'B' and resid 377 through 378 removed outlier: 3.558A pdb=" N PHE B 398 " --> pdb=" O TYR B 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 435 through 436 removed outlier: 5.727A pdb=" N ILE B 442 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD7, first strand: chain 'E' and resid 49 through 50 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 71 current: chain 'E' and resid 164 through 166 Processing sheet with id=AD8, first strand: chain 'E' and resid 206 through 210 removed outlier: 7.050A pdb=" N THR E 206 " --> pdb=" O TRP E 109 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TRP E 109 " --> pdb=" O THR E 206 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP E 208 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU E 498 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE1, first strand: chain 'I' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 72 current: chain 'I' and resid 164 through 168 Processing sheet with id=AE2, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AE3, first strand: chain 'I' and resid 215 through 218 removed outlier: 3.640A pdb=" N GLY I 235 " --> pdb=" O ASP I 215 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR I 217 " --> pdb=" O TYR I 233 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR I 233 " --> pdb=" O THR I 217 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 276 through 277 Processing sheet with id=AE5, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.209A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 345 through 346 Processing sheet with id=AE7, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AE8, first strand: chain 'I' and resid 415 through 416 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 166 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 216 through 218 Processing sheet with id=AF3, first strand: chain 'F' and resid 276 through 277 Processing sheet with id=AF4, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.731A 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 463 through 464 removed outlier: 3.768A pdb=" N TYR F 464 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 470 through 472 removed outlier: 6.867A pdb=" N ASP F 471 " --> pdb=" O CYS F 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 69 through 72 removed outlier: 4.191A pdb=" N TRP C 528 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C 147 " --> pdb=" O TRP C 528 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 68 through 73 removed outlier: 5.184A pdb=" N THR D 523 " --> pdb=" O MET D 73 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.30 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: 8075 1.34 - 1.46: 6375 1.46 - 1.58: 11897 1.58 - 1.71: 3 1.71 - 1.83: 169 Bond restraints: 26519 Sorted by residual: bond pdb=" C LEU G 578 " pdb=" N ALA G 579 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.06e+01 bond pdb=" C ALA B 503 " pdb=" N PRO B 504 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.66e+00 bond pdb=" CB TRP A 120 " pdb=" CG TRP A 120 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.40e+00 bond pdb=" N GLY C 496 " pdb=" CA GLY C 496 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.76e+00 bond pdb=" N GLY I 37 " pdb=" CA GLY I 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 ... (remaining 26514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 33403 1.64 - 3.27: 2339 3.27 - 4.91: 364 4.91 - 6.55: 128 6.55 - 8.18: 17 Bond angle restraints: 36251 Sorted by residual: angle pdb=" N GLY F 286 " pdb=" CA GLY F 286 " pdb=" C GLY F 286 " ideal model delta sigma weight residual 111.56 116.78 -5.22 1.01e+00 9.80e-01 2.67e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 110.43 116.00 -5.57 1.35e+00 5.49e-01 1.70e+01 angle pdb=" N GLY F 320 " pdb=" CA GLY F 320 " pdb=" C GLY F 320 " ideal model delta sigma weight residual 113.99 119.25 -5.26 1.28e+00 6.10e-01 1.69e+01 angle pdb=" CA UNK L 58 " pdb=" C UNK L 58 " pdb=" N UNK L 59 " ideal model delta sigma weight residual 116.20 124.28 -8.08 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N GLY I 320 " pdb=" CA GLY I 320 " pdb=" C GLY I 320 " ideal model delta sigma weight residual 113.86 119.66 -5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 36246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14476 17.99 - 35.99: 855 35.99 - 53.98: 128 53.98 - 71.98: 43 71.98 - 89.97: 33 Dihedral angle restraints: 15535 sinusoidal: 5954 harmonic: 9581 Sorted by residual: dihedral pdb=" CA ASP B 100 " pdb=" C ASP B 100 " pdb=" N ILE B 101 " pdb=" CA ILE B 101 " ideal model delta harmonic sigma weight residual -180.00 -147.67 -32.33 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta harmonic sigma weight residual 180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA TYR G 233 " pdb=" C TYR G 233 " pdb=" N HIS G 234 " pdb=" CA HIS G 234 " ideal model delta harmonic sigma weight residual 180.00 -150.37 -29.63 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 15532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2375 0.042 - 0.084: 1125 0.084 - 0.126: 352 0.126 - 0.168: 109 0.168 - 0.210: 12 Chirality restraints: 3973 Sorted by residual: chirality pdb=" CA ILE C 204 " pdb=" N ILE C 204 " pdb=" C ILE C 204 " pdb=" CB ILE C 204 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 145 " pdb=" N ILE C 145 " pdb=" C ILE C 145 " pdb=" CB ILE C 145 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE F 219 " pdb=" N ILE F 219 " pdb=" C ILE F 219 " pdb=" CB ILE F 219 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3970 not shown) Planarity restraints: 4735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.09e+01 pdb=" NE ARG A 408 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 107 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO B 108 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 216 " 0.240 9.50e-02 1.11e+02 1.08e-01 7.16e+00 pdb=" NE ARG G 216 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 216 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 216 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 216 " 0.010 2.00e-02 2.50e+03 ... (remaining 4732 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7518 2.82 - 3.34: 23984 3.34 - 3.86: 42817 3.86 - 4.38: 50900 4.38 - 4.90: 85398 Nonbonded interactions: 210617 Sorted by model distance: nonbonded pdb=" OH TYR B 343 " pdb=" OD1 ASN I 321 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN G 443 " pdb=" OG1 THR G 445 " model vdw 2.334 3.040 nonbonded pdb=" OG SER A 348 " pdb=" N THR A 349 " model vdw 2.354 3.120 nonbonded pdb=" N ASP B 239 " pdb=" OD1 ASP B 239 " model vdw 2.370 3.120 nonbonded pdb=" O LEU F 128 " pdb=" OG1 THR F 132 " model vdw 2.391 3.040 ... (remaining 210612 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' and (resid 45 through 153 or resid 165 through 251 or resid 254 throu \ gh 291 or resid 305 through 356 or resid 376 through 404 or resid 408 through 45 \ 6 or resid 461 through 473 or resid 479 through 490 or resid 494 through 581)) selection = (chain 'B' and (resid 45 through 153 or resid 165 through 356 or resid 376 throu \ gh 404 or resid 408 through 456 or resid 461 through 581)) selection = (chain 'F' and (resid 45 through 251 or resid 254 through 291 or resid 305 throu \ gh 356 or resid 376 through 404 or resid 408 through 456 or resid 461 through 47 \ 3 or resid 479 through 490 or resid 494 through 581)) selection = (chain 'G' and (resid 45 through 153 or resid 165 through 251 or resid 254 throu \ gh 291 or resid 305 through 356 or resid 376 through 404 or resid 408 through 45 \ 6 or resid 461 through 473 or resid 479 through 490 or resid 494 through 581)) selection = (chain 'I' and (resid 45 through 153 or resid 165 through 251 or resid 254 throu \ gh 291 or resid 305 through 356 or resid 376 through 473 or resid 479 through 49 \ 0 or resid 494 through 581)) } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.660 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 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 : 0.008 0.090 26524 Z= 0.380 Angle : 0.967 8.184 36261 Z= 0.527 Chirality : 0.054 0.210 3973 Planarity : 0.007 0.132 4735 Dihedral : 13.015 89.974 9314 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.99 % Allowed : 5.13 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 2990 helix: -1.98 (0.38), residues: 112 sheet: -0.69 (0.18), residues: 705 loop : -0.66 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 191 TYR 0.032 0.003 TYR G 524 PHE 0.043 0.003 PHE A 448 TRP 0.026 0.003 TRP I 545 HIS 0.008 0.002 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00841 (26519) covalent geometry : angle 0.96609 (36251) SS BOND : bond 0.00537 ( 5) SS BOND : angle 2.34603 ( 10) hydrogen bonds : bond 0.23097 ( 329) hydrogen bonds : angle 8.38678 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 834 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 50 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7280 (mt-10) REVERT: G 59 VAL cc_start: 0.8861 (t) cc_final: 0.8342 (m) REVERT: G 60 GLU cc_start: 0.7127 (tt0) cc_final: 0.6836 (tt0) REVERT: G 125 ASP cc_start: 0.6855 (m-30) cc_final: 0.6470 (m-30) REVERT: G 135 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6767 (mt-10) REVERT: G 174 MET cc_start: 0.7432 (mtp) cc_final: 0.7215 (mtp) REVERT: G 177 LEU cc_start: 0.7952 (tp) cc_final: 0.7721 (tp) REVERT: G 197 PHE cc_start: 0.7761 (m-10) cc_final: 0.7412 (m-80) REVERT: G 198 TYR cc_start: 0.8411 (m-80) cc_final: 0.8194 (m-10) REVERT: G 271 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7733 (mtpp) REVERT: G 330 ILE cc_start: 0.8187 (tp) cc_final: 0.7910 (tp) REVERT: G 382 ARG cc_start: 0.6031 (mtm180) cc_final: 0.5719 (mtm180) REVERT: G 387 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7696 (ttmm) REVERT: G 397 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7961 (mtm180) REVERT: G 492 ASN cc_start: 0.7956 (m-40) cc_final: 0.7650 (m-40) REVERT: G 536 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7851 (ttpp) REVERT: G 559 PHE cc_start: 0.8285 (m-80) cc_final: 0.7537 (m-80) REVERT: G 569 MET cc_start: 0.7257 (mmm) cc_final: 0.7052 (mmm) REVERT: G 570 LYS cc_start: 0.7967 (ptpt) cc_final: 0.7583 (ptpt) REVERT: A 56 ASN cc_start: 0.7626 (m110) cc_final: 0.7382 (m110) REVERT: A 99 ASP cc_start: 0.6934 (t70) cc_final: 0.6278 (t70) REVERT: A 100 ASP cc_start: 0.7145 (m-30) cc_final: 0.6556 (m-30) REVERT: A 109 TRP cc_start: 0.8297 (m100) cc_final: 0.7861 (m100) REVERT: A 142 GLU cc_start: 0.7504 (pt0) cc_final: 0.7192 (pt0) REVERT: A 174 MET cc_start: 0.7025 (mtp) cc_final: 0.6417 (mtp) REVERT: A 183 MET cc_start: 0.7201 (mmm) cc_final: 0.6671 (mmm) REVERT: A 192 SER cc_start: 0.7582 (t) cc_final: 0.7274 (t) REVERT: A 211 TYR cc_start: 0.7393 (m-80) cc_final: 0.7085 (m-10) REVERT: A 218 LEU cc_start: 0.8598 (tp) cc_final: 0.8284 (tt) REVERT: A 219 ILE cc_start: 0.8567 (mm) cc_final: 0.8327 (mm) REVERT: A 274 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7525 (mmm-85) REVERT: A 303 PHE cc_start: 0.7997 (m-80) cc_final: 0.7602 (m-80) REVERT: A 306 ILE cc_start: 0.8607 (tp) cc_final: 0.8313 (tt) REVERT: A 415 ILE cc_start: 0.8387 (mm) cc_final: 0.8186 (mm) REVERT: A 436 ILE cc_start: 0.9015 (pt) cc_final: 0.8657 (mt) REVERT: A 458 ASN cc_start: 0.8002 (m110) cc_final: 0.7794 (m110) REVERT: A 471 ASP cc_start: 0.7069 (t0) cc_final: 0.6302 (t0) REVERT: A 530 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6651 (ttpp) REVERT: A 533 LEU cc_start: 0.8315 (tp) cc_final: 0.8112 (tp) REVERT: A 543 HIS cc_start: 0.6915 (m170) cc_final: 0.6655 (m170) REVERT: A 553 ILE cc_start: 0.8641 (tt) cc_final: 0.8305 (tt) REVERT: A 559 PHE cc_start: 0.8444 (m-80) cc_final: 0.8172 (m-10) REVERT: A 570 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7700 (ptpt) REVERT: A 575 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7979 (mtpt) REVERT: A 582 LYS cc_start: 0.8237 (ttpp) cc_final: 0.8036 (ttpp) REVERT: B 93 ASN cc_start: 0.8055 (m110) cc_final: 0.7328 (p0) REVERT: B 101 ILE cc_start: 0.7832 (pt) cc_final: 0.7597 (pt) REVERT: B 104 GLN cc_start: 0.7991 (pt0) cc_final: 0.7394 (pt0) REVERT: B 117 TRP cc_start: 0.7120 (m100) cc_final: 0.6219 (m100) REVERT: B 125 ASP cc_start: 0.8160 (m-30) cc_final: 0.7798 (m-30) REVERT: B 126 TRP cc_start: 0.7614 (t-100) cc_final: 0.7389 (t-100) REVERT: B 128 LEU cc_start: 0.9183 (tp) cc_final: 0.8964 (tp) REVERT: B 134 SER cc_start: 0.7612 (p) cc_final: 0.7241 (p) REVERT: B 135 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 143 GLN cc_start: 0.7531 (mt0) cc_final: 0.7137 (mt0) REVERT: B 150 LEU cc_start: 0.8494 (tp) cc_final: 0.8084 (tp) REVERT: B 151 LYS cc_start: 0.8193 (mttm) cc_final: 0.7920 (mttm) REVERT: B 173 LEU cc_start: 0.8157 (tp) cc_final: 0.7946 (tp) REVERT: B 174 MET cc_start: 0.6648 (mtp) cc_final: 0.6329 (mtp) REVERT: B 183 MET cc_start: 0.6823 (mmm) cc_final: 0.6227 (mmm) REVERT: B 190 MET cc_start: 0.7626 (tpp) cc_final: 0.7207 (tpp) REVERT: B 198 TYR cc_start: 0.6764 (m-80) cc_final: 0.6188 (m-80) REVERT: B 209 ARG cc_start: 0.7748 (pmt170) cc_final: 0.7548 (pmt170) REVERT: B 266 PHE cc_start: 0.7027 (t80) cc_final: 0.6355 (t80) REVERT: B 268 PHE cc_start: 0.7315 (m-80) cc_final: 0.6727 (m-80) REVERT: B 382 ARG cc_start: 0.7435 (mmt90) cc_final: 0.7173 (mmt-90) REVERT: B 469 ILE cc_start: 0.8066 (mt) cc_final: 0.7544 (mt) REVERT: B 470 TRP cc_start: 0.7994 (p90) cc_final: 0.7790 (p90) REVERT: B 471 ASP cc_start: 0.5225 (t0) cc_final: 0.4899 (t0) REVERT: B 498 LEU cc_start: 0.8508 (tp) cc_final: 0.8307 (tp) REVERT: B 499 PHE cc_start: 0.8449 (m-80) cc_final: 0.8159 (m-80) REVERT: B 501 LYS cc_start: 0.7774 (tttt) cc_final: 0.7126 (tttt) REVERT: B 509 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6339 (mm-30) REVERT: B 527 PHE cc_start: 0.7067 (p90) cc_final: 0.6554 (p90) REVERT: B 532 LYS cc_start: 0.7309 (tttm) cc_final: 0.7000 (tttm) REVERT: B 533 LEU cc_start: 0.7769 (tp) cc_final: 0.7408 (tp) REVERT: B 536 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7743 (ttpp) REVERT: B 551 MET cc_start: 0.5557 (mmt) cc_final: 0.5213 (mmt) REVERT: E 45 PHE cc_start: 0.7397 (t80) cc_final: 0.6847 (t80) REVERT: E 87 MET cc_start: 0.7129 (ttt) cc_final: 0.6884 (ttt) REVERT: E 129 ILE cc_start: 0.8958 (mt) cc_final: 0.8725 (mt) REVERT: E 143 GLN cc_start: 0.7550 (mt0) cc_final: 0.7080 (mt0) REVERT: E 166 ASN cc_start: 0.6737 (m110) cc_final: 0.6522 (m110) REVERT: E 190 MET cc_start: 0.5520 (mtm) cc_final: 0.5176 (mtm) REVERT: E 329 THR cc_start: 0.4936 (t) cc_final: 0.4472 (m) REVERT: E 331 MET cc_start: 0.7202 (pmm) cc_final: 0.6934 (pmm) REVERT: E 377 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6247 (mtp180) REVERT: E 378 TYR cc_start: 0.6998 (m-80) cc_final: 0.6391 (m-80) REVERT: E 398 PHE cc_start: 0.7596 (p90) cc_final: 0.7299 (p90) REVERT: E 400 TYR cc_start: 0.7661 (t80) cc_final: 0.7443 (t80) REVERT: E 527 PHE cc_start: 0.7358 (p90) cc_final: 0.7082 (p90) REVERT: E 549 GLN cc_start: 0.7850 (tt0) cc_final: 0.6976 (tt0) REVERT: E 561 TYR cc_start: 0.8188 (m-80) cc_final: 0.7455 (m-80) REVERT: I 47 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7704 (t0) REVERT: I 52 LYS cc_start: 0.7338 (ttmm) cc_final: 0.7060 (ttmm) REVERT: I 60 GLU cc_start: 0.7188 (tt0) cc_final: 0.6904 (tt0) REVERT: I 87 MET cc_start: 0.6075 (ttp) cc_final: 0.5696 (ttp) REVERT: I 115 ASN cc_start: 0.7611 (t0) cc_final: 0.7351 (t0) REVERT: I 143 GLN cc_start: 0.8195 (mt0) cc_final: 0.7916 (mt0) REVERT: I 144 GLU cc_start: 0.7244 (pt0) cc_final: 0.6939 (pt0) REVERT: I 147 ASN cc_start: 0.8063 (t0) cc_final: 0.7303 (t0) REVERT: I 174 MET cc_start: 0.7030 (mtp) cc_final: 0.6634 (mtp) REVERT: I 201 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7951 (mtpt) REVERT: I 261 PHE cc_start: 0.7863 (t80) cc_final: 0.7459 (t80) REVERT: I 268 PHE cc_start: 0.7657 (m-80) cc_final: 0.7120 (m-80) REVERT: I 273 CYS cc_start: 0.7447 (t) cc_final: 0.7156 (t) REVERT: I 331 MET cc_start: 0.7165 (ttm) cc_final: 0.6941 (ttm) REVERT: I 387 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8112 (ttmm) REVERT: I 427 ASP cc_start: 0.8314 (m-30) cc_final: 0.7944 (m-30) REVERT: I 444 TYR cc_start: 0.8120 (p90) cc_final: 0.7790 (p90) REVERT: I 468 GLN cc_start: 0.6753 (mm110) cc_final: 0.6518 (mm110) REVERT: I 518 MET cc_start: 0.6677 (ptp) cc_final: 0.6177 (ptp) REVERT: I 532 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7551 (ttpp) REVERT: I 538 LYS cc_start: 0.8163 (tttp) cc_final: 0.7868 (ttmm) REVERT: I 539 LEU cc_start: 0.8624 (mt) cc_final: 0.8345 (mp) REVERT: I 543 HIS cc_start: 0.7176 (m170) cc_final: 0.6971 (m170) REVERT: I 544 THR cc_start: 0.7971 (p) cc_final: 0.7483 (p) REVERT: I 546 ASN cc_start: 0.8032 (p0) cc_final: 0.7709 (p0) REVERT: I 550 GLN cc_start: 0.7969 (mt0) cc_final: 0.7685 (mt0) REVERT: I 551 MET cc_start: 0.6694 (tmm) cc_final: 0.5495 (tmm) REVERT: I 558 GLN cc_start: 0.8140 (tt0) cc_final: 0.7881 (tt0) REVERT: I 559 PHE cc_start: 0.7862 (m-80) cc_final: 0.7648 (m-10) REVERT: I 573 TYR cc_start: 0.8200 (p90) cc_final: 0.7668 (p90) REVERT: I 574 GLU cc_start: 0.7427 (tp30) cc_final: 0.6914 (tp30) REVERT: I 575 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7881 (mtmm) REVERT: I 581 ARG cc_start: 0.6875 (ttm170) cc_final: 0.6309 (ttm170) REVERT: F 51 PHE cc_start: 0.6676 (m-80) cc_final: 0.6286 (m-80) REVERT: F 52 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7363 (ttmm) REVERT: F 53 PHE cc_start: 0.7264 (m-80) cc_final: 0.7059 (m-80) REVERT: F 54 LEU cc_start: 0.8225 (mt) cc_final: 0.7989 (mt) REVERT: F 59 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.7743 (m) REVERT: F 60 GLU cc_start: 0.7612 (tt0) cc_final: 0.7131 (tt0) REVERT: F 96 MET cc_start: 0.7373 (mpp) cc_final: 0.7130 (mpp) REVERT: F 143 GLN cc_start: 0.7348 (mp10) cc_final: 0.6786 (mp10) REVERT: F 180 ASN cc_start: 0.7703 (t0) cc_final: 0.7355 (t0) REVERT: F 218 LEU cc_start: 0.8221 (mt) cc_final: 0.7955 (mp) REVERT: F 232 ILE cc_start: 0.7414 (mt) cc_final: 0.6988 (mt) REVERT: F 243 PHE cc_start: 0.7766 (t80) cc_final: 0.7539 (t80) REVERT: F 244 TYR cc_start: 0.7522 (m-80) cc_final: 0.7282 (m-10) REVERT: F 266 PHE cc_start: 0.7586 (t80) cc_final: 0.7314 (t80) REVERT: F 271 LYS cc_start: 0.8256 (mtpp) cc_final: 0.8009 (mtpp) REVERT: F 282 ASN cc_start: 0.8164 (m110) cc_final: 0.7907 (m-40) REVERT: F 283 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7689 (tpp80) REVERT: F 338 TYR cc_start: 0.8382 (p90) cc_final: 0.8181 (p90) REVERT: F 404 GLN cc_start: 0.3889 (OUTLIER) cc_final: 0.3193 (tm-30) REVERT: F 405 ASP cc_start: 0.6062 (m-30) cc_final: 0.5676 (m-30) REVERT: F 430 LEU cc_start: 0.8341 (tp) cc_final: 0.8100 (tt) REVERT: F 431 LEU cc_start: 0.8489 (mt) cc_final: 0.8275 (mp) REVERT: F 450 THR cc_start: 0.8716 (p) cc_final: 0.8415 (t) REVERT: F 475 ASP cc_start: 0.7314 (t0) cc_final: 0.6731 (t0) REVERT: F 484 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8306 (m) REVERT: F 485 ASN cc_start: 0.7779 (p0) cc_final: 0.7402 (p0) REVERT: F 489 VAL cc_start: 0.8130 (m) cc_final: 0.7871 (m) REVERT: F 493 ASN cc_start: 0.8088 (m110) cc_final: 0.7855 (m-40) REVERT: F 538 LYS cc_start: 0.7563 (tptp) cc_final: 0.6704 (tppt) REVERT: F 551 MET cc_start: 0.6510 (ttt) cc_final: 0.6053 (ttt) REVERT: C 174 MET cc_start: 0.7001 (mtp) cc_final: 0.6320 (mtp) outliers start: 27 outliers final: 10 residues processed: 842 average time/residue: 0.1800 time to fit residues: 232.3453 Evaluate side-chains 813 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 799 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 484 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 0.8980 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 417 ASN ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN G 497 GLN A 403 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 508 ASN B 558 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.215950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.157600 restraints weight = 41466.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.163682 restraints weight = 17880.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167419 restraints weight = 10250.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.168939 restraints weight = 7561.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.170221 restraints weight = 6542.515| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 26524 Z= 0.334 Angle : 0.704 9.523 36261 Z= 0.366 Chirality : 0.048 0.184 3973 Planarity : 0.006 0.059 4735 Dihedral : 7.067 64.159 3523 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.53 % Allowed : 10.00 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 2990 helix: -1.15 (0.45), residues: 111 sheet: -0.67 (0.18), residues: 758 loop : -0.67 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 191 TYR 0.031 0.002 TYR G 451 PHE 0.026 0.002 PHE B 398 TRP 0.029 0.002 TRP F 545 HIS 0.008 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00708 (26519) covalent geometry : angle 0.70273 (36251) SS BOND : bond 0.01628 ( 5) SS BOND : angle 2.29015 ( 10) hydrogen bonds : bond 0.04664 ( 329) hydrogen bonds : angle 6.34948 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 810 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 59 VAL cc_start: 0.8792 (t) cc_final: 0.8376 (m) REVERT: G 85 ASN cc_start: 0.7626 (t0) cc_final: 0.6975 (t0) REVERT: G 125 ASP cc_start: 0.6574 (m-30) cc_final: 0.6228 (m-30) REVERT: G 211 TYR cc_start: 0.8207 (m-80) cc_final: 0.7564 (m-80) REVERT: G 248 ASN cc_start: 0.7611 (t0) cc_final: 0.7370 (t0) REVERT: G 249 SER cc_start: 0.8522 (t) cc_final: 0.8307 (t) REVERT: G 263 THR cc_start: 0.8042 (m) cc_final: 0.7736 (p) REVERT: G 282 ASN cc_start: 0.8246 (t0) cc_final: 0.7898 (t0) REVERT: G 332 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7576 (mmt90) REVERT: G 382 ARG cc_start: 0.5943 (mtm180) cc_final: 0.5625 (mtm180) REVERT: G 468 GLN cc_start: 0.7865 (mt0) cc_final: 0.7582 (mt0) REVERT: G 471 ASP cc_start: 0.7563 (t0) cc_final: 0.7248 (t0) REVERT: G 485 ASN cc_start: 0.7798 (p0) cc_final: 0.7112 (p0) REVERT: G 492 ASN cc_start: 0.7852 (m-40) cc_final: 0.7645 (m-40) REVERT: G 497 GLN cc_start: 0.8248 (mt0) cc_final: 0.7968 (mt0) REVERT: G 536 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8041 (ttpp) REVERT: G 560 ASN cc_start: 0.7735 (m-40) cc_final: 0.7434 (m-40) REVERT: G 561 TYR cc_start: 0.8535 (m-80) cc_final: 0.8152 (m-80) REVERT: G 575 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7602 (mmtt) REVERT: A 56 ASN cc_start: 0.7583 (m110) cc_final: 0.7376 (m110) REVERT: A 98 LEU cc_start: 0.7815 (mt) cc_final: 0.7051 (mt) REVERT: A 100 ASP cc_start: 0.7074 (m-30) cc_final: 0.6246 (m-30) REVERT: A 101 ILE cc_start: 0.8325 (mt) cc_final: 0.8115 (mp) REVERT: A 115 ASN cc_start: 0.7963 (t0) cc_final: 0.7674 (t0) REVERT: A 142 GLU cc_start: 0.7339 (pt0) cc_final: 0.7109 (pt0) REVERT: A 174 MET cc_start: 0.7092 (mtp) cc_final: 0.6727 (mtp) REVERT: A 183 MET cc_start: 0.7143 (mmm) cc_final: 0.6610 (mmm) REVERT: A 211 TYR cc_start: 0.7332 (m-80) cc_final: 0.7019 (m-80) REVERT: A 216 ARG cc_start: 0.6936 (ttt90) cc_final: 0.6337 (ttt90) REVERT: A 218 LEU cc_start: 0.8378 (tp) cc_final: 0.7968 (tt) REVERT: A 219 ILE cc_start: 0.8670 (mm) cc_final: 0.8429 (mm) REVERT: A 313 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8136 (mtm-85) REVERT: A 344 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7510 (p) REVERT: A 350 GLN cc_start: 0.7455 (mt0) cc_final: 0.7155 (mt0) REVERT: A 382 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6856 (mtm110) REVERT: A 411 GLU cc_start: 0.7441 (mp0) cc_final: 0.7190 (mp0) REVERT: A 413 ASP cc_start: 0.7309 (t0) cc_final: 0.7078 (t0) REVERT: A 439 LYS cc_start: 0.8302 (mptt) cc_final: 0.8009 (mptt) REVERT: A 458 ASN cc_start: 0.7954 (m110) cc_final: 0.7729 (m110) REVERT: A 530 LYS cc_start: 0.7379 (ttmt) cc_final: 0.7027 (ttpp) REVERT: A 543 HIS cc_start: 0.6798 (m170) cc_final: 0.6535 (m170) REVERT: A 570 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7707 (ptpt) REVERT: A 575 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7570 (mtpt) REVERT: B 70 HIS cc_start: 0.7848 (t70) cc_final: 0.7504 (t70) REVERT: B 80 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6702 (mtt-85) REVERT: B 101 ILE cc_start: 0.8188 (pt) cc_final: 0.7891 (pt) REVERT: B 125 ASP cc_start: 0.8307 (m-30) cc_final: 0.7891 (m-30) REVERT: B 135 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7150 (mt-10) REVERT: B 143 GLN cc_start: 0.7557 (mt0) cc_final: 0.7277 (mt0) REVERT: B 146 PHE cc_start: 0.8076 (p90) cc_final: 0.7859 (p90) REVERT: B 151 LYS cc_start: 0.8077 (mttm) cc_final: 0.7820 (mttm) REVERT: B 173 LEU cc_start: 0.8088 (tp) cc_final: 0.7884 (tp) REVERT: B 174 MET cc_start: 0.6580 (mtp) cc_final: 0.6303 (mtp) REVERT: B 178 ASP cc_start: 0.5856 (t0) cc_final: 0.5636 (t0) REVERT: B 183 MET cc_start: 0.6836 (mmm) cc_final: 0.6370 (mmm) REVERT: B 190 MET cc_start: 0.7841 (tpp) cc_final: 0.7408 (tpp) REVERT: B 198 TYR cc_start: 0.7134 (m-80) cc_final: 0.6617 (m-80) REVERT: B 237 ASP cc_start: 0.7180 (m-30) cc_final: 0.6632 (m-30) REVERT: B 247 GLU cc_start: 0.6170 (mp0) cc_final: 0.5525 (mp0) REVERT: B 266 PHE cc_start: 0.7192 (t80) cc_final: 0.6756 (t80) REVERT: B 382 ARG cc_start: 0.7618 (mmt90) cc_final: 0.6956 (mmt-90) REVERT: B 383 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7047 (tm-30) REVERT: B 469 ILE cc_start: 0.7995 (mt) cc_final: 0.7382 (mt) REVERT: B 470 TRP cc_start: 0.8008 (p90) cc_final: 0.7793 (p90) REVERT: B 499 PHE cc_start: 0.8405 (m-80) cc_final: 0.7745 (m-80) REVERT: B 501 LYS cc_start: 0.7890 (tttt) cc_final: 0.7265 (tttt) REVERT: B 509 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6362 (mm-30) REVERT: B 527 PHE cc_start: 0.6873 (p90) cc_final: 0.6524 (p90) REVERT: B 530 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8154 (ttmt) REVERT: B 532 LYS cc_start: 0.7278 (tttm) cc_final: 0.7061 (tttm) REVERT: B 533 LEU cc_start: 0.8069 (tp) cc_final: 0.7712 (tp) REVERT: B 551 MET cc_start: 0.5914 (mmt) cc_final: 0.5405 (mmt) REVERT: E 45 PHE cc_start: 0.7514 (t80) cc_final: 0.6913 (t80) REVERT: E 87 MET cc_start: 0.7100 (ttt) cc_final: 0.6797 (ttt) REVERT: E 129 ILE cc_start: 0.8875 (mt) cc_final: 0.8622 (mt) REVERT: E 166 ASN cc_start: 0.7020 (m110) cc_final: 0.6768 (m110) REVERT: E 190 MET cc_start: 0.5431 (mtm) cc_final: 0.5130 (mtm) REVERT: E 329 THR cc_start: 0.4310 (t) cc_final: 0.4047 (m) REVERT: E 378 TYR cc_start: 0.7069 (m-80) cc_final: 0.6336 (m-80) REVERT: E 398 PHE cc_start: 0.7828 (p90) cc_final: 0.7437 (p90) REVERT: E 400 TYR cc_start: 0.7792 (t80) cc_final: 0.7431 (t80) REVERT: E 455 THR cc_start: 0.4639 (p) cc_final: 0.4418 (p) REVERT: E 527 PHE cc_start: 0.7268 (p90) cc_final: 0.6858 (p90) REVERT: E 528 TRP cc_start: 0.6730 (m100) cc_final: 0.6463 (m100) REVERT: E 530 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7710 (tmtt) REVERT: E 561 TYR cc_start: 0.8239 (m-80) cc_final: 0.7495 (m-80) REVERT: E 565 ASN cc_start: 0.8319 (m-40) cc_final: 0.7503 (t0) REVERT: E 566 ILE cc_start: 0.8385 (pt) cc_final: 0.8052 (pt) REVERT: I 47 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7586 (t0) REVERT: I 52 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7525 (ttmm) REVERT: I 53 PHE cc_start: 0.7889 (m-80) cc_final: 0.7485 (m-80) REVERT: I 87 MET cc_start: 0.6295 (ttp) cc_final: 0.5715 (ttp) REVERT: I 115 ASN cc_start: 0.7807 (t0) cc_final: 0.7187 (t0) REVERT: I 144 GLU cc_start: 0.7398 (pt0) cc_final: 0.7102 (pt0) REVERT: I 174 MET cc_start: 0.6956 (mtp) cc_final: 0.6500 (mtp) REVERT: I 193 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7040 (mt-10) REVERT: I 261 PHE cc_start: 0.7953 (t80) cc_final: 0.7690 (t80) REVERT: I 268 PHE cc_start: 0.7584 (m-80) cc_final: 0.7247 (m-80) REVERT: I 273 CYS cc_start: 0.7391 (t) cc_final: 0.7152 (t) REVERT: I 319 MET cc_start: 0.7419 (tpt) cc_final: 0.7128 (tpp) REVERT: I 331 MET cc_start: 0.7283 (ttm) cc_final: 0.7077 (ttm) REVERT: I 396 GLU cc_start: 0.7575 (tt0) cc_final: 0.7337 (tt0) REVERT: I 427 ASP cc_start: 0.8439 (m-30) cc_final: 0.8200 (m-30) REVERT: I 518 MET cc_start: 0.6823 (ptp) cc_final: 0.6306 (ptp) REVERT: I 535 PHE cc_start: 0.8486 (m-80) cc_final: 0.7864 (m-80) REVERT: I 538 LYS cc_start: 0.8210 (tttp) cc_final: 0.7792 (ttmm) REVERT: I 544 THR cc_start: 0.7958 (p) cc_final: 0.7239 (t) REVERT: I 546 ASN cc_start: 0.7929 (p0) cc_final: 0.7373 (p0) REVERT: I 551 MET cc_start: 0.6610 (tmm) cc_final: 0.5598 (tmm) REVERT: I 573 TYR cc_start: 0.8167 (p90) cc_final: 0.7632 (p90) REVERT: I 575 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7700 (mtmm) REVERT: F 51 PHE cc_start: 0.6879 (m-80) cc_final: 0.6676 (m-80) REVERT: F 52 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7599 (ttmm) REVERT: F 59 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8427 (p) REVERT: F 60 GLU cc_start: 0.7468 (tt0) cc_final: 0.7164 (tt0) REVERT: F 96 MET cc_start: 0.7367 (mpp) cc_final: 0.7015 (mpp) REVERT: F 101 ILE cc_start: 0.8392 (mm) cc_final: 0.8090 (mm) REVERT: F 143 GLN cc_start: 0.7328 (mp10) cc_final: 0.6941 (mp10) REVERT: F 180 ASN cc_start: 0.7529 (t0) cc_final: 0.7162 (t0) REVERT: F 213 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7506 (tm-30) REVERT: F 242 GLN cc_start: 0.7281 (mt0) cc_final: 0.6991 (mt0) REVERT: F 243 PHE cc_start: 0.7895 (t80) cc_final: 0.7593 (t80) REVERT: F 244 TYR cc_start: 0.7413 (m-80) cc_final: 0.6620 (m-80) REVERT: F 248 ASN cc_start: 0.7120 (m-40) cc_final: 0.6803 (t0) REVERT: F 266 PHE cc_start: 0.7943 (t80) cc_final: 0.7592 (t80) REVERT: F 271 LYS cc_start: 0.8257 (mtpp) cc_final: 0.8008 (mtpp) REVERT: F 276 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7244 (m) REVERT: F 282 ASN cc_start: 0.8070 (m110) cc_final: 0.7801 (m-40) REVERT: F 311 ASP cc_start: 0.7138 (p0) cc_final: 0.6884 (p0) REVERT: F 327 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6984 (mm-30) REVERT: F 335 GLU cc_start: 0.6805 (tt0) cc_final: 0.6554 (tt0) REVERT: F 404 GLN cc_start: 0.4078 (OUTLIER) cc_final: 0.2875 (tt0) REVERT: F 405 ASP cc_start: 0.6171 (m-30) cc_final: 0.5864 (m-30) REVERT: F 473 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7025 (mm-30) REVERT: F 475 ASP cc_start: 0.7349 (t0) cc_final: 0.6760 (t0) REVERT: F 485 ASN cc_start: 0.7944 (p0) cc_final: 0.7682 (p0) REVERT: F 489 VAL cc_start: 0.8356 (m) cc_final: 0.8131 (m) REVERT: F 493 ASN cc_start: 0.8022 (m110) cc_final: 0.7798 (p0) REVERT: F 551 MET cc_start: 0.6607 (ttt) cc_final: 0.6074 (ttt) REVERT: C 174 MET cc_start: 0.7113 (mtp) cc_final: 0.6513 (mtp) outliers start: 69 outliers final: 42 residues processed: 825 average time/residue: 0.1727 time to fit residues: 221.6973 Evaluate side-chains 818 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 770 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 491 GLN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 524 TYR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 444 TYR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 85 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 242 optimal weight: 0.1980 chunk 271 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 40.0000 chunk 147 optimal weight: 40.0000 chunk 138 optimal weight: 0.0870 chunk 206 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 248 ASN G 280 GLN G 491 GLN G 505 ASN A 48 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.217585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160204 restraints weight = 41350.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166181 restraints weight = 17805.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170181 restraints weight = 10310.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.171617 restraints weight = 7466.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.172689 restraints weight = 6460.690| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26524 Z= 0.158 Angle : 0.600 8.006 36261 Z= 0.305 Chirality : 0.043 0.147 3973 Planarity : 0.005 0.055 4735 Dihedral : 6.165 59.858 3518 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.93 % Allowed : 12.93 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 2990 helix: -0.79 (0.47), residues: 106 sheet: -0.56 (0.18), residues: 769 loop : -0.48 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 274 TYR 0.028 0.002 TYR B 464 PHE 0.030 0.002 PHE B 141 TRP 0.034 0.001 TRP F 545 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00347 (26519) covalent geometry : angle 0.59901 (36251) SS BOND : bond 0.00238 ( 5) SS BOND : angle 2.49221 ( 10) hydrogen bonds : bond 0.03745 ( 329) hydrogen bonds : angle 5.98656 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 784 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.8007 (t0) REVERT: G 59 VAL cc_start: 0.8817 (t) cc_final: 0.8524 (m) REVERT: G 89 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7950 (mmmm) REVERT: G 101 ILE cc_start: 0.8669 (mt) cc_final: 0.7193 (mt) REVERT: G 125 ASP cc_start: 0.6513 (m-30) cc_final: 0.6178 (m-30) REVERT: G 197 PHE cc_start: 0.7917 (m-80) cc_final: 0.7667 (m-80) REVERT: G 211 TYR cc_start: 0.8230 (m-80) cc_final: 0.7879 (m-80) REVERT: G 338 TYR cc_start: 0.8704 (p90) cc_final: 0.8438 (p90) REVERT: G 350 GLN cc_start: 0.7316 (mt0) cc_final: 0.7003 (mt0) REVERT: G 380 PHE cc_start: 0.8077 (p90) cc_final: 0.7645 (p90) REVERT: G 382 ARG cc_start: 0.5773 (mtm180) cc_final: 0.5194 (mtm180) REVERT: G 471 ASP cc_start: 0.7601 (t0) cc_final: 0.7242 (t0) REVERT: G 485 ASN cc_start: 0.7753 (p0) cc_final: 0.7042 (p0) REVERT: G 536 LYS cc_start: 0.8456 (ttpp) cc_final: 0.8113 (ttpp) REVERT: G 559 PHE cc_start: 0.7929 (m-80) cc_final: 0.7284 (m-80) REVERT: G 560 ASN cc_start: 0.7745 (m-40) cc_final: 0.7416 (m-40) REVERT: G 561 TYR cc_start: 0.8471 (m-80) cc_final: 0.8152 (m-80) REVERT: A 56 ASN cc_start: 0.7395 (m110) cc_final: 0.7193 (m110) REVERT: A 100 ASP cc_start: 0.7112 (m-30) cc_final: 0.6602 (m-30) REVERT: A 115 ASN cc_start: 0.7918 (t0) cc_final: 0.7636 (t0) REVERT: A 174 MET cc_start: 0.7073 (mtp) cc_final: 0.6830 (mtp) REVERT: A 183 MET cc_start: 0.7061 (mmm) cc_final: 0.6528 (mmm) REVERT: A 197 PHE cc_start: 0.8036 (m-10) cc_final: 0.7607 (m-10) REVERT: A 211 TYR cc_start: 0.7292 (m-80) cc_final: 0.6968 (m-80) REVERT: A 216 ARG cc_start: 0.6926 (ttt90) cc_final: 0.6598 (ttt90) REVERT: A 218 LEU cc_start: 0.8358 (tp) cc_final: 0.7970 (tt) REVERT: A 265 THR cc_start: 0.7810 (p) cc_final: 0.7450 (p) REVERT: A 344 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (p) REVERT: A 350 GLN cc_start: 0.7409 (mt0) cc_final: 0.7169 (mt0) REVERT: A 382 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6664 (mtm110) REVERT: A 387 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7547 (ttpt) REVERT: A 397 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7959 (mtt-85) REVERT: A 439 LYS cc_start: 0.8247 (mptt) cc_final: 0.7958 (mptt) REVERT: A 475 ASP cc_start: 0.7441 (t70) cc_final: 0.6823 (t0) REVERT: A 530 LYS cc_start: 0.7256 (ttmt) cc_final: 0.6963 (ttpp) REVERT: A 543 HIS cc_start: 0.6790 (m170) cc_final: 0.6513 (m170) REVERT: A 570 LYS cc_start: 0.7878 (ptpt) cc_final: 0.7644 (ptpt) REVERT: A 575 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7659 (mtpt) REVERT: B 80 ARG cc_start: 0.7214 (mtt-85) cc_final: 0.6559 (mtt-85) REVERT: B 101 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7802 (pt) REVERT: B 143 GLN cc_start: 0.7610 (mt0) cc_final: 0.7281 (mt0) REVERT: B 151 LYS cc_start: 0.7948 (mttm) cc_final: 0.7733 (mttm) REVERT: B 174 MET cc_start: 0.6713 (mtp) cc_final: 0.6414 (mtp) REVERT: B 183 MET cc_start: 0.6875 (mmm) cc_final: 0.6332 (mmm) REVERT: B 190 MET cc_start: 0.7831 (tpp) cc_final: 0.7411 (tpp) REVERT: B 198 TYR cc_start: 0.7062 (m-80) cc_final: 0.6486 (m-80) REVERT: B 237 ASP cc_start: 0.7192 (m-30) cc_final: 0.6684 (m-30) REVERT: B 247 GLU cc_start: 0.6209 (mp0) cc_final: 0.5859 (mp0) REVERT: B 377 ARG cc_start: 0.6897 (mmm-85) cc_final: 0.6676 (mmm-85) REVERT: B 382 ARG cc_start: 0.7449 (mmt90) cc_final: 0.7175 (mmt-90) REVERT: B 383 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7093 (tm-30) REVERT: B 469 ILE cc_start: 0.7977 (mt) cc_final: 0.7339 (mt) REVERT: B 501 LYS cc_start: 0.7933 (tttt) cc_final: 0.7315 (tttt) REVERT: B 509 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6283 (mm-30) REVERT: B 527 PHE cc_start: 0.6875 (p90) cc_final: 0.6526 (p90) REVERT: B 530 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8086 (ttmt) REVERT: B 533 LEU cc_start: 0.8119 (tp) cc_final: 0.7696 (tp) REVERT: B 551 MET cc_start: 0.5866 (mmt) cc_final: 0.5343 (mmt) REVERT: B 553 ILE cc_start: 0.5877 (OUTLIER) cc_final: 0.5675 (mt) REVERT: E 45 PHE cc_start: 0.7395 (t80) cc_final: 0.6849 (t80) REVERT: E 46 ASN cc_start: 0.7641 (t0) cc_final: 0.7437 (t0) REVERT: E 129 ILE cc_start: 0.8864 (mt) cc_final: 0.8659 (mt) REVERT: E 166 ASN cc_start: 0.7002 (m110) cc_final: 0.6727 (m110) REVERT: E 190 MET cc_start: 0.5519 (mtm) cc_final: 0.5147 (mtm) REVERT: E 329 THR cc_start: 0.4413 (t) cc_final: 0.4071 (m) REVERT: E 378 TYR cc_start: 0.7101 (m-80) cc_final: 0.6368 (m-80) REVERT: E 398 PHE cc_start: 0.7829 (p90) cc_final: 0.7435 (p90) REVERT: E 400 TYR cc_start: 0.7790 (t80) cc_final: 0.7442 (t80) REVERT: E 455 THR cc_start: 0.4547 (p) cc_final: 0.4312 (p) REVERT: E 530 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7640 (tmtt) REVERT: E 557 ASN cc_start: 0.8437 (p0) cc_final: 0.7376 (p0) REVERT: E 561 TYR cc_start: 0.8248 (m-80) cc_final: 0.7324 (m-80) REVERT: E 565 ASN cc_start: 0.8342 (m-40) cc_final: 0.7442 (t0) REVERT: E 566 ILE cc_start: 0.8334 (pt) cc_final: 0.8041 (pt) REVERT: I 47 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.6967 (t0) REVERT: I 52 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7531 (ttmm) REVERT: I 87 MET cc_start: 0.6384 (ttp) cc_final: 0.5878 (ttp) REVERT: I 101 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8052 (pp) REVERT: I 115 ASN cc_start: 0.7737 (t0) cc_final: 0.7070 (t0) REVERT: I 174 MET cc_start: 0.7028 (mtp) cc_final: 0.6608 (mtp) REVERT: I 193 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7018 (mt-10) REVERT: I 268 PHE cc_start: 0.7630 (m-80) cc_final: 0.7006 (m-80) REVERT: I 319 MET cc_start: 0.7225 (tpt) cc_final: 0.7012 (tpp) REVERT: I 331 MET cc_start: 0.7262 (ttm) cc_final: 0.7035 (ttm) REVERT: I 396 GLU cc_start: 0.7495 (tt0) cc_final: 0.7093 (tt0) REVERT: I 427 ASP cc_start: 0.8419 (m-30) cc_final: 0.8184 (m-30) REVERT: I 535 PHE cc_start: 0.8411 (m-80) cc_final: 0.7972 (m-80) REVERT: I 538 LYS cc_start: 0.8251 (tttp) cc_final: 0.7896 (ttmm) REVERT: I 544 THR cc_start: 0.7874 (p) cc_final: 0.7445 (p) REVERT: I 546 ASN cc_start: 0.7998 (p0) cc_final: 0.7653 (p0) REVERT: I 551 MET cc_start: 0.6456 (tmm) cc_final: 0.4673 (tmm) REVERT: I 573 TYR cc_start: 0.8309 (p90) cc_final: 0.7818 (p90) REVERT: I 574 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6715 (tt0) REVERT: I 575 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7628 (mtmm) REVERT: F 52 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7590 (ttmm) REVERT: F 59 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8550 (p) REVERT: F 60 GLU cc_start: 0.7513 (tt0) cc_final: 0.7184 (tt0) REVERT: F 101 ILE cc_start: 0.8315 (mm) cc_final: 0.8073 (mm) REVERT: F 143 GLN cc_start: 0.7357 (mp10) cc_final: 0.6940 (mp10) REVERT: F 180 ASN cc_start: 0.7500 (t0) cc_final: 0.7141 (t0) REVERT: F 243 PHE cc_start: 0.7930 (t80) cc_final: 0.7544 (t80) REVERT: F 244 TYR cc_start: 0.7393 (m-80) cc_final: 0.6539 (m-80) REVERT: F 248 ASN cc_start: 0.7063 (m-40) cc_final: 0.6831 (t0) REVERT: F 266 PHE cc_start: 0.7880 (t80) cc_final: 0.7584 (t80) REVERT: F 271 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7930 (mtpp) REVERT: F 280 GLN cc_start: 0.7759 (mm110) cc_final: 0.7524 (mm110) REVERT: F 282 ASN cc_start: 0.7930 (m110) cc_final: 0.7627 (m-40) REVERT: F 283 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7782 (tpt-90) REVERT: F 311 ASP cc_start: 0.6919 (p0) cc_final: 0.6468 (p0) REVERT: F 327 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6750 (mm-30) REVERT: F 405 ASP cc_start: 0.6042 (m-30) cc_final: 0.5695 (m-30) REVERT: F 450 THR cc_start: 0.8785 (p) cc_final: 0.8507 (t) REVERT: F 475 ASP cc_start: 0.7287 (t0) cc_final: 0.6621 (t0) REVERT: F 484 VAL cc_start: 0.8353 (m) cc_final: 0.7891 (p) REVERT: F 485 ASN cc_start: 0.7792 (p0) cc_final: 0.7440 (p0) REVERT: F 551 MET cc_start: 0.6609 (ttt) cc_final: 0.6079 (ttt) REVERT: F 569 MET cc_start: 0.5687 (mmm) cc_final: 0.5466 (mmm) REVERT: C 174 MET cc_start: 0.7131 (mtp) cc_final: 0.6516 (mtp) REVERT: C 236 THR cc_start: 0.5562 (OUTLIER) cc_final: 0.5092 (p) outliers start: 80 outliers final: 53 residues processed: 810 average time/residue: 0.1818 time to fit residues: 226.1387 Evaluate side-chains 829 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 767 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 443 ASN Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 490 CYS Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 10 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 294 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN A 115 ASN A 546 ASN B 386 GLN B 508 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.221794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.166632 restraints weight = 40938.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.172457 restraints weight = 18160.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.173782 restraints weight = 10504.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.174495 restraints weight = 11039.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.174475 restraints weight = 8863.930| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26524 Z= 0.150 Angle : 0.581 9.239 36261 Z= 0.293 Chirality : 0.043 0.176 3973 Planarity : 0.005 0.054 4735 Dihedral : 5.629 59.590 3510 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.55 % Allowed : 13.96 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 2990 helix: -0.83 (0.46), residues: 106 sheet: -0.57 (0.18), residues: 786 loop : -0.35 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 274 TYR 0.029 0.002 TYR B 464 PHE 0.030 0.002 PHE B 398 TRP 0.042 0.001 TRP F 545 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00331 (26519) covalent geometry : angle 0.57917 (36251) SS BOND : bond 0.00461 ( 5) SS BOND : angle 2.69953 ( 10) hydrogen bonds : bond 0.03400 ( 329) hydrogen bonds : angle 5.78793 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 773 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8030 (t0) REVERT: G 59 VAL cc_start: 0.8799 (t) cc_final: 0.8507 (m) REVERT: G 101 ILE cc_start: 0.8473 (mt) cc_final: 0.8014 (mt) REVERT: G 125 ASP cc_start: 0.6553 (m-30) cc_final: 0.6283 (m-30) REVERT: G 135 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: G 142 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6371 (mm-30) REVERT: G 151 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7691 (mtpp) REVERT: G 211 TYR cc_start: 0.8258 (m-80) cc_final: 0.7684 (m-80) REVERT: G 248 ASN cc_start: 0.7573 (t0) cc_final: 0.7228 (t0) REVERT: G 338 TYR cc_start: 0.8700 (p90) cc_final: 0.8453 (p90) REVERT: G 380 PHE cc_start: 0.8024 (p90) cc_final: 0.7617 (p90) REVERT: G 382 ARG cc_start: 0.5773 (mtm180) cc_final: 0.5159 (mtm180) REVERT: G 390 THR cc_start: 0.8598 (t) cc_final: 0.8325 (p) REVERT: G 471 ASP cc_start: 0.7587 (t0) cc_final: 0.7188 (t0) REVERT: G 473 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6500 (tm-30) REVERT: G 536 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8090 (ttpp) REVERT: G 548 ILE cc_start: 0.8392 (pt) cc_final: 0.7979 (pt) REVERT: G 559 PHE cc_start: 0.7915 (m-80) cc_final: 0.7637 (m-80) REVERT: G 560 ASN cc_start: 0.7741 (m-40) cc_final: 0.7393 (m-40) REVERT: G 561 TYR cc_start: 0.8471 (m-80) cc_final: 0.8206 (m-80) REVERT: A 56 ASN cc_start: 0.7346 (m110) cc_final: 0.7137 (m110) REVERT: A 98 LEU cc_start: 0.7720 (mt) cc_final: 0.7046 (tp) REVERT: A 100 ASP cc_start: 0.7174 (m-30) cc_final: 0.6668 (m-30) REVERT: A 183 MET cc_start: 0.7092 (mmm) cc_final: 0.6556 (mmm) REVERT: A 211 TYR cc_start: 0.7345 (m-80) cc_final: 0.7005 (m-80) REVERT: A 216 ARG cc_start: 0.6894 (ttt90) cc_final: 0.6603 (ttt90) REVERT: A 218 LEU cc_start: 0.8283 (tp) cc_final: 0.7912 (tt) REVERT: A 265 THR cc_start: 0.7519 (p) cc_final: 0.7264 (p) REVERT: A 344 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7687 (p) REVERT: A 350 GLN cc_start: 0.7437 (mt0) cc_final: 0.7171 (mt0) REVERT: A 382 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6514 (mtm110) REVERT: A 387 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7513 (ttpt) REVERT: A 397 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7930 (mtt-85) REVERT: A 403 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7192 (m-70) REVERT: A 439 LYS cc_start: 0.8156 (mptt) cc_final: 0.7876 (mptt) REVERT: A 475 ASP cc_start: 0.7407 (t70) cc_final: 0.6801 (t0) REVERT: A 530 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6961 (ttpp) REVERT: A 543 HIS cc_start: 0.6657 (m170) cc_final: 0.6419 (m170) REVERT: A 570 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7563 (ptpt) REVERT: A 575 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7632 (mtpt) REVERT: B 80 ARG cc_start: 0.7173 (mtt-85) cc_final: 0.6423 (mtt-85) REVERT: B 101 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7809 (pt) REVERT: B 125 ASP cc_start: 0.8467 (m-30) cc_final: 0.7994 (m-30) REVERT: B 143 GLN cc_start: 0.7558 (mt0) cc_final: 0.7346 (mt0) REVERT: B 144 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6584 (pt0) REVERT: B 151 LYS cc_start: 0.8007 (mttm) cc_final: 0.7711 (mttm) REVERT: B 174 MET cc_start: 0.6813 (mtp) cc_final: 0.6391 (mtp) REVERT: B 178 ASP cc_start: 0.5859 (t0) cc_final: 0.5539 (t0) REVERT: B 183 MET cc_start: 0.6980 (mmm) cc_final: 0.6489 (mmm) REVERT: B 190 MET cc_start: 0.7967 (tpp) cc_final: 0.7500 (tpp) REVERT: B 198 TYR cc_start: 0.7176 (m-80) cc_final: 0.6465 (m-80) REVERT: B 237 ASP cc_start: 0.7275 (m-30) cc_final: 0.6857 (m-30) REVERT: B 247 GLU cc_start: 0.6292 (mp0) cc_final: 0.6055 (mp0) REVERT: B 266 PHE cc_start: 0.7178 (t80) cc_final: 0.6641 (t80) REVERT: B 382 ARG cc_start: 0.7542 (mmt90) cc_final: 0.6932 (mmp80) REVERT: B 383 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7066 (tm-30) REVERT: B 501 LYS cc_start: 0.7710 (tttt) cc_final: 0.7114 (tttt) REVERT: B 509 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6369 (mm-30) REVERT: B 527 PHE cc_start: 0.6991 (p90) cc_final: 0.6578 (p90) REVERT: B 530 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7785 (ttmt) REVERT: B 533 LEU cc_start: 0.7849 (tp) cc_final: 0.7516 (tp) REVERT: B 536 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7635 (ttpp) REVERT: B 551 MET cc_start: 0.5852 (mmt) cc_final: 0.5333 (mmt) REVERT: E 45 PHE cc_start: 0.7493 (t80) cc_final: 0.6733 (t80) REVERT: E 46 ASN cc_start: 0.7562 (t0) cc_final: 0.7138 (t0) REVERT: E 64 ASN cc_start: 0.6743 (p0) cc_final: 0.6502 (p0) REVERT: E 121 PHE cc_start: 0.7876 (m-80) cc_final: 0.7183 (m-10) REVERT: E 129 ILE cc_start: 0.8775 (mt) cc_final: 0.8552 (mt) REVERT: E 165 TYR cc_start: 0.7713 (m-80) cc_final: 0.7185 (m-80) REVERT: E 166 ASN cc_start: 0.7165 (m110) cc_final: 0.6910 (m110) REVERT: E 190 MET cc_start: 0.5574 (mtm) cc_final: 0.5131 (mtm) REVERT: E 329 THR cc_start: 0.4544 (t) cc_final: 0.4188 (m) REVERT: E 378 TYR cc_start: 0.7241 (m-80) cc_final: 0.6396 (m-80) REVERT: E 398 PHE cc_start: 0.7969 (p90) cc_final: 0.7480 (p90) REVERT: E 400 TYR cc_start: 0.7800 (t80) cc_final: 0.7426 (t80) REVERT: E 527 PHE cc_start: 0.7228 (p90) cc_final: 0.6776 (p90) REVERT: E 528 TRP cc_start: 0.6776 (m100) cc_final: 0.6509 (m100) REVERT: E 557 ASN cc_start: 0.8285 (p0) cc_final: 0.7318 (p0) REVERT: E 560 ASN cc_start: 0.8122 (p0) cc_final: 0.7620 (p0) REVERT: E 561 TYR cc_start: 0.8280 (m-80) cc_final: 0.7376 (m-80) REVERT: E 565 ASN cc_start: 0.8497 (m-40) cc_final: 0.8152 (m-40) REVERT: I 47 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7013 (t0) REVERT: I 52 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7461 (ttmm) REVERT: I 53 PHE cc_start: 0.7849 (m-80) cc_final: 0.7593 (m-80) REVERT: I 87 MET cc_start: 0.6680 (ttp) cc_final: 0.6237 (ttp) REVERT: I 115 ASN cc_start: 0.7708 (t0) cc_final: 0.7025 (t0) REVERT: I 174 MET cc_start: 0.7062 (mtp) cc_final: 0.6535 (mtp) REVERT: I 201 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7832 (ttpt) REVERT: I 268 PHE cc_start: 0.7656 (m-80) cc_final: 0.6977 (m-80) REVERT: I 319 MET cc_start: 0.7209 (tpt) cc_final: 0.6992 (tpp) REVERT: I 331 MET cc_start: 0.7273 (ttm) cc_final: 0.7033 (ttm) REVERT: I 396 GLU cc_start: 0.7425 (tt0) cc_final: 0.7000 (tt0) REVERT: I 427 ASP cc_start: 0.8430 (m-30) cc_final: 0.8201 (m-30) REVERT: I 444 TYR cc_start: 0.7520 (p90) cc_final: 0.7261 (p90) REVERT: I 518 MET cc_start: 0.6690 (ptp) cc_final: 0.6489 (ptp) REVERT: I 530 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8226 (ttpt) REVERT: I 535 PHE cc_start: 0.8459 (m-80) cc_final: 0.7948 (m-80) REVERT: I 538 LYS cc_start: 0.8257 (tttp) cc_final: 0.7964 (ttmm) REVERT: I 539 LEU cc_start: 0.8554 (mt) cc_final: 0.8278 (mp) REVERT: I 544 THR cc_start: 0.7940 (p) cc_final: 0.7560 (p) REVERT: I 546 ASN cc_start: 0.7964 (p0) cc_final: 0.7657 (p0) REVERT: I 550 GLN cc_start: 0.7716 (mt0) cc_final: 0.7469 (mm-40) REVERT: I 573 TYR cc_start: 0.8281 (p90) cc_final: 0.7832 (p90) REVERT: I 575 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7641 (mtmm) REVERT: F 52 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7572 (ttmm) REVERT: F 59 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8470 (p) REVERT: F 60 GLU cc_start: 0.7461 (tt0) cc_final: 0.7171 (tt0) REVERT: F 101 ILE cc_start: 0.8317 (mm) cc_final: 0.8059 (mm) REVERT: F 143 GLN cc_start: 0.7513 (mp10) cc_final: 0.6844 (mp10) REVERT: F 180 ASN cc_start: 0.7551 (t0) cc_final: 0.7171 (t0) REVERT: F 242 GLN cc_start: 0.7379 (mt0) cc_final: 0.7132 (tt0) REVERT: F 244 TYR cc_start: 0.7194 (m-80) cc_final: 0.6768 (m-80) REVERT: F 248 ASN cc_start: 0.7081 (m110) cc_final: 0.6766 (t0) REVERT: F 271 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7896 (mtpp) REVERT: F 280 GLN cc_start: 0.7765 (mm110) cc_final: 0.7518 (mm-40) REVERT: F 283 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7810 (tpt-90) REVERT: F 311 ASP cc_start: 0.6821 (p0) cc_final: 0.6481 (p0) REVERT: F 327 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6749 (mm-30) REVERT: F 336 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8318 (t) REVERT: F 425 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8163 (p) REVERT: F 475 ASP cc_start: 0.7242 (t0) cc_final: 0.6569 (t0) REVERT: F 484 VAL cc_start: 0.8315 (m) cc_final: 0.7897 (p) REVERT: F 485 ASN cc_start: 0.7814 (p0) cc_final: 0.7453 (p0) REVERT: F 538 LYS cc_start: 0.7612 (tppt) cc_final: 0.7199 (tppt) REVERT: F 551 MET cc_start: 0.6569 (ttt) cc_final: 0.5971 (ttt) REVERT: F 569 MET cc_start: 0.5907 (mmm) cc_final: 0.5562 (mmm) REVERT: C 174 MET cc_start: 0.7066 (mtp) cc_final: 0.6403 (mtp) REVERT: C 236 THR cc_start: 0.5292 (p) cc_final: 0.4883 (p) outliers start: 97 outliers final: 70 residues processed: 804 average time/residue: 0.1791 time to fit residues: 222.1364 Evaluate side-chains 834 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 754 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 444 TYR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 490 CYS Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 159 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 304 optimal weight: 40.0000 chunk 198 optimal weight: 40.0000 chunk 42 optimal weight: 0.0970 chunk 53 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN G 492 ASN A 115 ASN A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.221673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.165003 restraints weight = 40932.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.170821 restraints weight = 17675.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174523 restraints weight = 10378.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.175893 restraints weight = 7568.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.176737 restraints weight = 6576.491| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26524 Z= 0.178 Angle : 0.583 11.154 36261 Z= 0.296 Chirality : 0.043 0.157 3973 Planarity : 0.005 0.052 4735 Dihedral : 5.553 58.909 3510 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.77 % Allowed : 14.91 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 2990 helix: -0.64 (0.48), residues: 101 sheet: -0.53 (0.18), residues: 766 loop : -0.33 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 377 TYR 0.029 0.002 TYR B 464 PHE 0.032 0.002 PHE I 146 TRP 0.040 0.001 TRP F 545 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00387 (26519) covalent geometry : angle 0.57926 (36251) SS BOND : bond 0.00418 ( 5) SS BOND : angle 4.15921 ( 10) hydrogen bonds : bond 0.03458 ( 329) hydrogen bonds : angle 5.73745 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 758 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8054 (t0) REVERT: G 59 VAL cc_start: 0.8829 (t) cc_final: 0.8448 (m) REVERT: G 85 ASN cc_start: 0.7561 (t0) cc_final: 0.7195 (t0) REVERT: G 101 ILE cc_start: 0.8531 (mt) cc_final: 0.7928 (mt) REVERT: G 125 ASP cc_start: 0.6500 (m-30) cc_final: 0.6224 (m-30) REVERT: G 135 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: G 142 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6531 (mm-30) REVERT: G 216 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7190 (ttt-90) REVERT: G 248 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7390 (t0) REVERT: G 319 MET cc_start: 0.2182 (OUTLIER) cc_final: 0.1829 (ptm) REVERT: G 380 PHE cc_start: 0.7988 (p90) cc_final: 0.7431 (p90) REVERT: G 382 ARG cc_start: 0.5756 (mtm180) cc_final: 0.5324 (mtm180) REVERT: G 390 THR cc_start: 0.8618 (t) cc_final: 0.8259 (p) REVERT: G 466 ASN cc_start: 0.7906 (m110) cc_final: 0.7670 (m110) REVERT: G 471 ASP cc_start: 0.7558 (t0) cc_final: 0.7181 (t0) REVERT: G 473 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6542 (tm-30) REVERT: G 536 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8064 (ttpp) REVERT: G 560 ASN cc_start: 0.7718 (m-40) cc_final: 0.7362 (m-40) REVERT: G 581 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7910 (ttp-110) REVERT: A 98 LEU cc_start: 0.7705 (mt) cc_final: 0.7002 (tp) REVERT: A 100 ASP cc_start: 0.7072 (m-30) cc_final: 0.6721 (m-30) REVERT: A 183 MET cc_start: 0.7078 (mmm) cc_final: 0.6578 (mmm) REVERT: A 211 TYR cc_start: 0.7313 (m-80) cc_final: 0.6994 (m-80) REVERT: A 218 LEU cc_start: 0.8308 (tp) cc_final: 0.7983 (tt) REVERT: A 265 THR cc_start: 0.7545 (p) cc_final: 0.7295 (p) REVERT: A 344 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7725 (p) REVERT: A 350 GLN cc_start: 0.7412 (mt0) cc_final: 0.7207 (mt0) REVERT: A 382 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6559 (mtm110) REVERT: A 397 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7821 (mtt-85) REVERT: A 403 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7187 (m-70) REVERT: A 433 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 439 LYS cc_start: 0.8099 (mptt) cc_final: 0.7792 (mptt) REVERT: A 475 ASP cc_start: 0.7413 (t70) cc_final: 0.6803 (t0) REVERT: A 530 LYS cc_start: 0.7282 (ttmt) cc_final: 0.7002 (ttpp) REVERT: A 575 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7628 (mtpt) REVERT: B 80 ARG cc_start: 0.7180 (mtt-85) cc_final: 0.6473 (mtt-85) REVERT: B 101 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7948 (pt) REVERT: B 117 TRP cc_start: 0.6869 (m100) cc_final: 0.6341 (m100) REVERT: B 125 ASP cc_start: 0.8232 (m-30) cc_final: 0.7844 (m-30) REVERT: B 145 ILE cc_start: 0.8130 (mt) cc_final: 0.7744 (mm) REVERT: B 151 LYS cc_start: 0.7979 (mttm) cc_final: 0.7728 (mttm) REVERT: B 174 MET cc_start: 0.6788 (mtp) cc_final: 0.6467 (mtp) REVERT: B 178 ASP cc_start: 0.5941 (t0) cc_final: 0.5649 (t0) REVERT: B 183 MET cc_start: 0.6873 (mmm) cc_final: 0.6472 (mmm) REVERT: B 190 MET cc_start: 0.7837 (tpp) cc_final: 0.7415 (tpp) REVERT: B 198 TYR cc_start: 0.7142 (m-80) cc_final: 0.6562 (m-10) REVERT: B 266 PHE cc_start: 0.7284 (t80) cc_final: 0.6882 (t80) REVERT: B 354 LYS cc_start: 0.7525 (mmtp) cc_final: 0.6951 (mmtp) REVERT: B 377 ARG cc_start: 0.6846 (mmm-85) cc_final: 0.6467 (tpp80) REVERT: B 382 ARG cc_start: 0.7521 (mmt90) cc_final: 0.7223 (mmp80) REVERT: B 383 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7448 (tm-30) REVERT: B 501 LYS cc_start: 0.7937 (tttt) cc_final: 0.7453 (tttt) REVERT: B 509 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6206 (mm-30) REVERT: B 527 PHE cc_start: 0.6855 (p90) cc_final: 0.6445 (p90) REVERT: B 530 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8008 (ttmt) REVERT: B 532 LYS cc_start: 0.7271 (tttm) cc_final: 0.6886 (tttm) REVERT: B 533 LEU cc_start: 0.7890 (tp) cc_final: 0.7624 (tp) REVERT: B 536 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7623 (ttpp) REVERT: B 551 MET cc_start: 0.5690 (mmt) cc_final: 0.5105 (mmt) REVERT: E 45 PHE cc_start: 0.7466 (t80) cc_final: 0.6757 (t80) REVERT: E 121 PHE cc_start: 0.7653 (m-80) cc_final: 0.7145 (m-10) REVERT: E 129 ILE cc_start: 0.8825 (mt) cc_final: 0.8599 (mt) REVERT: E 165 TYR cc_start: 0.7738 (m-80) cc_final: 0.7233 (m-80) REVERT: E 166 ASN cc_start: 0.7078 (m110) cc_final: 0.6849 (m110) REVERT: E 190 MET cc_start: 0.5635 (mtm) cc_final: 0.5203 (mtm) REVERT: E 329 THR cc_start: 0.4775 (t) cc_final: 0.4356 (m) REVERT: E 378 TYR cc_start: 0.7148 (m-80) cc_final: 0.6419 (m-80) REVERT: E 398 PHE cc_start: 0.7943 (p90) cc_final: 0.7511 (p90) REVERT: E 400 TYR cc_start: 0.7824 (t80) cc_final: 0.7463 (t80) REVERT: E 527 PHE cc_start: 0.7272 (p90) cc_final: 0.6831 (p90) REVERT: E 557 ASN cc_start: 0.8555 (p0) cc_final: 0.7603 (p0) REVERT: E 561 TYR cc_start: 0.8299 (m-80) cc_final: 0.7670 (m-80) REVERT: E 565 ASN cc_start: 0.8410 (m-40) cc_final: 0.7299 (t0) REVERT: I 47 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7123 (t0) REVERT: I 52 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7494 (ttmm) REVERT: I 87 MET cc_start: 0.6863 (ttp) cc_final: 0.6374 (ttp) REVERT: I 115 ASN cc_start: 0.7681 (t0) cc_final: 0.7002 (t0) REVERT: I 174 MET cc_start: 0.6957 (mtp) cc_final: 0.6530 (mtp) REVERT: I 201 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7879 (ttpt) REVERT: I 268 PHE cc_start: 0.7564 (m-80) cc_final: 0.7170 (m-80) REVERT: I 331 MET cc_start: 0.7198 (ttm) cc_final: 0.6978 (ttm) REVERT: I 444 TYR cc_start: 0.7916 (p90) cc_final: 0.7522 (p90) REVERT: I 518 MET cc_start: 0.6728 (ptp) cc_final: 0.6523 (ptp) REVERT: I 535 PHE cc_start: 0.8484 (m-80) cc_final: 0.8041 (m-80) REVERT: I 538 LYS cc_start: 0.8235 (tttp) cc_final: 0.7923 (ttmm) REVERT: I 539 LEU cc_start: 0.8537 (mt) cc_final: 0.8200 (mp) REVERT: I 544 THR cc_start: 0.7975 (p) cc_final: 0.7586 (p) REVERT: I 546 ASN cc_start: 0.7969 (p0) cc_final: 0.7664 (p0) REVERT: I 549 GLN cc_start: 0.7904 (tt0) cc_final: 0.7510 (tt0) REVERT: I 573 TYR cc_start: 0.8313 (p90) cc_final: 0.7864 (p90) REVERT: I 575 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7686 (mtmm) REVERT: I 581 ARG cc_start: 0.6990 (ttm170) cc_final: 0.6364 (ttm170) REVERT: F 52 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7500 (ttmm) REVERT: F 59 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8013 (p) REVERT: F 60 GLU cc_start: 0.7388 (tt0) cc_final: 0.7080 (tt0) REVERT: F 101 ILE cc_start: 0.8284 (mm) cc_final: 0.8029 (mm) REVERT: F 143 GLN cc_start: 0.7575 (mp10) cc_final: 0.7083 (mp10) REVERT: F 180 ASN cc_start: 0.7523 (t0) cc_final: 0.7162 (t0) REVERT: F 244 TYR cc_start: 0.7121 (m-80) cc_final: 0.6771 (m-80) REVERT: F 245 THR cc_start: 0.7779 (t) cc_final: 0.7537 (p) REVERT: F 248 ASN cc_start: 0.7144 (m110) cc_final: 0.6787 (t0) REVERT: F 271 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7919 (mtpp) REVERT: F 280 GLN cc_start: 0.7854 (mm110) cc_final: 0.7602 (mm-40) REVERT: F 283 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.7779 (tpt-90) REVERT: F 311 ASP cc_start: 0.6799 (p0) cc_final: 0.6519 (p0) REVERT: F 327 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6708 (mm-30) REVERT: F 336 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8303 (t) REVERT: F 425 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8123 (p) REVERT: F 475 ASP cc_start: 0.7220 (t0) cc_final: 0.6650 (t0) REVERT: F 484 VAL cc_start: 0.8357 (m) cc_final: 0.7993 (p) REVERT: F 551 MET cc_start: 0.6633 (ttt) cc_final: 0.6179 (ttt) REVERT: F 569 MET cc_start: 0.5705 (mmm) cc_final: 0.5487 (mmm) REVERT: C 174 MET cc_start: 0.7148 (mtp) cc_final: 0.6535 (mtp) REVERT: C 236 THR cc_start: 0.5456 (OUTLIER) cc_final: 0.4975 (p) outliers start: 103 outliers final: 71 residues processed: 792 average time/residue: 0.1793 time to fit residues: 219.5952 Evaluate side-chains 837 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 751 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 299 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 165 optimal weight: 50.0000 chunk 206 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 199 optimal weight: 0.0020 chunk 152 optimal weight: 50.0000 chunk 240 optimal weight: 0.1980 chunk 216 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 301 optimal weight: 0.6980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 ASN ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 386 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN F 318 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.219293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163063 restraints weight = 41225.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.169045 restraints weight = 17677.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172812 restraints weight = 10176.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.174191 restraints weight = 7322.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.174212 restraints weight = 6373.795| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26524 Z= 0.131 Angle : 0.567 8.778 36261 Z= 0.285 Chirality : 0.042 0.150 3973 Planarity : 0.005 0.060 4735 Dihedral : 5.284 60.015 3510 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.59 % Allowed : 16.26 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 2990 helix: -0.79 (0.46), residues: 106 sheet: -0.48 (0.19), residues: 748 loop : -0.28 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 274 TYR 0.033 0.001 TYR B 464 PHE 0.028 0.002 PHE B 141 TRP 0.029 0.001 TRP E 528 HIS 0.005 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00289 (26519) covalent geometry : angle 0.56458 (36251) SS BOND : bond 0.00331 ( 5) SS BOND : angle 3.16489 ( 10) hydrogen bonds : bond 0.03204 ( 329) hydrogen bonds : angle 5.61651 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 766 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7988 (t0) REVERT: G 59 VAL cc_start: 0.8727 (t) cc_final: 0.8394 (m) REVERT: G 100 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7112 (t0) REVERT: G 135 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: G 142 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6595 (mm-30) REVERT: G 211 TYR cc_start: 0.8244 (m-80) cc_final: 0.7714 (m-80) REVERT: G 216 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7128 (ttt-90) REVERT: G 248 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7218 (t0) REVERT: G 319 MET cc_start: 0.2072 (OUTLIER) cc_final: 0.1733 (ptm) REVERT: G 338 TYR cc_start: 0.8740 (p90) cc_final: 0.8450 (p90) REVERT: G 380 PHE cc_start: 0.7883 (p90) cc_final: 0.7462 (p90) REVERT: G 382 ARG cc_start: 0.5727 (mtm180) cc_final: 0.5115 (mtm180) REVERT: G 390 THR cc_start: 0.8625 (t) cc_final: 0.8344 (p) REVERT: G 466 ASN cc_start: 0.7892 (m110) cc_final: 0.7647 (m110) REVERT: G 471 ASP cc_start: 0.7540 (t0) cc_final: 0.7172 (t0) REVERT: G 473 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6538 (tm-30) REVERT: G 536 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8058 (ttpp) REVERT: G 559 PHE cc_start: 0.7942 (m-80) cc_final: 0.7663 (m-80) REVERT: G 560 ASN cc_start: 0.7785 (m-40) cc_final: 0.7365 (m-40) REVERT: G 561 TYR cc_start: 0.8535 (m-80) cc_final: 0.8258 (m-80) REVERT: G 581 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7934 (ttp-110) REVERT: A 47 ASN cc_start: 0.7974 (t160) cc_final: 0.7642 (t160) REVERT: A 98 LEU cc_start: 0.7647 (mt) cc_final: 0.6990 (tp) REVERT: A 100 ASP cc_start: 0.6993 (m-30) cc_final: 0.6784 (m-30) REVERT: A 174 MET cc_start: 0.7353 (mtp) cc_final: 0.6816 (mtp) REVERT: A 183 MET cc_start: 0.7068 (mmm) cc_final: 0.6570 (mmm) REVERT: A 211 TYR cc_start: 0.7296 (m-80) cc_final: 0.7071 (m-80) REVERT: A 218 LEU cc_start: 0.8277 (tp) cc_final: 0.7939 (tt) REVERT: A 265 THR cc_start: 0.7462 (p) cc_final: 0.7213 (p) REVERT: A 344 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7806 (p) REVERT: A 350 GLN cc_start: 0.7488 (mt0) cc_final: 0.7195 (mt0) REVERT: A 382 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6651 (mtm110) REVERT: A 397 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7771 (mtt-85) REVERT: A 433 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 439 LYS cc_start: 0.8153 (mptt) cc_final: 0.7912 (mptt) REVERT: A 475 ASP cc_start: 0.7385 (t70) cc_final: 0.6745 (t0) REVERT: A 530 LYS cc_start: 0.7234 (ttmt) cc_final: 0.6866 (ttpp) REVERT: A 544 THR cc_start: 0.8002 (t) cc_final: 0.7723 (t) REVERT: A 574 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6461 (mm-30) REVERT: A 575 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7589 (mtpt) REVERT: B 80 ARG cc_start: 0.7179 (mtt-85) cc_final: 0.6462 (mtt-85) REVERT: B 101 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7928 (pt) REVERT: B 117 TRP cc_start: 0.6852 (m100) cc_final: 0.6364 (m100) REVERT: B 125 ASP cc_start: 0.8218 (m-30) cc_final: 0.7827 (m-30) REVERT: B 145 ILE cc_start: 0.8104 (mt) cc_final: 0.7698 (mm) REVERT: B 151 LYS cc_start: 0.7971 (mttm) cc_final: 0.7766 (mttm) REVERT: B 174 MET cc_start: 0.6802 (mtp) cc_final: 0.6454 (mtp) REVERT: B 178 ASP cc_start: 0.5914 (t0) cc_final: 0.5608 (t0) REVERT: B 183 MET cc_start: 0.6901 (mmm) cc_final: 0.6501 (mmm) REVERT: B 190 MET cc_start: 0.7826 (tpp) cc_final: 0.7389 (tpp) REVERT: B 198 TYR cc_start: 0.7071 (m-80) cc_final: 0.6509 (m-10) REVERT: B 266 PHE cc_start: 0.7331 (t80) cc_final: 0.6950 (t80) REVERT: B 354 LYS cc_start: 0.7528 (mmtp) cc_final: 0.6929 (mmtp) REVERT: B 377 ARG cc_start: 0.6865 (mmm-85) cc_final: 0.6097 (mmm-85) REVERT: B 382 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7123 (mmp80) REVERT: B 383 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7443 (tm-30) REVERT: B 397 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7740 (ptp90) REVERT: B 501 LYS cc_start: 0.7862 (tttt) cc_final: 0.7358 (tttt) REVERT: B 508 ASN cc_start: 0.8334 (t0) cc_final: 0.8132 (t0) REVERT: B 509 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6252 (mm-30) REVERT: B 527 PHE cc_start: 0.6755 (p90) cc_final: 0.6388 (p90) REVERT: B 530 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8006 (ttmt) REVERT: B 532 LYS cc_start: 0.7291 (tttm) cc_final: 0.6862 (tttm) REVERT: B 533 LEU cc_start: 0.7923 (tp) cc_final: 0.7678 (tp) REVERT: B 536 LYS cc_start: 0.7893 (ttpp) cc_final: 0.7598 (ttpp) REVERT: B 551 MET cc_start: 0.5669 (mmt) cc_final: 0.5081 (mmt) REVERT: E 45 PHE cc_start: 0.7270 (t80) cc_final: 0.6596 (t80) REVERT: E 121 PHE cc_start: 0.7652 (m-80) cc_final: 0.7142 (m-10) REVERT: E 129 ILE cc_start: 0.8802 (mt) cc_final: 0.8583 (mt) REVERT: E 165 TYR cc_start: 0.7777 (m-80) cc_final: 0.7260 (m-80) REVERT: E 166 ASN cc_start: 0.7082 (m110) cc_final: 0.6858 (m110) REVERT: E 190 MET cc_start: 0.5783 (mtm) cc_final: 0.5311 (mtm) REVERT: E 329 THR cc_start: 0.5023 (t) cc_final: 0.4653 (m) REVERT: E 378 TYR cc_start: 0.7191 (m-80) cc_final: 0.6439 (m-80) REVERT: E 398 PHE cc_start: 0.7950 (p90) cc_final: 0.7503 (p90) REVERT: E 400 TYR cc_start: 0.7794 (t80) cc_final: 0.7412 (t80) REVERT: E 527 PHE cc_start: 0.7282 (p90) cc_final: 0.6814 (p90) REVERT: E 557 ASN cc_start: 0.8478 (p0) cc_final: 0.7515 (p0) REVERT: E 561 TYR cc_start: 0.8309 (m-80) cc_final: 0.7622 (m-80) REVERT: E 565 ASN cc_start: 0.8433 (m-40) cc_final: 0.7222 (t0) REVERT: I 47 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7059 (t0) REVERT: I 52 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7475 (ttmm) REVERT: I 87 MET cc_start: 0.6868 (ttp) cc_final: 0.6407 (ttp) REVERT: I 115 ASN cc_start: 0.7657 (t0) cc_final: 0.7217 (t0) REVERT: I 174 MET cc_start: 0.7111 (mtp) cc_final: 0.6645 (mtp) REVERT: I 201 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7894 (ttpt) REVERT: I 268 PHE cc_start: 0.7571 (m-80) cc_final: 0.7081 (m-80) REVERT: I 319 MET cc_start: 0.5529 (tpp) cc_final: 0.4564 (tpp) REVERT: I 331 MET cc_start: 0.7168 (ttm) cc_final: 0.6934 (ttm) REVERT: I 444 TYR cc_start: 0.7954 (p90) cc_final: 0.7534 (p90) REVERT: I 468 GLN cc_start: 0.7200 (mm110) cc_final: 0.6910 (mm110) REVERT: I 518 MET cc_start: 0.6691 (ptp) cc_final: 0.6466 (ptp) REVERT: I 535 PHE cc_start: 0.8443 (m-80) cc_final: 0.7924 (m-80) REVERT: I 538 LYS cc_start: 0.8225 (tttp) cc_final: 0.7807 (ttpp) REVERT: I 544 THR cc_start: 0.7965 (p) cc_final: 0.7612 (p) REVERT: I 546 ASN cc_start: 0.8001 (p0) cc_final: 0.7703 (p0) REVERT: I 550 GLN cc_start: 0.7954 (mm110) cc_final: 0.7515 (mm-40) REVERT: I 573 TYR cc_start: 0.8329 (p90) cc_final: 0.7877 (p90) REVERT: I 575 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7692 (mtmm) REVERT: I 581 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6441 (ttm170) REVERT: F 52 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7553 (ttmm) REVERT: F 60 GLU cc_start: 0.7370 (tt0) cc_final: 0.7062 (tt0) REVERT: F 101 ILE cc_start: 0.8314 (mm) cc_final: 0.8056 (mm) REVERT: F 180 ASN cc_start: 0.7521 (t0) cc_final: 0.7137 (t0) REVERT: F 248 ASN cc_start: 0.7153 (m110) cc_final: 0.6796 (t0) REVERT: F 271 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7904 (mtpp) REVERT: F 280 GLN cc_start: 0.7685 (mm110) cc_final: 0.7020 (mm-40) REVERT: F 283 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7631 (tpt-90) REVERT: F 311 ASP cc_start: 0.6765 (p0) cc_final: 0.6441 (p0) REVERT: F 327 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6673 (mm-30) REVERT: F 336 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8331 (t) REVERT: F 425 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8108 (p) REVERT: F 450 THR cc_start: 0.8797 (p) cc_final: 0.8435 (t) REVERT: F 475 ASP cc_start: 0.7241 (t0) cc_final: 0.6639 (t0) REVERT: F 484 VAL cc_start: 0.8307 (m) cc_final: 0.7905 (p) REVERT: F 551 MET cc_start: 0.6524 (ttt) cc_final: 0.6141 (ttt) REVERT: F 569 MET cc_start: 0.5692 (mmm) cc_final: 0.5453 (mmm) REVERT: C 174 MET cc_start: 0.7116 (mtp) cc_final: 0.6530 (mtp) REVERT: C 236 THR cc_start: 0.5452 (OUTLIER) cc_final: 0.4976 (p) REVERT: C 250 VAL cc_start: 0.7311 (t) cc_final: 0.7081 (t) outliers start: 98 outliers final: 69 residues processed: 799 average time/residue: 0.1795 time to fit residues: 222.7416 Evaluate side-chains 832 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 749 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 466 ASN Chi-restraints excluded: chain I residue 556 ASP Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 310 GLN Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 444 TYR Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 178 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 169 optimal weight: 40.0000 chunk 226 optimal weight: 0.0070 chunk 190 optimal weight: 0.3980 chunk 206 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 2.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN A 143 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.218479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.161282 restraints weight = 40882.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.167080 restraints weight = 17902.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.170685 restraints weight = 10562.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172043 restraints weight = 7706.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172050 restraints weight = 6704.798| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26524 Z= 0.171 Angle : 0.578 9.266 36261 Z= 0.290 Chirality : 0.043 0.164 3973 Planarity : 0.005 0.053 4735 Dihedral : 5.257 59.502 3509 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.85 % Allowed : 16.37 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 2990 helix: -0.46 (0.48), residues: 101 sheet: -0.50 (0.19), residues: 755 loop : -0.30 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 540 TYR 0.032 0.002 TYR B 464 PHE 0.028 0.002 PHE G 353 TRP 0.054 0.001 TRP E 528 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00371 (26519) covalent geometry : angle 0.57658 (36251) SS BOND : bond 0.00191 ( 5) SS BOND : angle 2.68682 ( 10) hydrogen bonds : bond 0.03241 ( 329) hydrogen bonds : angle 5.58561 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 737 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8031 (t0) REVERT: G 59 VAL cc_start: 0.8746 (t) cc_final: 0.8394 (m) REVERT: G 100 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7047 (t0) REVERT: G 135 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: G 151 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7682 (mtpp) REVERT: G 216 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6754 (ttt-90) REVERT: G 218 LEU cc_start: 0.8486 (tp) cc_final: 0.8286 (tp) REVERT: G 248 ASN cc_start: 0.7569 (t0) cc_final: 0.7304 (t0) REVERT: G 319 MET cc_start: 0.2095 (OUTLIER) cc_final: 0.1775 (ptm) REVERT: G 380 PHE cc_start: 0.7973 (p90) cc_final: 0.7273 (p90) REVERT: G 382 ARG cc_start: 0.5776 (mtm180) cc_final: 0.5201 (mtm180) REVERT: G 390 THR cc_start: 0.8584 (t) cc_final: 0.8289 (p) REVERT: G 466 ASN cc_start: 0.7926 (m110) cc_final: 0.7518 (m110) REVERT: G 471 ASP cc_start: 0.7530 (t0) cc_final: 0.7157 (t0) REVERT: G 473 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6569 (tm-30) REVERT: G 485 ASN cc_start: 0.7810 (p0) cc_final: 0.7086 (p0) REVERT: G 536 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8052 (ttpp) REVERT: G 559 PHE cc_start: 0.7968 (m-80) cc_final: 0.7687 (m-80) REVERT: G 560 ASN cc_start: 0.7709 (m-40) cc_final: 0.7317 (m-40) REVERT: A 47 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7656 (t160) REVERT: A 98 LEU cc_start: 0.7722 (mt) cc_final: 0.7039 (tp) REVERT: A 100 ASP cc_start: 0.7003 (m-30) cc_final: 0.6793 (m-30) REVERT: A 174 MET cc_start: 0.7381 (mtp) cc_final: 0.6920 (mtp) REVERT: A 183 MET cc_start: 0.7131 (mmm) cc_final: 0.6641 (mmm) REVERT: A 211 TYR cc_start: 0.7330 (m-80) cc_final: 0.6995 (m-80) REVERT: A 218 LEU cc_start: 0.8283 (tp) cc_final: 0.7954 (tt) REVERT: A 265 THR cc_start: 0.7445 (p) cc_final: 0.7206 (p) REVERT: A 344 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7890 (p) REVERT: A 346 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6920 (mp0) REVERT: A 350 GLN cc_start: 0.7421 (mt0) cc_final: 0.7193 (mt0) REVERT: A 382 ARG cc_start: 0.7120 (mtm110) cc_final: 0.6723 (mtm110) REVERT: A 403 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7001 (m-70) REVERT: A 433 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7956 (p) REVERT: A 475 ASP cc_start: 0.7421 (t70) cc_final: 0.6798 (t0) REVERT: A 530 LYS cc_start: 0.7319 (ttmt) cc_final: 0.6918 (ttpp) REVERT: A 569 MET cc_start: 0.5601 (mmm) cc_final: 0.5371 (mmm) REVERT: A 574 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6493 (mm-30) REVERT: A 575 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7600 (mtpt) REVERT: B 80 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6468 (mtt-85) REVERT: B 101 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7925 (pt) REVERT: B 117 TRP cc_start: 0.6909 (m100) cc_final: 0.6431 (m100) REVERT: B 125 ASP cc_start: 0.8290 (m-30) cc_final: 0.7923 (m-30) REVERT: B 145 ILE cc_start: 0.8115 (mt) cc_final: 0.7788 (mm) REVERT: B 151 LYS cc_start: 0.7993 (mttm) cc_final: 0.7768 (mttm) REVERT: B 174 MET cc_start: 0.6806 (mtp) cc_final: 0.6507 (mtp) REVERT: B 183 MET cc_start: 0.6951 (mmm) cc_final: 0.6396 (mmm) REVERT: B 190 MET cc_start: 0.7818 (tpp) cc_final: 0.7390 (tpp) REVERT: B 197 PHE cc_start: 0.7030 (m-10) cc_final: 0.6402 (m-10) REVERT: B 198 TYR cc_start: 0.7170 (m-80) cc_final: 0.6564 (m-80) REVERT: B 266 PHE cc_start: 0.7314 (t80) cc_final: 0.7027 (t80) REVERT: B 354 LYS cc_start: 0.7557 (mmtp) cc_final: 0.6936 (mmtp) REVERT: B 377 ARG cc_start: 0.6795 (mmm-85) cc_final: 0.6211 (tpp80) REVERT: B 382 ARG cc_start: 0.7535 (mmt90) cc_final: 0.7026 (mmp80) REVERT: B 383 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7456 (tm-30) REVERT: B 501 LYS cc_start: 0.7903 (tttt) cc_final: 0.7429 (tttt) REVERT: B 509 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6250 (mm-30) REVERT: B 527 PHE cc_start: 0.6878 (p90) cc_final: 0.6507 (p90) REVERT: B 530 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: B 532 LYS cc_start: 0.7332 (tttm) cc_final: 0.6900 (tttm) REVERT: B 533 LEU cc_start: 0.7936 (tp) cc_final: 0.7696 (tp) REVERT: B 536 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7600 (ttpp) REVERT: B 551 MET cc_start: 0.5700 (mmt) cc_final: 0.5083 (mmt) REVERT: E 45 PHE cc_start: 0.7183 (t80) cc_final: 0.6573 (t80) REVERT: E 121 PHE cc_start: 0.7635 (m-80) cc_final: 0.7175 (m-10) REVERT: E 165 TYR cc_start: 0.7756 (m-80) cc_final: 0.7239 (m-80) REVERT: E 190 MET cc_start: 0.5810 (mtm) cc_final: 0.5371 (mtm) REVERT: E 329 THR cc_start: 0.5153 (t) cc_final: 0.4778 (m) REVERT: E 378 TYR cc_start: 0.7212 (m-80) cc_final: 0.6436 (m-80) REVERT: E 398 PHE cc_start: 0.7948 (p90) cc_final: 0.7504 (p90) REVERT: E 400 TYR cc_start: 0.7807 (t80) cc_final: 0.7430 (t80) REVERT: E 527 PHE cc_start: 0.7376 (p90) cc_final: 0.6925 (p90) REVERT: E 557 ASN cc_start: 0.8462 (p0) cc_final: 0.7643 (p0) REVERT: E 561 TYR cc_start: 0.8301 (m-80) cc_final: 0.7669 (m-80) REVERT: E 565 ASN cc_start: 0.8421 (m-40) cc_final: 0.7137 (t0) REVERT: I 47 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7107 (t0) REVERT: I 52 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7472 (ttmm) REVERT: I 87 MET cc_start: 0.6940 (ttp) cc_final: 0.6503 (ttp) REVERT: I 115 ASN cc_start: 0.7734 (t0) cc_final: 0.7261 (t0) REVERT: I 174 MET cc_start: 0.7114 (mtp) cc_final: 0.6737 (mtp) REVERT: I 201 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7889 (ttpt) REVERT: I 268 PHE cc_start: 0.7512 (m-80) cc_final: 0.7201 (m-80) REVERT: I 319 MET cc_start: 0.5335 (tpp) cc_final: 0.4561 (tpp) REVERT: I 331 MET cc_start: 0.7179 (ttm) cc_final: 0.6950 (ttm) REVERT: I 383 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: I 444 TYR cc_start: 0.8007 (p90) cc_final: 0.7661 (p90) REVERT: I 468 GLN cc_start: 0.7320 (mm110) cc_final: 0.7020 (mm110) REVERT: I 518 MET cc_start: 0.6603 (ptp) cc_final: 0.6367 (ptp) REVERT: I 535 PHE cc_start: 0.8485 (m-80) cc_final: 0.7957 (m-80) REVERT: I 538 LYS cc_start: 0.8227 (tttp) cc_final: 0.7846 (ttpp) REVERT: I 539 LEU cc_start: 0.8489 (mt) cc_final: 0.8269 (mp) REVERT: I 544 THR cc_start: 0.7964 (p) cc_final: 0.7599 (p) REVERT: I 546 ASN cc_start: 0.7982 (p0) cc_final: 0.7715 (p0) REVERT: I 550 GLN cc_start: 0.7909 (mm110) cc_final: 0.7389 (mm-40) REVERT: I 561 TYR cc_start: 0.7985 (m-80) cc_final: 0.7740 (m-80) REVERT: I 573 TYR cc_start: 0.8296 (p90) cc_final: 0.7859 (p90) REVERT: I 575 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7710 (mtmm) REVERT: I 581 ARG cc_start: 0.7045 (ttm170) cc_final: 0.6357 (ttm170) REVERT: F 52 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7493 (ttmm) REVERT: F 59 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8305 (p) REVERT: F 60 GLU cc_start: 0.7221 (tt0) cc_final: 0.6888 (tt0) REVERT: F 101 ILE cc_start: 0.8349 (mm) cc_final: 0.8085 (mm) REVERT: F 143 GLN cc_start: 0.7608 (mp10) cc_final: 0.7340 (mp10) REVERT: F 180 ASN cc_start: 0.7490 (t0) cc_final: 0.7015 (t0) REVERT: F 248 ASN cc_start: 0.7127 (m110) cc_final: 0.6770 (t0) REVERT: F 271 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7900 (mtpp) REVERT: F 280 GLN cc_start: 0.7628 (mm110) cc_final: 0.6987 (mm-40) REVERT: F 283 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7650 (tpt-90) REVERT: F 311 ASP cc_start: 0.6769 (p0) cc_final: 0.6546 (p0) REVERT: F 327 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6661 (mm-30) REVERT: F 425 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8093 (p) REVERT: F 475 ASP cc_start: 0.7219 (t0) cc_final: 0.6533 (t0) REVERT: F 484 VAL cc_start: 0.8262 (m) cc_final: 0.7846 (p) REVERT: F 551 MET cc_start: 0.6500 (ttt) cc_final: 0.6161 (ttt) REVERT: F 569 MET cc_start: 0.5698 (mmm) cc_final: 0.5423 (mmm) REVERT: C 174 MET cc_start: 0.7139 (mtp) cc_final: 0.6566 (mtp) REVERT: C 236 THR cc_start: 0.5474 (OUTLIER) cc_final: 0.4985 (p) REVERT: C 250 VAL cc_start: 0.7349 (t) cc_final: 0.7115 (t) outliers start: 105 outliers final: 78 residues processed: 771 average time/residue: 0.1708 time to fit residues: 205.5267 Evaluate side-chains 827 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 733 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain G residue 570 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 310 GLN Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 444 TYR Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 278 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 ASN G 248 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 ASN I 543 HIS ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.217173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.160301 restraints weight = 41268.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.166040 restraints weight = 17971.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.169735 restraints weight = 10530.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.171154 restraints weight = 7718.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.171167 restraints weight = 6652.568| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 26524 Z= 0.211 Angle : 0.596 8.044 36261 Z= 0.302 Chirality : 0.044 0.187 3973 Planarity : 0.005 0.061 4735 Dihedral : 5.346 59.564 3509 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.85 % Allowed : 16.81 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 2990 helix: -0.37 (0.48), residues: 100 sheet: -0.50 (0.19), residues: 767 loop : -0.38 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 274 TYR 0.034 0.002 TYR B 464 PHE 0.029 0.002 PHE B 141 TRP 0.043 0.001 TRP E 528 HIS 0.005 0.001 HIS I 543 Details of bonding type rmsd covalent geometry : bond 0.00455 (26519) covalent geometry : angle 0.59432 (36251) SS BOND : bond 0.00274 ( 5) SS BOND : angle 2.88794 ( 10) hydrogen bonds : bond 0.03414 ( 329) hydrogen bonds : angle 5.65739 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 752 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8028 (t0) REVERT: G 59 VAL cc_start: 0.8818 (t) cc_final: 0.8417 (m) REVERT: G 100 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7166 (t0) REVERT: G 135 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: G 142 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6720 (mm-30) REVERT: G 151 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7708 (mtpp) REVERT: G 185 PHE cc_start: 0.8032 (t80) cc_final: 0.7749 (t80) REVERT: G 216 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6775 (ttt-90) REVERT: G 218 LEU cc_start: 0.8520 (tp) cc_final: 0.8319 (tp) REVERT: G 248 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7228 (t0) REVERT: G 319 MET cc_start: 0.2273 (OUTLIER) cc_final: 0.2002 (ptm) REVERT: G 331 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: G 380 PHE cc_start: 0.8009 (p90) cc_final: 0.7319 (p90) REVERT: G 382 ARG cc_start: 0.5804 (mtm180) cc_final: 0.5238 (mtm180) REVERT: G 466 ASN cc_start: 0.7959 (m110) cc_final: 0.7561 (m110) REVERT: G 471 ASP cc_start: 0.7500 (t0) cc_final: 0.7247 (t0) REVERT: G 473 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6585 (tm-30) REVERT: G 485 ASN cc_start: 0.7813 (p0) cc_final: 0.7227 (p0) REVERT: G 536 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8008 (ttpp) REVERT: G 560 ASN cc_start: 0.7725 (m-40) cc_final: 0.7285 (m-40) REVERT: A 47 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7695 (t160) REVERT: A 62 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8066 (m) REVERT: A 98 LEU cc_start: 0.7765 (mt) cc_final: 0.7052 (tp) REVERT: A 100 ASP cc_start: 0.7061 (m-30) cc_final: 0.6793 (m-30) REVERT: A 174 MET cc_start: 0.7309 (mtp) cc_final: 0.6854 (mtp) REVERT: A 183 MET cc_start: 0.7157 (mmm) cc_final: 0.6728 (mmm) REVERT: A 211 TYR cc_start: 0.7340 (m-80) cc_final: 0.7004 (m-80) REVERT: A 218 LEU cc_start: 0.8287 (tp) cc_final: 0.7958 (tt) REVERT: A 344 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 346 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6912 (mp0) REVERT: A 382 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6610 (mtm110) REVERT: A 403 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6985 (m-70) REVERT: A 433 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7977 (p) REVERT: A 475 ASP cc_start: 0.7438 (t70) cc_final: 0.6824 (t0) REVERT: A 530 LYS cc_start: 0.7438 (ttmt) cc_final: 0.7026 (ttpp) REVERT: A 569 MET cc_start: 0.5648 (mmm) cc_final: 0.5377 (mmm) REVERT: A 574 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6372 (mm-30) REVERT: A 575 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7595 (mtpt) REVERT: B 80 ARG cc_start: 0.7163 (mtt-85) cc_final: 0.6452 (mtt-85) REVERT: B 101 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7908 (pt) REVERT: B 104 GLN cc_start: 0.7997 (pt0) cc_final: 0.7443 (pt0) REVERT: B 117 TRP cc_start: 0.6903 (m100) cc_final: 0.6480 (m100) REVERT: B 125 ASP cc_start: 0.8261 (m-30) cc_final: 0.7909 (m-30) REVERT: B 174 MET cc_start: 0.6780 (mtp) cc_final: 0.6443 (mtp) REVERT: B 183 MET cc_start: 0.6919 (mmm) cc_final: 0.6432 (mmm) REVERT: B 190 MET cc_start: 0.7774 (tpp) cc_final: 0.7338 (tpp) REVERT: B 198 TYR cc_start: 0.7192 (m-80) cc_final: 0.6620 (m-80) REVERT: B 266 PHE cc_start: 0.7305 (t80) cc_final: 0.6975 (t80) REVERT: B 354 LYS cc_start: 0.7518 (mmtp) cc_final: 0.6882 (mmtp) REVERT: B 377 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6168 (tpp80) REVERT: B 382 ARG cc_start: 0.7568 (mmt90) cc_final: 0.7053 (mmp80) REVERT: B 383 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7269 (tm-30) REVERT: B 501 LYS cc_start: 0.7958 (tttt) cc_final: 0.7448 (tttt) REVERT: B 527 PHE cc_start: 0.6864 (p90) cc_final: 0.6533 (p90) REVERT: B 530 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8145 (ttmt) REVERT: B 532 LYS cc_start: 0.7415 (tttm) cc_final: 0.6882 (tttm) REVERT: B 533 LEU cc_start: 0.7955 (tp) cc_final: 0.7681 (tp) REVERT: B 536 LYS cc_start: 0.7863 (ttpp) cc_final: 0.7600 (ttpp) REVERT: B 551 MET cc_start: 0.5730 (mmt) cc_final: 0.5119 (mmt) REVERT: E 45 PHE cc_start: 0.7180 (t80) cc_final: 0.6602 (t80) REVERT: E 64 ASN cc_start: 0.6886 (p0) cc_final: 0.6681 (p0) REVERT: E 121 PHE cc_start: 0.7631 (m-80) cc_final: 0.6946 (m-10) REVERT: E 165 TYR cc_start: 0.7798 (m-80) cc_final: 0.7489 (m-80) REVERT: E 190 MET cc_start: 0.5868 (mtm) cc_final: 0.5414 (mtm) REVERT: E 329 THR cc_start: 0.5134 (t) cc_final: 0.4781 (m) REVERT: E 378 TYR cc_start: 0.7203 (m-80) cc_final: 0.6416 (m-80) REVERT: E 398 PHE cc_start: 0.7939 (p90) cc_final: 0.7486 (p90) REVERT: E 400 TYR cc_start: 0.7804 (t80) cc_final: 0.7514 (t80) REVERT: E 527 PHE cc_start: 0.7377 (p90) cc_final: 0.6895 (p90) REVERT: E 535 PHE cc_start: 0.7618 (m-80) cc_final: 0.7226 (m-80) REVERT: E 557 ASN cc_start: 0.8448 (p0) cc_final: 0.7656 (p0) REVERT: E 561 TYR cc_start: 0.8301 (m-80) cc_final: 0.7686 (m-80) REVERT: E 565 ASN cc_start: 0.8436 (m-40) cc_final: 0.8209 (m-40) REVERT: I 47 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7143 (t0) REVERT: I 52 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7437 (ttmm) REVERT: I 115 ASN cc_start: 0.7733 (t0) cc_final: 0.7254 (t0) REVERT: I 174 MET cc_start: 0.6987 (mtp) cc_final: 0.6592 (mtp) REVERT: I 201 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7896 (ttpt) REVERT: I 268 PHE cc_start: 0.7520 (m-80) cc_final: 0.7195 (m-80) REVERT: I 319 MET cc_start: 0.5690 (tpp) cc_final: 0.4984 (tpp) REVERT: I 331 MET cc_start: 0.7174 (ttm) cc_final: 0.6936 (ttm) REVERT: I 383 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: I 444 TYR cc_start: 0.7960 (p90) cc_final: 0.7604 (p90) REVERT: I 468 GLN cc_start: 0.7366 (mm110) cc_final: 0.7045 (mm110) REVERT: I 518 MET cc_start: 0.6631 (ptp) cc_final: 0.6374 (ptp) REVERT: I 535 PHE cc_start: 0.8504 (m-80) cc_final: 0.8064 (m-80) REVERT: I 538 LYS cc_start: 0.8234 (tttp) cc_final: 0.7984 (tttp) REVERT: I 539 LEU cc_start: 0.8493 (mt) cc_final: 0.8271 (mp) REVERT: I 544 THR cc_start: 0.8043 (p) cc_final: 0.7671 (p) REVERT: I 546 ASN cc_start: 0.7967 (p0) cc_final: 0.7681 (p0) REVERT: I 550 GLN cc_start: 0.7895 (mm110) cc_final: 0.7301 (mm110) REVERT: I 573 TYR cc_start: 0.8267 (p90) cc_final: 0.7819 (p90) REVERT: I 575 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7721 (mtmm) REVERT: F 52 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7566 (ttmm) REVERT: F 60 GLU cc_start: 0.7353 (tt0) cc_final: 0.7042 (tt0) REVERT: F 101 ILE cc_start: 0.8363 (mm) cc_final: 0.8086 (mm) REVERT: F 143 GLN cc_start: 0.7546 (mp10) cc_final: 0.7268 (mp10) REVERT: F 248 ASN cc_start: 0.7220 (m110) cc_final: 0.6871 (t0) REVERT: F 271 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7920 (mtpp) REVERT: F 280 GLN cc_start: 0.7743 (mm110) cc_final: 0.7482 (mm110) REVERT: F 283 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7721 (tpt-90) REVERT: F 311 ASP cc_start: 0.6852 (p0) cc_final: 0.6649 (p0) REVERT: F 314 ARG cc_start: 0.7496 (ptp90) cc_final: 0.7287 (ptp90) REVERT: F 327 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6637 (mm-30) REVERT: F 332 ARG cc_start: 0.7337 (mtt90) cc_final: 0.7043 (mtt90) REVERT: F 425 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8098 (p) REVERT: F 475 ASP cc_start: 0.7217 (t0) cc_final: 0.6549 (t0) REVERT: F 484 VAL cc_start: 0.8239 (m) cc_final: 0.7937 (p) REVERT: F 551 MET cc_start: 0.6519 (ttt) cc_final: 0.6138 (ttt) REVERT: F 569 MET cc_start: 0.5664 (mmm) cc_final: 0.5397 (mmm) REVERT: C 174 MET cc_start: 0.7248 (mtp) cc_final: 0.6741 (mtp) REVERT: C 236 THR cc_start: 0.5458 (OUTLIER) cc_final: 0.5059 (p) REVERT: C 250 VAL cc_start: 0.7320 (t) cc_final: 0.7091 (t) outliers start: 105 outliers final: 67 residues processed: 783 average time/residue: 0.1698 time to fit residues: 208.3742 Evaluate side-chains 833 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 747 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 310 GLN Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 chunk 160 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 286 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN A 115 ASN A 143 GLN A 446 ASN A 546 ASN B 47 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN C 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.219621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.163526 restraints weight = 41340.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.169284 restraints weight = 17909.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173095 restraints weight = 10443.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.174514 restraints weight = 7602.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.174968 restraints weight = 6555.023| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26524 Z= 0.098 Angle : 0.559 9.726 36261 Z= 0.280 Chirality : 0.041 0.272 3973 Planarity : 0.005 0.066 4735 Dihedral : 4.923 59.151 3507 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.15 % Allowed : 18.28 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2990 helix: -0.48 (0.46), residues: 106 sheet: -0.35 (0.20), residues: 714 loop : -0.30 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 274 TYR 0.031 0.001 TYR B 464 PHE 0.027 0.001 PHE B 398 TRP 0.037 0.001 TRP B 470 HIS 0.004 0.001 HIS F 277 Details of bonding type rmsd covalent geometry : bond 0.00224 (26519) covalent geometry : angle 0.55796 (36251) SS BOND : bond 0.00251 ( 5) SS BOND : angle 2.13238 ( 10) hydrogen bonds : bond 0.02966 ( 329) hydrogen bonds : angle 5.56279 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 764 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7937 (t0) REVERT: G 59 VAL cc_start: 0.8722 (t) cc_final: 0.8398 (m) REVERT: G 83 VAL cc_start: 0.8402 (p) cc_final: 0.8097 (m) REVERT: G 130 VAL cc_start: 0.8396 (t) cc_final: 0.8190 (t) REVERT: G 135 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: G 151 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7657 (mtpp) REVERT: G 185 PHE cc_start: 0.8027 (t80) cc_final: 0.7736 (t80) REVERT: G 319 MET cc_start: 0.2144 (OUTLIER) cc_final: 0.1682 (ptm) REVERT: G 338 TYR cc_start: 0.8735 (p90) cc_final: 0.8426 (p90) REVERT: G 380 PHE cc_start: 0.7895 (p90) cc_final: 0.7152 (p90) REVERT: G 382 ARG cc_start: 0.5557 (mtm180) cc_final: 0.4935 (mtm180) REVERT: G 466 ASN cc_start: 0.7843 (m110) cc_final: 0.7373 (m110) REVERT: G 471 ASP cc_start: 0.7493 (t0) cc_final: 0.7159 (t0) REVERT: G 473 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6460 (tm-30) REVERT: G 536 LYS cc_start: 0.8454 (ttpp) cc_final: 0.7964 (ttpp) REVERT: G 560 ASN cc_start: 0.7792 (m-40) cc_final: 0.7345 (m-40) REVERT: A 47 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7615 (t160) REVERT: A 62 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8038 (m) REVERT: A 66 SER cc_start: 0.7682 (m) cc_final: 0.7359 (m) REVERT: A 92 VAL cc_start: 0.8296 (t) cc_final: 0.8017 (p) REVERT: A 98 LEU cc_start: 0.7605 (mt) cc_final: 0.7009 (tp) REVERT: A 100 ASP cc_start: 0.6848 (m-30) cc_final: 0.6630 (m-30) REVERT: A 174 MET cc_start: 0.7322 (mtp) cc_final: 0.6910 (mtp) REVERT: A 183 MET cc_start: 0.7046 (mmm) cc_final: 0.6569 (mmm) REVERT: A 211 TYR cc_start: 0.7265 (m-80) cc_final: 0.7018 (m-80) REVERT: A 344 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7822 (p) REVERT: A 397 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7790 (mtt-85) REVERT: A 433 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 439 LYS cc_start: 0.8063 (mptt) cc_final: 0.7758 (mptt) REVERT: A 475 ASP cc_start: 0.7282 (t70) cc_final: 0.6636 (t0) REVERT: A 530 LYS cc_start: 0.7199 (ttmt) cc_final: 0.6856 (ttpp) REVERT: A 569 MET cc_start: 0.5583 (mmm) cc_final: 0.5366 (mmm) REVERT: A 574 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6295 (mm-30) REVERT: A 575 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7578 (mtpt) REVERT: B 67 ARG cc_start: 0.6966 (mmt-90) cc_final: 0.6655 (mtt90) REVERT: B 80 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6483 (mtt-85) REVERT: B 101 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7915 (pt) REVERT: B 104 GLN cc_start: 0.7999 (pt0) cc_final: 0.7525 (pt0) REVERT: B 117 TRP cc_start: 0.6896 (m100) cc_final: 0.6555 (m100) REVERT: B 125 ASP cc_start: 0.8210 (m-30) cc_final: 0.7863 (m-30) REVERT: B 151 LYS cc_start: 0.7939 (mttm) cc_final: 0.7724 (mttm) REVERT: B 174 MET cc_start: 0.6718 (mtp) cc_final: 0.6430 (mtp) REVERT: B 178 ASP cc_start: 0.5939 (t0) cc_final: 0.5659 (t0) REVERT: B 183 MET cc_start: 0.6892 (mmm) cc_final: 0.6509 (mmm) REVERT: B 190 MET cc_start: 0.7757 (tpp) cc_final: 0.7305 (tpp) REVERT: B 197 PHE cc_start: 0.6996 (m-10) cc_final: 0.6531 (m-10) REVERT: B 198 TYR cc_start: 0.7172 (m-80) cc_final: 0.6637 (m-80) REVERT: B 266 PHE cc_start: 0.7355 (t80) cc_final: 0.6988 (t80) REVERT: B 354 LYS cc_start: 0.7560 (mmtp) cc_final: 0.6898 (mmtp) REVERT: B 377 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6032 (tpp80) REVERT: B 380 PHE cc_start: 0.6581 (p90) cc_final: 0.5375 (p90) REVERT: B 382 ARG cc_start: 0.7509 (mmt90) cc_final: 0.7298 (mmp80) REVERT: B 383 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7244 (tm-30) REVERT: B 501 LYS cc_start: 0.7945 (tttt) cc_final: 0.7457 (tttt) REVERT: B 527 PHE cc_start: 0.6820 (p90) cc_final: 0.6500 (p90) REVERT: B 530 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8047 (ttmt) REVERT: B 532 LYS cc_start: 0.7074 (tttm) cc_final: 0.6689 (tttm) REVERT: B 533 LEU cc_start: 0.7951 (tp) cc_final: 0.7700 (tp) REVERT: B 536 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7572 (ttpp) REVERT: B 551 MET cc_start: 0.5831 (mmt) cc_final: 0.5193 (mmt) REVERT: E 45 PHE cc_start: 0.7078 (t80) cc_final: 0.6482 (t80) REVERT: E 121 PHE cc_start: 0.7687 (m-80) cc_final: 0.7094 (m-10) REVERT: E 122 ASN cc_start: 0.7439 (t0) cc_final: 0.6017 (p0) REVERT: E 165 TYR cc_start: 0.7777 (m-80) cc_final: 0.7230 (m-80) REVERT: E 190 MET cc_start: 0.5827 (mtm) cc_final: 0.5364 (mtm) REVERT: E 329 THR cc_start: 0.5348 (t) cc_final: 0.4980 (m) REVERT: E 378 TYR cc_start: 0.7141 (m-80) cc_final: 0.6377 (m-80) REVERT: E 398 PHE cc_start: 0.7910 (p90) cc_final: 0.7450 (p90) REVERT: E 400 TYR cc_start: 0.7829 (t80) cc_final: 0.7437 (t80) REVERT: E 527 PHE cc_start: 0.7321 (p90) cc_final: 0.7021 (p90) REVERT: E 530 LYS cc_start: 0.8317 (tmtt) cc_final: 0.7638 (tmtt) REVERT: E 535 PHE cc_start: 0.7602 (m-80) cc_final: 0.7276 (m-80) REVERT: E 557 ASN cc_start: 0.8433 (p0) cc_final: 0.7640 (p0) REVERT: E 559 PHE cc_start: 0.7156 (m-80) cc_final: 0.6918 (m-80) REVERT: E 561 TYR cc_start: 0.8365 (m-80) cc_final: 0.7707 (m-80) REVERT: I 47 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7117 (t0) REVERT: I 52 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7427 (ttmm) REVERT: I 115 ASN cc_start: 0.7707 (t0) cc_final: 0.7244 (t0) REVERT: I 127 GLN cc_start: 0.7714 (tt0) cc_final: 0.7448 (tt0) REVERT: I 174 MET cc_start: 0.7090 (mtp) cc_final: 0.6800 (mtp) REVERT: I 201 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7934 (ttpt) REVERT: I 268 PHE cc_start: 0.7461 (m-80) cc_final: 0.7162 (m-80) REVERT: I 319 MET cc_start: 0.5699 (tpp) cc_final: 0.5046 (tpp) REVERT: I 331 MET cc_start: 0.7176 (ttm) cc_final: 0.6917 (ttm) REVERT: I 444 TYR cc_start: 0.8049 (p90) cc_final: 0.7750 (p90) REVERT: I 468 GLN cc_start: 0.7312 (mm110) cc_final: 0.7030 (mm110) REVERT: I 518 MET cc_start: 0.6594 (ptp) cc_final: 0.6334 (ptp) REVERT: I 538 LYS cc_start: 0.8205 (tttp) cc_final: 0.7974 (ttmm) REVERT: I 550 GLN cc_start: 0.7887 (mm110) cc_final: 0.7398 (mm-40) REVERT: I 573 TYR cc_start: 0.8324 (p90) cc_final: 0.7898 (p90) REVERT: I 575 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7649 (mtmm) REVERT: F 52 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7431 (ttmm) REVERT: F 60 GLU cc_start: 0.7281 (tt0) cc_final: 0.6928 (tt0) REVERT: F 101 ILE cc_start: 0.8298 (mm) cc_final: 0.8025 (mm) REVERT: F 242 GLN cc_start: 0.7357 (mt0) cc_final: 0.6883 (tt0) REVERT: F 248 ASN cc_start: 0.7157 (m110) cc_final: 0.6838 (t0) REVERT: F 271 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7855 (mtpp) REVERT: F 283 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7673 (tpt-90) REVERT: F 311 ASP cc_start: 0.6719 (p0) cc_final: 0.6405 (p0) REVERT: F 314 ARG cc_start: 0.7281 (ptp90) cc_final: 0.7080 (ptp90) REVERT: F 327 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6441 (mm-30) REVERT: F 332 ARG cc_start: 0.7267 (mtt90) cc_final: 0.7067 (mtt90) REVERT: F 405 ASP cc_start: 0.5778 (m-30) cc_final: 0.5517 (m-30) REVERT: F 425 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8094 (p) REVERT: F 475 ASP cc_start: 0.7220 (t0) cc_final: 0.6613 (t0) REVERT: F 484 VAL cc_start: 0.8118 (m) cc_final: 0.7737 (p) REVERT: F 551 MET cc_start: 0.6410 (ttt) cc_final: 0.6022 (ttt) REVERT: C 174 MET cc_start: 0.7254 (mtp) cc_final: 0.6736 (mtp) REVERT: C 236 THR cc_start: 0.5363 (OUTLIER) cc_final: 0.4891 (p) REVERT: C 250 VAL cc_start: 0.7312 (t) cc_final: 0.7078 (t) outliers start: 86 outliers final: 58 residues processed: 791 average time/residue: 0.1728 time to fit residues: 212.0456 Evaluate side-chains 825 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 754 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 383 GLN Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 310 GLN Chi-restraints excluded: chain F residue 312 LYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 497 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 279 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 271 optimal weight: 0.0980 chunk 85 optimal weight: 20.0000 chunk 249 optimal weight: 50.0000 chunk 252 optimal weight: 1.9990 chunk 191 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN G 517 ASN ** G 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN A 350 GLN A 546 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN I 565 ASN F 72 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.215595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157330 restraints weight = 40922.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163021 restraints weight = 18023.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166672 restraints weight = 10714.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.168268 restraints weight = 7842.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169163 restraints weight = 6772.786| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 26524 Z= 0.352 Angle : 0.675 15.445 36261 Z= 0.346 Chirality : 0.047 0.312 3973 Planarity : 0.005 0.064 4735 Dihedral : 5.464 60.020 3505 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.93 % Allowed : 19.01 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 2990 helix: -0.17 (0.49), residues: 99 sheet: -0.55 (0.19), residues: 771 loop : -0.47 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 216 TYR 0.037 0.002 TYR B 464 PHE 0.038 0.002 PHE G 353 TRP 0.038 0.002 TRP E 528 HIS 0.009 0.001 HIS F 277 Details of bonding type rmsd covalent geometry : bond 0.00745 (26519) covalent geometry : angle 0.67365 (36251) SS BOND : bond 0.00256 ( 5) SS BOND : angle 2.71452 ( 10) hydrogen bonds : bond 0.03827 ( 329) hydrogen bonds : angle 5.80477 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 753 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (t0) REVERT: G 59 VAL cc_start: 0.8818 (t) cc_final: 0.8433 (m) REVERT: G 135 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: G 151 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7707 (mtpp) REVERT: G 185 PHE cc_start: 0.8030 (t80) cc_final: 0.7781 (t80) REVERT: G 217 THR cc_start: 0.7895 (p) cc_final: 0.7491 (p) REVERT: G 319 MET cc_start: 0.2441 (OUTLIER) cc_final: 0.2099 (ptm) REVERT: G 380 PHE cc_start: 0.8097 (p90) cc_final: 0.7403 (p90) REVERT: G 382 ARG cc_start: 0.5856 (mtm180) cc_final: 0.5248 (mtm180) REVERT: G 466 ASN cc_start: 0.8017 (m110) cc_final: 0.7641 (m110) REVERT: G 471 ASP cc_start: 0.7458 (t0) cc_final: 0.7252 (t0) REVERT: G 473 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6571 (tm-30) REVERT: G 485 ASN cc_start: 0.7824 (p0) cc_final: 0.7290 (p0) REVERT: G 536 LYS cc_start: 0.8428 (ttpp) cc_final: 0.7951 (ttpp) REVERT: G 559 PHE cc_start: 0.8183 (m-80) cc_final: 0.7751 (m-80) REVERT: G 560 ASN cc_start: 0.7735 (m-40) cc_final: 0.7360 (m-40) REVERT: A 47 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7754 (t160) REVERT: A 65 SER cc_start: 0.8329 (p) cc_final: 0.7977 (p) REVERT: A 98 LEU cc_start: 0.7825 (mt) cc_final: 0.7137 (tp) REVERT: A 100 ASP cc_start: 0.7006 (m-30) cc_final: 0.6741 (m-30) REVERT: A 174 MET cc_start: 0.7384 (mtp) cc_final: 0.6927 (mtp) REVERT: A 183 MET cc_start: 0.7210 (mmm) cc_final: 0.6816 (mmm) REVERT: A 211 TYR cc_start: 0.7368 (m-80) cc_final: 0.7004 (m-80) REVERT: A 218 LEU cc_start: 0.8310 (tp) cc_final: 0.7975 (tt) REVERT: A 293 SER cc_start: 0.8216 (m) cc_final: 0.7902 (p) REVERT: A 344 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 382 ARG cc_start: 0.7321 (mtm110) cc_final: 0.6889 (mtm110) REVERT: A 403 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7015 (m-70) REVERT: A 433 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 475 ASP cc_start: 0.7487 (t70) cc_final: 0.6922 (t0) REVERT: A 569 MET cc_start: 0.5650 (mmm) cc_final: 0.5431 (mmm) REVERT: A 574 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6447 (mm-30) REVERT: A 575 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7603 (mtpt) REVERT: B 67 ARG cc_start: 0.7258 (mmt-90) cc_final: 0.6142 (mtt-85) REVERT: B 80 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6520 (mtt-85) REVERT: B 101 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7869 (pt) REVERT: B 117 TRP cc_start: 0.6925 (m100) cc_final: 0.6580 (m100) REVERT: B 125 ASP cc_start: 0.8298 (m-30) cc_final: 0.7943 (m-30) REVERT: B 151 LYS cc_start: 0.8039 (mttm) cc_final: 0.7807 (mttm) REVERT: B 174 MET cc_start: 0.6784 (mtp) cc_final: 0.6480 (mtp) REVERT: B 183 MET cc_start: 0.6949 (mmm) cc_final: 0.6452 (mmm) REVERT: B 190 MET cc_start: 0.7700 (tpp) cc_final: 0.7277 (tpp) REVERT: B 198 TYR cc_start: 0.7210 (m-80) cc_final: 0.6427 (m-80) REVERT: B 266 PHE cc_start: 0.7345 (t80) cc_final: 0.6917 (t80) REVERT: B 338 TYR cc_start: 0.6500 (p90) cc_final: 0.6227 (p90) REVERT: B 354 LYS cc_start: 0.7549 (mmtp) cc_final: 0.6884 (mmtp) REVERT: B 377 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6194 (tpp80) REVERT: B 380 PHE cc_start: 0.6646 (p90) cc_final: 0.5462 (p90) REVERT: B 382 ARG cc_start: 0.7646 (mmt90) cc_final: 0.7294 (mmp80) REVERT: B 383 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7301 (tm-30) REVERT: B 501 LYS cc_start: 0.7955 (tttt) cc_final: 0.7482 (tttt) REVERT: B 527 PHE cc_start: 0.6963 (p90) cc_final: 0.6545 (p90) REVERT: B 530 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8140 (ttmt) REVERT: B 532 LYS cc_start: 0.7337 (tttm) cc_final: 0.6954 (tttm) REVERT: B 533 LEU cc_start: 0.7939 (tp) cc_final: 0.7700 (tp) REVERT: B 536 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7647 (ttpp) REVERT: B 551 MET cc_start: 0.5704 (mmt) cc_final: 0.5134 (mmt) REVERT: E 45 PHE cc_start: 0.7280 (t80) cc_final: 0.6666 (t80) REVERT: E 127 GLN cc_start: 0.7705 (tp40) cc_final: 0.7372 (tp40) REVERT: E 165 TYR cc_start: 0.7831 (m-80) cc_final: 0.7246 (m-80) REVERT: E 190 MET cc_start: 0.5904 (mtm) cc_final: 0.5422 (mtm) REVERT: E 329 THR cc_start: 0.5383 (t) cc_final: 0.4992 (m) REVERT: E 378 TYR cc_start: 0.7199 (m-80) cc_final: 0.6405 (m-80) REVERT: E 398 PHE cc_start: 0.7960 (p90) cc_final: 0.7486 (p90) REVERT: E 400 TYR cc_start: 0.7784 (t80) cc_final: 0.7433 (t80) REVERT: E 527 PHE cc_start: 0.7431 (p90) cc_final: 0.6989 (p90) REVERT: E 530 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7642 (tmtt) REVERT: E 535 PHE cc_start: 0.7644 (m-80) cc_final: 0.7349 (m-80) REVERT: E 561 TYR cc_start: 0.8372 (m-80) cc_final: 0.7789 (m-80) REVERT: E 565 ASN cc_start: 0.8420 (m-40) cc_final: 0.7139 (t0) REVERT: I 47 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7248 (t0) REVERT: I 52 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7377 (ttmm) REVERT: I 115 ASN cc_start: 0.7696 (t0) cc_final: 0.7217 (t0) REVERT: I 174 MET cc_start: 0.7092 (mtp) cc_final: 0.6736 (mtp) REVERT: I 201 LYS cc_start: 0.8241 (mtpt) cc_final: 0.8003 (ttpt) REVERT: I 268 PHE cc_start: 0.7513 (m-80) cc_final: 0.7231 (m-80) REVERT: I 319 MET cc_start: 0.5886 (tpp) cc_final: 0.5270 (tpp) REVERT: I 331 MET cc_start: 0.7170 (ttm) cc_final: 0.6922 (ttm) REVERT: I 383 GLN cc_start: 0.7729 (mt0) cc_final: 0.7342 (mt0) REVERT: I 444 TYR cc_start: 0.7928 (p90) cc_final: 0.7640 (p90) REVERT: I 468 GLN cc_start: 0.7435 (mm110) cc_final: 0.7197 (mm110) REVERT: I 518 MET cc_start: 0.6629 (ptp) cc_final: 0.6359 (ptp) REVERT: I 535 PHE cc_start: 0.8532 (m-80) cc_final: 0.8066 (m-80) REVERT: I 538 LYS cc_start: 0.8228 (tttp) cc_final: 0.7986 (tttp) REVERT: I 539 LEU cc_start: 0.8449 (mt) cc_final: 0.8232 (mp) REVERT: I 550 GLN cc_start: 0.7890 (mm110) cc_final: 0.7246 (mm-40) REVERT: I 551 MET cc_start: 0.6405 (tmm) cc_final: 0.6138 (tmm) REVERT: I 573 TYR cc_start: 0.8274 (p90) cc_final: 0.7804 (p90) REVERT: I 575 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7724 (mtmm) REVERT: F 52 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7557 (ttmm) REVERT: F 60 GLU cc_start: 0.7417 (tt0) cc_final: 0.7038 (tt0) REVERT: F 101 ILE cc_start: 0.8395 (mm) cc_final: 0.8107 (mm) REVERT: F 143 GLN cc_start: 0.7791 (mp10) cc_final: 0.7178 (mp10) REVERT: F 242 GLN cc_start: 0.7303 (mt0) cc_final: 0.6864 (tt0) REVERT: F 248 ASN cc_start: 0.7225 (m110) cc_final: 0.6958 (t0) REVERT: F 271 LYS cc_start: 0.8236 (mtpp) cc_final: 0.8003 (mtpp) REVERT: F 276 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7449 (m) REVERT: F 327 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6718 (mm-30) REVERT: F 332 ARG cc_start: 0.7513 (mtt90) cc_final: 0.7237 (mtt90) REVERT: F 350 GLN cc_start: 0.7761 (mp10) cc_final: 0.7395 (mp10) REVERT: F 405 ASP cc_start: 0.5791 (m-30) cc_final: 0.5514 (m-30) REVERT: F 425 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8114 (p) REVERT: F 475 ASP cc_start: 0.7246 (t0) cc_final: 0.6596 (t0) REVERT: F 484 VAL cc_start: 0.8318 (m) cc_final: 0.8045 (p) REVERT: F 569 MET cc_start: 0.5665 (mmm) cc_final: 0.5320 (mmm) REVERT: C 174 MET cc_start: 0.7308 (mtp) cc_final: 0.6786 (mtp) REVERT: C 250 VAL cc_start: 0.7360 (t) cc_final: 0.7134 (t) outliers start: 80 outliers final: 55 residues processed: 781 average time/residue: 0.1696 time to fit residues: 207.5528 Evaluate side-chains 814 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 746 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 415 ILE Chi-restraints excluded: chain G residue 424 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 538 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 444 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 310 GLN Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 162 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 134 optimal weight: 50.0000 chunk 169 optimal weight: 30.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN ** G 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.217267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159742 restraints weight = 40651.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.165446 restraints weight = 17841.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168964 restraints weight = 10650.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170477 restraints weight = 7839.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171560 restraints weight = 6778.595| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26524 Z= 0.175 Angle : 0.612 14.063 36261 Z= 0.308 Chirality : 0.043 0.297 3973 Planarity : 0.005 0.067 4735 Dihedral : 5.231 59.114 3505 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.78 % Allowed : 19.27 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 2990 helix: -0.24 (0.48), residues: 99 sheet: -0.52 (0.19), residues: 755 loop : -0.42 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 274 TYR 0.039 0.002 TYR B 464 PHE 0.031 0.002 PHE A 448 TRP 0.034 0.001 TRP E 528 HIS 0.007 0.001 HIS F 277 Details of bonding type rmsd covalent geometry : bond 0.00383 (26519) covalent geometry : angle 0.61022 (36251) SS BOND : bond 0.00277 ( 5) SS BOND : angle 2.46957 ( 10) hydrogen bonds : bond 0.03364 ( 329) hydrogen bonds : angle 5.73017 ( 615) =============================================================================== Job complete usr+sys time: 5533.92 seconds wall clock time: 95 minutes 39.43 seconds (5739.43 seconds total)