Starting phenix.real_space_refine on Sun Jun 22 09:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uts_26788/06_2025/7uts_26788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uts_26788/06_2025/7uts_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uts_26788/06_2025/7uts_26788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uts_26788/06_2025/7uts_26788.map" model { file = "/net/cci-nas-00/data/ceres_data/7uts_26788/06_2025/7uts_26788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uts_26788/06_2025/7uts_26788.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.76, per 1000 atoms: 0.57 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: 5.75 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.36 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: 8.38 Time building geometry restraints manager: 6.98 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 55.920 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP I 545 HIS 0.008 0.002 HIS A 137 PHE 0.043 0.003 PHE A 448 TYR 0.032 0.003 TYR G 524 ARG 0.008 0.001 ARG G 191 Details of bonding type rmsd hydrogen bonds : bond 0.23097 ( 329) hydrogen bonds : angle 8.38678 ( 615) SS BOND : bond 0.00537 ( 5) SS BOND : angle 2.34603 ( 10) covalent geometry : bond 0.00841 (26519) covalent geometry : angle 0.96609 (36251) *********************** 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 : 2.618 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: 0.6301 (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: 0.8252 (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: 0.7119 (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: 0.7172 (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: 0.7359 (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: 0.7339 (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: 0.6940 (ttm) REVERT: I 387 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8112 (ttmm) REVERT: I 427 ASP cc_start: 0.8315 (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: 0.8346 (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: 0.7708 (p0) REVERT: I 550 GLN cc_start: 0.7970 (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: 0.7263 (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: 0.8477 (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: 0.4042 time to fit residues: 518.1297 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 : 2.842 ------------------------------------------------------------------------------- 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 274 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 84 optimal weight: 40.0000 chunk 166 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 189 optimal weight: 40.0000 chunk 295 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4456 r_free = 0.4456 target = 0.217103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159088 restraints weight = 41091.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165141 restraints weight = 17689.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.168972 restraints weight = 10212.323| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 26524 Z= 0.244 Angle : 0.656 9.187 36261 Z= 0.339 Chirality : 0.046 0.165 3973 Planarity : 0.005 0.052 4735 Dihedral : 6.843 63.331 3523 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 10.26 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 2990 helix: -1.00 (0.45), residues: 111 sheet: -0.59 (0.18), residues: 784 loop : -0.55 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 545 HIS 0.007 0.001 HIS B 137 PHE 0.025 0.002 PHE B 398 TYR 0.023 0.002 TYR F 342 ARG 0.008 0.001 ARG F 408 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 329) hydrogen bonds : angle 6.25570 ( 615) SS BOND : bond 0.00781 ( 5) SS BOND : angle 3.27084 ( 10) covalent geometry : bond 0.00524 (26519) covalent geometry : angle 0.65390 (36251) *********************** 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 862 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 801 time to evaluate : 2.442 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 59 VAL cc_start: 0.8795 (t) cc_final: 0.8393 (m) REVERT: G 125 ASP cc_start: 0.6526 (m-30) cc_final: 0.6209 (m-30) REVERT: G 151 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7692 (mtpp) REVERT: G 211 TYR cc_start: 0.8221 (m-80) cc_final: 0.7558 (m-80) REVERT: G 248 ASN cc_start: 0.7622 (t0) cc_final: 0.7382 (t0) REVERT: G 249 SER cc_start: 0.8546 (t) cc_final: 0.8328 (t) REVERT: G 263 THR cc_start: 0.8047 (m) cc_final: 0.7733 (p) REVERT: G 271 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7652 (mtpp) REVERT: G 282 ASN cc_start: 0.8191 (t0) cc_final: 0.7852 (t0) REVERT: G 332 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7530 (mmt90) REVERT: G 338 TYR cc_start: 0.8652 (p90) cc_final: 0.8431 (p90) REVERT: G 382 ARG cc_start: 0.5941 (mtm180) cc_final: 0.5614 (mtm180) REVERT: G 458 ASN cc_start: 0.7383 (m-40) cc_final: 0.7122 (m110) REVERT: G 468 GLN cc_start: 0.7841 (mt0) cc_final: 0.7578 (mt0) REVERT: G 471 ASP cc_start: 0.7548 (t0) cc_final: 0.7220 (t0) REVERT: G 485 ASN cc_start: 0.7806 (p0) cc_final: 0.7162 (p0) REVERT: G 492 ASN cc_start: 0.7843 (m-40) cc_final: 0.7601 (m-40) REVERT: G 536 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8044 (ttpp) REVERT: G 559 PHE cc_start: 0.8041 (m-80) cc_final: 0.7388 (m-80) REVERT: G 560 ASN cc_start: 0.7729 (m-40) cc_final: 0.7443 (m-40) REVERT: G 561 TYR cc_start: 0.8508 (m-80) cc_final: 0.8179 (m-80) REVERT: A 56 ASN cc_start: 0.7545 (m110) cc_final: 0.7333 (m110) REVERT: A 98 LEU cc_start: 0.7749 (mt) cc_final: 0.6982 (mt) REVERT: A 100 ASP cc_start: 0.7063 (m-30) cc_final: 0.6423 (m-30) REVERT: A 115 ASN cc_start: 0.7926 (t0) cc_final: 0.7709 (t0) REVERT: A 142 GLU cc_start: 0.7302 (pt0) cc_final: 0.7081 (pt0) REVERT: A 174 MET cc_start: 0.7079 (mtp) cc_final: 0.6770 (mpp) REVERT: A 183 MET cc_start: 0.7135 (mmm) cc_final: 0.6593 (mmm) REVERT: A 211 TYR cc_start: 0.7344 (m-80) cc_final: 0.7015 (m-80) REVERT: A 216 ARG cc_start: 0.6981 (ttt90) cc_final: 0.6435 (ttt90) REVERT: A 218 LEU cc_start: 0.8397 (tp) cc_final: 0.7989 (tt) REVERT: A 219 ILE cc_start: 0.8674 (mm) cc_final: 0.8436 (mm) REVERT: A 344 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7508 (p) REVERT: A 346 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6825 (mt-10) REVERT: A 350 GLN cc_start: 0.7441 (mt0) cc_final: 0.7112 (mt0) REVERT: A 382 ARG cc_start: 0.7125 (mtm110) cc_final: 0.6669 (mtm110) REVERT: A 409 TYR cc_start: 0.7732 (t80) cc_final: 0.7517 (t80) REVERT: A 411 GLU cc_start: 0.7430 (mp0) cc_final: 0.7166 (mp0) REVERT: A 413 ASP cc_start: 0.7323 (t0) cc_final: 0.7122 (t0) REVERT: A 439 LYS cc_start: 0.8202 (mptt) cc_final: 0.7881 (mptt) REVERT: A 458 ASN cc_start: 0.7961 (m110) cc_final: 0.7695 (m110) REVERT: A 530 LYS cc_start: 0.7297 (ttmt) cc_final: 0.6923 (ttpp) REVERT: A 543 HIS cc_start: 0.6835 (m170) cc_final: 0.6534 (m170) REVERT: A 570 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7733 (ptpt) REVERT: A 575 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7540 (mtpt) REVERT: B 70 HIS cc_start: 0.7872 (t70) cc_final: 0.7529 (t70) REVERT: B 80 ARG cc_start: 0.7241 (mtt-85) cc_final: 0.6723 (mtt-85) REVERT: B 101 ILE cc_start: 0.8211 (pt) cc_final: 0.7913 (pt) REVERT: B 104 GLN cc_start: 0.8034 (pt0) cc_final: 0.7347 (pt0) REVERT: B 125 ASP cc_start: 0.8336 (m-30) cc_final: 0.7887 (m-30) REVERT: B 135 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7136 (mt-10) REVERT: B 143 GLN cc_start: 0.7511 (mt0) cc_final: 0.7269 (mt0) REVERT: B 145 ILE cc_start: 0.8263 (mt) cc_final: 0.7786 (mm) REVERT: B 146 PHE cc_start: 0.8069 (p90) cc_final: 0.7843 (p90) REVERT: B 151 LYS cc_start: 0.8045 (mttm) cc_final: 0.7786 (mttm) REVERT: B 173 LEU cc_start: 0.8095 (tp) cc_final: 0.7893 (tp) REVERT: B 174 MET cc_start: 0.6578 (mtp) cc_final: 0.6296 (mtp) REVERT: B 178 ASP cc_start: 0.5841 (t0) cc_final: 0.5638 (t0) REVERT: B 183 MET cc_start: 0.6831 (mmm) cc_final: 0.6363 (mmm) REVERT: B 190 MET cc_start: 0.7870 (tpp) cc_final: 0.7437 (tpp) REVERT: B 198 TYR cc_start: 0.7117 (m-80) cc_final: 0.6575 (m-80) REVERT: B 247 GLU cc_start: 0.6214 (mp0) cc_final: 0.5824 (mp0) REVERT: B 266 PHE cc_start: 0.7216 (t80) cc_final: 0.6776 (t80) REVERT: B 382 ARG cc_start: 0.7524 (mmt90) cc_final: 0.6976 (mmt-90) REVERT: B 383 GLN cc_start: 0.7745 (tp-100) cc_final: 0.6882 (tm-30) REVERT: B 469 ILE cc_start: 0.7977 (mt) cc_final: 0.7377 (mt) REVERT: B 470 TRP cc_start: 0.8000 (p90) cc_final: 0.7720 (p90) REVERT: B 499 PHE cc_start: 0.8400 (m-80) cc_final: 0.7683 (m-80) REVERT: B 501 LYS cc_start: 0.7894 (tttt) cc_final: 0.7274 (tttt) REVERT: B 509 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6407 (mm-30) REVERT: B 527 PHE cc_start: 0.6872 (p90) cc_final: 0.6482 (p90) REVERT: B 530 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (ttmt) REVERT: B 532 LYS cc_start: 0.7193 (tttm) cc_final: 0.6863 (tttm) REVERT: B 533 LEU cc_start: 0.8052 (tp) cc_final: 0.7660 (tp) REVERT: B 551 MET cc_start: 0.5785 (mmt) cc_final: 0.5254 (mmt) REVERT: E 45 PHE cc_start: 0.7500 (t80) cc_final: 0.6873 (t80) REVERT: E 129 ILE cc_start: 0.8865 (mt) cc_final: 0.8614 (mt) REVERT: E 166 ASN cc_start: 0.7009 (m110) cc_final: 0.6758 (m110) REVERT: E 190 MET cc_start: 0.5414 (mtm) cc_final: 0.5105 (mtm) REVERT: E 377 ARG cc_start: 0.6706 (mtm-85) cc_final: 0.6148 (mtm-85) REVERT: E 378 TYR cc_start: 0.7075 (m-80) cc_final: 0.6308 (m-80) REVERT: E 398 PHE cc_start: 0.7963 (p90) cc_final: 0.7540 (p90) REVERT: E 400 TYR cc_start: 0.7804 (t80) cc_final: 0.7467 (t80) REVERT: E 527 PHE cc_start: 0.7278 (p90) cc_final: 0.6876 (p90) REVERT: E 528 TRP cc_start: 0.6721 (m100) cc_final: 0.6427 (m100) REVERT: E 530 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7714 (tmtt) REVERT: E 561 TYR cc_start: 0.8233 (m-80) cc_final: 0.7485 (m-80) REVERT: E 565 ASN cc_start: 0.8316 (m-40) cc_final: 0.7477 (t0) REVERT: E 566 ILE cc_start: 0.8339 (pt) cc_final: 0.8003 (pt) REVERT: I 47 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7425 (t0) REVERT: I 52 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7501 (ttmm) REVERT: I 53 PHE cc_start: 0.7905 (m-80) cc_final: 0.7471 (m-80) REVERT: I 87 MET cc_start: 0.6258 (ttp) cc_final: 0.5850 (ttp) REVERT: I 115 ASN cc_start: 0.7822 (t0) cc_final: 0.7240 (t0) REVERT: I 127 GLN cc_start: 0.7926 (tt0) cc_final: 0.7720 (tt0) REVERT: I 144 GLU cc_start: 0.7295 (pt0) cc_final: 0.7065 (pt0) REVERT: I 174 MET cc_start: 0.7011 (mtp) cc_final: 0.6509 (mtp) REVERT: I 193 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7033 (mt-10) REVERT: I 268 PHE cc_start: 0.7567 (m-80) cc_final: 0.7072 (m-80) REVERT: I 273 CYS cc_start: 0.7389 (t) cc_final: 0.7187 (t) REVERT: I 319 MET cc_start: 0.7351 (tpt) cc_final: 0.7075 (tpp) REVERT: I 331 MET cc_start: 0.7287 (ttm) cc_final: 0.7069 (ttm) REVERT: I 396 GLU cc_start: 0.7536 (tt0) cc_final: 0.7316 (tt0) REVERT: I 427 ASP cc_start: 0.8402 (m-30) cc_final: 0.8176 (m-30) REVERT: I 518 MET cc_start: 0.6828 (ptp) cc_final: 0.6289 (ptp) REVERT: I 535 PHE cc_start: 0.8507 (m-80) cc_final: 0.7873 (m-80) REVERT: I 538 LYS cc_start: 0.8229 (tttp) cc_final: 0.7949 (ttmm) REVERT: I 544 THR cc_start: 0.7918 (p) cc_final: 0.7219 (t) REVERT: I 546 ASN cc_start: 0.7940 (p0) cc_final: 0.7414 (p0) REVERT: I 549 GLN cc_start: 0.7900 (tt0) cc_final: 0.7539 (tt0) REVERT: I 551 MET cc_start: 0.6604 (tmm) cc_final: 0.5612 (tmm) REVERT: I 573 TYR cc_start: 0.8177 (p90) cc_final: 0.7650 (p90) REVERT: I 575 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7660 (mtmm) REVERT: F 52 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7540 (ttmm) REVERT: F 59 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8265 (p) REVERT: F 60 GLU cc_start: 0.7406 (tt0) cc_final: 0.7066 (tt0) REVERT: F 96 MET cc_start: 0.7324 (mpp) cc_final: 0.6982 (mpp) REVERT: F 101 ILE cc_start: 0.8330 (mm) cc_final: 0.8061 (mm) REVERT: F 143 GLN cc_start: 0.7416 (mp10) cc_final: 0.6939 (mp10) REVERT: F 180 ASN cc_start: 0.7493 (t0) cc_final: 0.7168 (t0) REVERT: F 242 GLN cc_start: 0.7262 (mt0) cc_final: 0.7045 (mt0) REVERT: F 243 PHE cc_start: 0.7911 (t80) cc_final: 0.7627 (t80) REVERT: F 244 TYR cc_start: 0.7382 (m-80) cc_final: 0.6562 (m-80) REVERT: F 248 ASN cc_start: 0.7057 (m-40) cc_final: 0.6809 (t0) REVERT: F 271 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7979 (mtpp) REVERT: F 273 CYS cc_start: 0.7810 (t) cc_final: 0.7587 (p) REVERT: F 282 ASN cc_start: 0.8045 (m110) cc_final: 0.7744 (m-40) REVERT: F 283 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7867 (tpt-90) REVERT: F 311 ASP cc_start: 0.7047 (p0) cc_final: 0.6791 (p0) REVERT: F 327 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6971 (mm-30) REVERT: F 335 GLU cc_start: 0.6731 (tt0) cc_final: 0.6505 (tt0) REVERT: F 405 ASP cc_start: 0.6133 (m-30) cc_final: 0.5760 (m-30) REVERT: F 473 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6938 (mm-30) REVERT: F 475 ASP cc_start: 0.7370 (t0) cc_final: 0.6788 (t0) REVERT: F 485 ASN cc_start: 0.7913 (p0) cc_final: 0.7592 (p0) REVERT: F 489 VAL cc_start: 0.8306 (m) cc_final: 0.8073 (m) REVERT: F 551 MET cc_start: 0.6559 (ttt) cc_final: 0.6010 (ttt) REVERT: C 174 MET cc_start: 0.7088 (mtp) cc_final: 0.6481 (mtp) REVERT: C 236 THR cc_start: 0.4612 (p) cc_final: 0.4149 (p) outliers start: 61 outliers final: 38 residues processed: 815 average time/residue: 0.3967 time to fit residues: 493.5885 Evaluate side-chains 824 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 782 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 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 418 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 71 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 578 LEU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 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 275 LEU Chi-restraints excluded: chain I residue 571 ILE 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 425 THR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain C residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 246 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 134 optimal weight: 50.0000 chunk 301 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN G 280 GLN G 491 GLN G 505 ASN A 48 GLN A 546 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 ASN F 416 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.221630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.165011 restraints weight = 40565.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.170856 restraints weight = 17665.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173967 restraints weight = 10374.441| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26524 Z= 0.185 Angle : 0.605 8.783 36261 Z= 0.309 Chirality : 0.044 0.162 3973 Planarity : 0.005 0.051 4735 Dihedral : 6.033 60.489 3514 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 12.71 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 2990 helix: -1.00 (0.46), residues: 116 sheet: -0.57 (0.18), residues: 784 loop : -0.44 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 545 HIS 0.007 0.001 HIS B 137 PHE 0.028 0.002 PHE B 398 TYR 0.029 0.002 TYR B 464 ARG 0.010 0.001 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 329) hydrogen bonds : angle 5.96412 ( 615) SS BOND : bond 0.00212 ( 5) SS BOND : angle 2.76742 ( 10) covalent geometry : bond 0.00402 (26519) covalent geometry : angle 0.60371 (36251) *********************** 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 875 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 792 time to evaluate : 2.567 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: 0.8299 (OUTLIER) cc_final: 0.8072 (t0) REVERT: G 59 VAL cc_start: 0.8815 (t) cc_final: 0.8526 (m) REVERT: G 80 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7388 (mtm-85) REVERT: G 88 ASP cc_start: 0.7663 (p0) cc_final: 0.7452 (p0) REVERT: G 89 LYS cc_start: 0.8274 (mmmm) cc_final: 0.7923 (mtpp) REVERT: G 125 ASP cc_start: 0.6601 (m-30) cc_final: 0.6325 (m-30) REVERT: G 197 PHE cc_start: 0.7903 (m-80) cc_final: 0.7649 (m-80) REVERT: G 211 TYR cc_start: 0.8227 (m-80) cc_final: 0.7866 (m-80) REVERT: G 248 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7259 (t0) REVERT: G 249 SER cc_start: 0.8584 (t) cc_final: 0.8368 (t) REVERT: G 271 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7701 (mtpp) REVERT: G 338 TYR cc_start: 0.8696 (p90) cc_final: 0.8467 (p90) REVERT: G 380 PHE cc_start: 0.8100 (p90) cc_final: 0.7655 (p90) REVERT: G 382 ARG cc_start: 0.5785 (mtm180) cc_final: 0.5215 (mtm180) REVERT: G 471 ASP cc_start: 0.7610 (t0) cc_final: 0.7216 (t0) REVERT: G 485 ASN cc_start: 0.7807 (p0) cc_final: 0.7078 (p0) REVERT: G 497 GLN cc_start: 0.8148 (mt0) cc_final: 0.7913 (mt0) REVERT: G 536 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8088 (ttpp) REVERT: G 559 PHE cc_start: 0.8020 (m-80) cc_final: 0.7322 (m-80) REVERT: G 560 ASN cc_start: 0.7753 (m-40) cc_final: 0.7420 (m-40) REVERT: G 561 TYR cc_start: 0.8505 (m-80) cc_final: 0.8249 (m-80) REVERT: A 56 ASN cc_start: 0.7414 (m110) cc_final: 0.7201 (m110) REVERT: A 100 ASP cc_start: 0.6763 (m-30) cc_final: 0.6217 (m-30) REVERT: A 115 ASN cc_start: 0.7903 (t0) cc_final: 0.7644 (t0) REVERT: A 174 MET cc_start: 0.7137 (mtp) cc_final: 0.6816 (mtp) REVERT: A 183 MET cc_start: 0.7067 (mmm) cc_final: 0.6545 (mmm) REVERT: A 197 PHE cc_start: 0.8022 (m-10) cc_final: 0.7601 (m-10) REVERT: A 211 TYR cc_start: 0.7331 (m-80) cc_final: 0.7009 (m-80) REVERT: A 218 LEU cc_start: 0.8384 (tp) cc_final: 0.8070 (tt) REVERT: A 265 THR cc_start: 0.7829 (p) cc_final: 0.7475 (p) REVERT: A 344 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7484 (p) REVERT: A 346 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6852 (mt-10) REVERT: A 350 GLN cc_start: 0.7479 (mt0) cc_final: 0.7142 (mt0) REVERT: A 382 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6627 (mtm110) REVERT: A 439 LYS cc_start: 0.8275 (mptt) cc_final: 0.7979 (mptt) REVERT: A 475 ASP cc_start: 0.7459 (t70) cc_final: 0.6853 (t0) REVERT: A 530 LYS cc_start: 0.7285 (ttmt) cc_final: 0.6905 (ttpp) REVERT: A 543 HIS cc_start: 0.6794 (m170) cc_final: 0.6543 (m170) REVERT: A 570 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7632 (ptpt) REVERT: A 575 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7659 (mtpt) REVERT: B 80 ARG cc_start: 0.7239 (mtt-85) cc_final: 0.6556 (mtt-85) REVERT: B 101 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7769 (pt) REVERT: B 143 GLN cc_start: 0.7560 (mt0) cc_final: 0.7113 (mt0) REVERT: B 145 ILE cc_start: 0.8197 (mt) cc_final: 0.7744 (mm) REVERT: B 151 LYS cc_start: 0.7966 (mttm) cc_final: 0.7731 (mttm) REVERT: B 174 MET cc_start: 0.6594 (mtp) cc_final: 0.6328 (mtp) REVERT: B 183 MET cc_start: 0.6918 (mmm) cc_final: 0.6338 (mmm) REVERT: B 190 MET cc_start: 0.7889 (tpp) cc_final: 0.7456 (tpp) REVERT: B 198 TYR cc_start: 0.7095 (m-80) cc_final: 0.6473 (m-80) REVERT: B 237 ASP cc_start: 0.7196 (m-30) cc_final: 0.6650 (m-30) REVERT: B 247 GLU cc_start: 0.6270 (mp0) cc_final: 0.5918 (mp0) REVERT: B 377 ARG cc_start: 0.6842 (mmm-85) cc_final: 0.6630 (mmm-85) REVERT: B 382 ARG cc_start: 0.7450 (mmt90) cc_final: 0.7203 (mmt-90) REVERT: B 383 GLN cc_start: 0.7794 (tp-100) cc_final: 0.6959 (tm-30) REVERT: B 469 ILE cc_start: 0.7972 (mt) cc_final: 0.7361 (mt) REVERT: B 470 TRP cc_start: 0.8005 (p90) cc_final: 0.7759 (p90) REVERT: B 501 LYS cc_start: 0.7864 (tttt) cc_final: 0.7243 (tttt) REVERT: B 509 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6348 (mm-30) REVERT: B 527 PHE cc_start: 0.6949 (p90) cc_final: 0.6553 (p90) REVERT: B 530 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8048 (ttmt) REVERT: B 533 LEU cc_start: 0.8060 (tp) cc_final: 0.7616 (tp) REVERT: B 551 MET cc_start: 0.5772 (mmt) cc_final: 0.5282 (mmt) REVERT: B 553 ILE cc_start: 0.5980 (OUTLIER) cc_final: 0.5735 (mt) REVERT: E 45 PHE cc_start: 0.7450 (t80) cc_final: 0.6880 (t80) REVERT: E 129 ILE cc_start: 0.8859 (mt) cc_final: 0.8646 (mt) REVERT: E 166 ASN cc_start: 0.7055 (m110) cc_final: 0.6787 (m110) REVERT: E 190 MET cc_start: 0.5502 (mtm) cc_final: 0.5126 (mtm) REVERT: E 378 TYR cc_start: 0.7100 (m-80) cc_final: 0.6363 (m-80) REVERT: E 398 PHE cc_start: 0.7816 (p90) cc_final: 0.7411 (p90) REVERT: E 400 TYR cc_start: 0.7804 (t80) cc_final: 0.7468 (t80) REVERT: E 527 PHE cc_start: 0.7285 (p90) cc_final: 0.7057 (p90) REVERT: E 530 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7653 (tmtt) REVERT: E 557 ASN cc_start: 0.8362 (p0) cc_final: 0.7274 (p0) REVERT: E 561 TYR cc_start: 0.8252 (m-80) cc_final: 0.7294 (m-80) REVERT: E 565 ASN cc_start: 0.8416 (m-40) cc_final: 0.7412 (t0) REVERT: E 566 ILE cc_start: 0.8303 (pt) cc_final: 0.7959 (pt) REVERT: I 47 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7093 (t0) REVERT: I 52 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7505 (ttmm) REVERT: I 66 SER cc_start: 0.7787 (m) cc_final: 0.7520 (m) REVERT: I 87 MET cc_start: 0.6380 (ttp) cc_final: 0.5793 (ttp) REVERT: I 101 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8032 (pp) REVERT: I 115 ASN cc_start: 0.7821 (t0) cc_final: 0.7163 (t0) REVERT: I 144 GLU cc_start: 0.7301 (pt0) cc_final: 0.7090 (pt0) REVERT: I 174 MET cc_start: 0.7072 (mtp) cc_final: 0.6586 (mtp) REVERT: I 193 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7059 (mt-10) REVERT: I 268 PHE cc_start: 0.7623 (m-80) cc_final: 0.6964 (m-80) REVERT: I 319 MET cc_start: 0.7260 (tpt) cc_final: 0.7031 (tpp) REVERT: I 331 MET cc_start: 0.7287 (ttm) cc_final: 0.7049 (ttm) REVERT: I 383 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7523 (mt0) REVERT: I 396 GLU cc_start: 0.7521 (tt0) cc_final: 0.7107 (tt0) REVERT: I 427 ASP cc_start: 0.8430 (m-30) cc_final: 0.8196 (m-30) REVERT: I 535 PHE cc_start: 0.8404 (m-80) cc_final: 0.7929 (m-80) REVERT: I 544 THR cc_start: 0.7893 (p) cc_final: 0.7480 (p) REVERT: I 546 ASN cc_start: 0.7964 (p0) cc_final: 0.7645 (p0) REVERT: I 549 GLN cc_start: 0.7917 (tt0) cc_final: 0.7541 (tt0) REVERT: I 551 MET cc_start: 0.6504 (tmm) cc_final: 0.4903 (tmm) REVERT: I 572 VAL cc_start: 0.8811 (p) cc_final: 0.8582 (m) REVERT: I 573 TYR cc_start: 0.8300 (p90) cc_final: 0.7785 (p90) REVERT: I 574 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: I 575 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7690 (mtmm) REVERT: I 576 SER cc_start: 0.7900 (t) cc_final: 0.7639 (p) REVERT: F 52 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7570 (ttmm) REVERT: F 59 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8346 (p) REVERT: F 60 GLU cc_start: 0.7460 (tt0) cc_final: 0.7159 (tt0) REVERT: F 101 ILE cc_start: 0.8305 (mm) cc_final: 0.8040 (mm) REVERT: F 143 GLN cc_start: 0.7404 (mp10) cc_final: 0.6809 (mp10) REVERT: F 180 ASN cc_start: 0.7537 (t0) cc_final: 0.7190 (t0) REVERT: F 213 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7437 (tm-30) REVERT: F 243 PHE cc_start: 0.7982 (t80) cc_final: 0.7584 (t80) REVERT: F 244 TYR cc_start: 0.7402 (m-80) cc_final: 0.6567 (m-80) REVERT: F 248 ASN cc_start: 0.7040 (m-40) cc_final: 0.6783 (t0) REVERT: F 266 PHE cc_start: 0.7909 (t80) cc_final: 0.7669 (t80) REVERT: F 271 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7925 (mtpp) REVERT: F 280 GLN cc_start: 0.7766 (mm110) cc_final: 0.7500 (mm110) REVERT: F 282 ASN cc_start: 0.7979 (m110) cc_final: 0.7723 (m-40) REVERT: F 283 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7820 (tpt-90) REVERT: F 311 ASP cc_start: 0.6985 (p0) cc_final: 0.6519 (p0) REVERT: F 312 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8059 (ptpp) REVERT: F 327 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6802 (mm-30) REVERT: F 335 GLU cc_start: 0.6860 (tt0) cc_final: 0.6602 (tt0) REVERT: F 405 ASP cc_start: 0.6102 (m-30) cc_final: 0.5737 (m-30) REVERT: F 475 ASP cc_start: 0.7316 (t0) cc_final: 0.6642 (t0) REVERT: F 484 VAL cc_start: 0.8379 (m) cc_final: 0.7896 (p) REVERT: F 551 MET cc_start: 0.6574 (ttt) cc_final: 0.6021 (ttt) REVERT: F 569 MET cc_start: 0.5775 (mmm) cc_final: 0.5520 (mmm) REVERT: C 174 MET cc_start: 0.7147 (mtp) cc_final: 0.6524 (mtp) REVERT: C 236 THR cc_start: 0.4747 (OUTLIER) cc_final: 0.4283 (p) outliers start: 83 outliers final: 53 residues processed: 819 average time/residue: 0.3873 time to fit residues: 487.8589 Evaluate side-chains 832 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 768 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain G residue 257 THR 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 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 A residue 73 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 297 SER Chi-restraints excluded: chain A residue 344 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 92 VAL Chi-restraints excluded: chain B residue 101 ILE 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 380 PHE Chi-restraints excluded: chain B residue 502 VAL 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 E residue 107 THR 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 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 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 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 107 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 168 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 250 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 196 optimal weight: 20.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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 491 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN B 386 GLN B 508 ASN E 248 ASN ** I 56 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** F 491 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.221122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.164305 restraints weight = 41159.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.170075 restraints weight = 17843.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173817 restraints weight = 10476.587| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 26524 Z= 0.217 Angle : 0.611 10.202 36261 Z= 0.310 Chirality : 0.044 0.173 3973 Planarity : 0.005 0.055 4735 Dihedral : 5.779 61.635 3510 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.52 % Allowed : 14.10 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 2990 helix: -0.58 (0.48), residues: 100 sheet: -0.56 (0.18), residues: 772 loop : -0.38 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 545 HIS 0.006 0.001 HIS B 137 PHE 0.031 0.002 PHE B 398 TYR 0.029 0.002 TYR B 464 ARG 0.011 0.001 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 329) hydrogen bonds : angle 5.87263 ( 615) SS BOND : bond 0.00630 ( 5) SS BOND : angle 2.78699 ( 10) covalent geometry : bond 0.00469 (26519) covalent geometry : angle 0.60927 (36251) *********************** 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: 96 poor density : 774 time to evaluate : 2.837 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 47 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (t0) REVERT: G 59 VAL cc_start: 0.8832 (t) cc_final: 0.8499 (m) REVERT: G 80 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: G 125 ASP cc_start: 0.6560 (m-30) cc_final: 0.6306 (m-30) REVERT: G 135 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: G 142 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6502 (mm-30) REVERT: G 151 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7703 (mtpp) REVERT: G 211 TYR cc_start: 0.8244 (m-80) cc_final: 0.7861 (m-80) REVERT: G 248 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7273 (t0) REVERT: G 271 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7707 (mtpp) REVERT: G 338 TYR cc_start: 0.8701 (p90) cc_final: 0.8424 (p90) REVERT: G 350 GLN cc_start: 0.7292 (mt0) cc_final: 0.6850 (mt0) REVERT: G 380 PHE cc_start: 0.8095 (p90) cc_final: 0.7676 (p90) REVERT: G 382 ARG cc_start: 0.5794 (mtm180) cc_final: 0.5228 (mtm180) REVERT: G 390 THR cc_start: 0.8647 (t) cc_final: 0.8343 (p) REVERT: G 471 ASP cc_start: 0.7611 (t0) cc_final: 0.7184 (t0) REVERT: G 473 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6568 (tm-30) REVERT: G 485 ASN cc_start: 0.7808 (p0) cc_final: 0.7082 (p0) REVERT: G 536 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8056 (ttpp) REVERT: G 559 PHE cc_start: 0.7986 (m-80) cc_final: 0.7334 (m-80) REVERT: G 560 ASN cc_start: 0.7696 (m-40) cc_final: 0.7361 (m-40) REVERT: G 561 TYR cc_start: 0.8521 (m-80) cc_final: 0.8219 (m-80) REVERT: G 581 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7911 (ttp-110) REVERT: A 100 ASP cc_start: 0.6860 (m-30) cc_final: 0.6320 (m-30) REVERT: A 115 ASN cc_start: 0.7957 (t0) cc_final: 0.7599 (t0) REVERT: A 174 MET cc_start: 0.7263 (mtp) cc_final: 0.6864 (mtp) REVERT: A 183 MET cc_start: 0.7088 (mmm) cc_final: 0.6560 (mmm) REVERT: A 211 TYR cc_start: 0.7325 (m-80) cc_final: 0.7013 (m-80) REVERT: A 218 LEU cc_start: 0.8332 (tp) cc_final: 0.7996 (tt) REVERT: A 265 THR cc_start: 0.7802 (p) cc_final: 0.7539 (p) REVERT: A 344 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7519 (p) REVERT: A 350 GLN cc_start: 0.7447 (mt0) cc_final: 0.7180 (mt0) REVERT: A 382 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6698 (mtm110) REVERT: A 387 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7791 (ttpt) REVERT: A 403 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7232 (m-70) REVERT: A 433 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (p) REVERT: A 436 ILE cc_start: 0.8995 (pt) cc_final: 0.8634 (mt) REVERT: A 439 LYS cc_start: 0.8167 (mptt) cc_final: 0.7901 (mptt) REVERT: A 475 ASP cc_start: 0.7467 (t70) cc_final: 0.6872 (t0) REVERT: A 530 LYS cc_start: 0.7338 (ttmt) cc_final: 0.7059 (ttpp) REVERT: A 543 HIS cc_start: 0.6822 (m170) cc_final: 0.6607 (m170) REVERT: A 570 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7537 (ptpt) REVERT: A 575 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7678 (mtpt) REVERT: B 80 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6539 (mtt-85) REVERT: B 101 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7946 (pt) REVERT: B 125 ASP cc_start: 0.8383 (m-30) cc_final: 0.7896 (m-30) REVERT: B 143 GLN cc_start: 0.7524 (mt0) cc_final: 0.7069 (mt0) REVERT: B 151 LYS cc_start: 0.7939 (mttm) cc_final: 0.7724 (mttm) REVERT: B 174 MET cc_start: 0.6806 (mtp) cc_final: 0.6417 (mtp) REVERT: B 178 ASP cc_start: 0.5949 (t0) cc_final: 0.5699 (t0) REVERT: B 183 MET cc_start: 0.6882 (mmm) cc_final: 0.6487 (mmm) REVERT: B 190 MET cc_start: 0.7889 (tpp) cc_final: 0.7442 (tpp) REVERT: B 198 TYR cc_start: 0.7071 (m-80) cc_final: 0.6493 (m-80) REVERT: B 237 ASP cc_start: 0.7291 (m-30) cc_final: 0.6628 (m-30) REVERT: B 247 GLU cc_start: 0.6268 (mp0) cc_final: 0.6005 (mp0) REVERT: B 266 PHE cc_start: 0.7252 (t80) cc_final: 0.6756 (t80) REVERT: B 306 ILE cc_start: 0.7774 (mp) cc_final: 0.7560 (pt) REVERT: B 377 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6465 (tpp80) REVERT: B 382 ARG cc_start: 0.7572 (mmt90) cc_final: 0.7034 (mmp80) REVERT: B 383 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7051 (tm-30) REVERT: B 469 ILE cc_start: 0.7983 (mt) cc_final: 0.7466 (mp) REVERT: B 470 TRP cc_start: 0.8009 (p90) cc_final: 0.7795 (p90) REVERT: B 501 LYS cc_start: 0.7926 (tttt) cc_final: 0.7317 (tttt) REVERT: B 509 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6276 (mm-30) REVERT: B 527 PHE cc_start: 0.6885 (p90) cc_final: 0.6519 (p90) REVERT: B 530 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8049 (ttmt) REVERT: B 533 LEU cc_start: 0.8061 (tp) cc_final: 0.7629 (tp) REVERT: B 551 MET cc_start: 0.5885 (mmt) cc_final: 0.5402 (mmt) REVERT: B 553 ILE cc_start: 0.5941 (OUTLIER) cc_final: 0.5723 (mt) REVERT: E 45 PHE cc_start: 0.7442 (t80) cc_final: 0.6774 (t80) REVERT: E 121 PHE cc_start: 0.7821 (m-80) cc_final: 0.7190 (m-10) REVERT: E 129 ILE cc_start: 0.8825 (mt) cc_final: 0.8614 (mt) REVERT: E 165 TYR cc_start: 0.7948 (m-80) cc_final: 0.7388 (m-80) REVERT: E 166 ASN cc_start: 0.6860 (m110) cc_final: 0.6623 (m110) REVERT: E 190 MET cc_start: 0.5500 (mtm) cc_final: 0.5106 (mtm) REVERT: E 329 THR cc_start: 0.4966 (t) cc_final: 0.4644 (m) REVERT: E 378 TYR cc_start: 0.7112 (m-80) cc_final: 0.6386 (m-80) REVERT: E 398 PHE cc_start: 0.7839 (p90) cc_final: 0.7441 (p90) REVERT: E 400 TYR cc_start: 0.7803 (t80) cc_final: 0.7466 (t80) REVERT: E 455 THR cc_start: 0.4434 (p) cc_final: 0.4178 (p) REVERT: E 528 TRP cc_start: 0.6690 (m100) cc_final: 0.6445 (m100) REVERT: E 561 TYR cc_start: 0.8276 (m-80) cc_final: 0.7495 (m-80) REVERT: E 565 ASN cc_start: 0.8400 (m-40) cc_final: 0.7426 (t0) REVERT: I 47 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.6977 (t0) REVERT: I 52 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7484 (ttmm) REVERT: I 53 PHE cc_start: 0.7891 (m-80) cc_final: 0.7650 (m-80) REVERT: I 87 MET cc_start: 0.6515 (ttp) cc_final: 0.6001 (ttp) REVERT: I 115 ASN cc_start: 0.7847 (t0) cc_final: 0.7150 (t0) REVERT: I 133 MET cc_start: 0.7358 (mmt) cc_final: 0.7094 (mmt) REVERT: I 144 GLU cc_start: 0.7404 (pt0) cc_final: 0.7195 (pt0) REVERT: I 174 MET cc_start: 0.7089 (mtp) cc_final: 0.6645 (mtp) REVERT: I 201 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7836 (ttpt) REVERT: I 268 PHE cc_start: 0.7603 (m-80) cc_final: 0.7178 (m-80) REVERT: I 331 MET cc_start: 0.7293 (ttm) cc_final: 0.7037 (ttm) REVERT: I 396 GLU cc_start: 0.7452 (tt0) cc_final: 0.7027 (tt0) REVERT: I 427 ASP cc_start: 0.8405 (m-30) cc_final: 0.8203 (m-30) REVERT: I 444 TYR cc_start: 0.7581 (p90) cc_final: 0.7288 (p90) REVERT: I 535 PHE cc_start: 0.8432 (m-80) cc_final: 0.7961 (m-80) REVERT: I 539 LEU cc_start: 0.8573 (mt) cc_final: 0.8224 (mp) REVERT: I 544 THR cc_start: 0.7944 (p) cc_final: 0.7538 (p) REVERT: I 546 ASN cc_start: 0.7934 (p0) cc_final: 0.7636 (p0) REVERT: I 549 GLN cc_start: 0.7986 (tt0) cc_final: 0.7588 (tt0) REVERT: I 573 TYR cc_start: 0.8261 (p90) cc_final: 0.7779 (p90) REVERT: I 575 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7669 (mtmm) REVERT: I 576 SER cc_start: 0.7906 (t) cc_final: 0.7608 (p) REVERT: F 52 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7610 (ttmm) REVERT: F 60 GLU cc_start: 0.7472 (tt0) cc_final: 0.7171 (tt0) REVERT: F 101 ILE cc_start: 0.8333 (mm) cc_final: 0.8031 (mm) REVERT: F 143 GLN cc_start: 0.7482 (mp10) cc_final: 0.6810 (mp10) REVERT: F 180 ASN cc_start: 0.7558 (t0) cc_final: 0.7188 (t0) REVERT: F 213 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7468 (tm-30) REVERT: F 244 TYR cc_start: 0.7188 (m-80) cc_final: 0.6938 (m-80) REVERT: F 248 ASN cc_start: 0.7106 (m110) cc_final: 0.6808 (t0) REVERT: F 266 PHE cc_start: 0.7873 (t80) cc_final: 0.7668 (t80) REVERT: F 271 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7966 (mtpp) REVERT: F 280 GLN cc_start: 0.7781 (mm110) cc_final: 0.7480 (mm-40) REVERT: F 282 ASN cc_start: 0.7957 (m110) cc_final: 0.7719 (m-40) REVERT: F 327 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6742 (mm-30) REVERT: F 335 GLU cc_start: 0.6919 (tt0) cc_final: 0.6709 (tt0) REVERT: F 405 ASP cc_start: 0.6048 (m-30) cc_final: 0.5679 (m-30) REVERT: F 475 ASP cc_start: 0.7242 (t0) cc_final: 0.6675 (t0) REVERT: F 484 VAL cc_start: 0.8368 (m) cc_final: 0.7956 (p) REVERT: F 485 ASN cc_start: 0.7710 (p0) cc_final: 0.7247 (p0) REVERT: F 551 MET cc_start: 0.6550 (ttt) cc_final: 0.6031 (ttt) REVERT: F 569 MET cc_start: 0.5771 (mmm) cc_final: 0.5514 (mmm) REVERT: C 174 MET cc_start: 0.7143 (mtp) cc_final: 0.6498 (mtp) REVERT: C 236 THR cc_start: 0.4801 (OUTLIER) cc_final: 0.4198 (p) outliers start: 96 outliers final: 68 residues processed: 805 average time/residue: 0.3934 time to fit residues: 487.1416 Evaluate side-chains 842 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 763 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 179 SER Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 230 THR 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 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 478 LEU 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 G residue 570 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 THR 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 354 LYS 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 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 92 VAL Chi-restraints excluded: chain B residue 101 ILE 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 380 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 538 LYS 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 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 558 GLN Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 574 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 317 THR Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 336 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 28 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 174 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 492 ASN G 497 GLN A 115 ASN A 546 ASN B 508 ASN B 558 GLN I 383 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 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 = 0.4441 r_free = 0.4441 target = 0.216134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158348 restraints weight = 41193.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164245 restraints weight = 17660.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.168058 restraints weight = 10288.851| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 26524 Z= 0.269 Angle : 0.636 11.737 36261 Z= 0.324 Chirality : 0.045 0.175 3973 Planarity : 0.005 0.056 4735 Dihedral : 5.813 62.232 3509 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.99 % Allowed : 14.84 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2990 helix: -0.49 (0.50), residues: 100 sheet: -0.66 (0.18), residues: 778 loop : -0.41 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 545 HIS 0.005 0.001 HIS F 277 PHE 0.032 0.002 PHE B 398 TYR 0.031 0.002 TYR B 464 ARG 0.023 0.001 ARG I 377 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 329) hydrogen bonds : angle 5.85684 ( 615) SS BOND : bond 0.00210 ( 5) SS BOND : angle 4.36170 ( 10) covalent geometry : bond 0.00574 (26519) covalent geometry : angle 0.63244 (36251) *********************** 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 876 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 767 time to evaluate : 2.503 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: symmetry clash REVERT: G 47 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8118 (t0) REVERT: G 59 VAL cc_start: 0.8881 (t) cc_final: 0.8513 (m) REVERT: G 80 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7336 (mtm-85) REVERT: G 125 ASP cc_start: 0.6533 (m-30) cc_final: 0.6261 (m-30) REVERT: G 135 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: G 151 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7740 (mtpp) REVERT: G 217 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7353 (p) REVERT: G 248 ASN cc_start: 0.7578 (t0) cc_final: 0.7314 (t0) REVERT: G 271 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7698 (mtpp) REVERT: G 319 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.1968 (ptm) REVERT: G 380 PHE cc_start: 0.8053 (p90) cc_final: 0.7601 (p90) REVERT: G 382 ARG cc_start: 0.5815 (mtm180) cc_final: 0.5252 (mtm180) REVERT: G 390 THR cc_start: 0.8623 (t) cc_final: 0.8263 (p) REVERT: G 471 ASP cc_start: 0.7533 (t0) cc_final: 0.7123 (t0) REVERT: G 473 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6599 (tm-30) REVERT: G 485 ASN cc_start: 0.7762 (p0) cc_final: 0.7059 (p0) REVERT: G 536 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8036 (ttpp) REVERT: G 559 PHE cc_start: 0.8016 (m-80) cc_final: 0.7351 (m-80) REVERT: G 560 ASN cc_start: 0.7706 (m-40) cc_final: 0.7341 (m-40) REVERT: G 581 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7958 (ttp-110) REVERT: A 99 ASP cc_start: 0.6950 (t0) cc_final: 0.6384 (t70) REVERT: A 100 ASP cc_start: 0.6787 (m-30) cc_final: 0.6133 (m-30) REVERT: A 115 ASN cc_start: 0.8010 (t0) cc_final: 0.7657 (t0) REVERT: A 183 MET cc_start: 0.7172 (mmm) cc_final: 0.6662 (mmm) REVERT: A 197 PHE cc_start: 0.8058 (m-10) cc_final: 0.7594 (m-10) REVERT: A 211 TYR cc_start: 0.7377 (m-80) cc_final: 0.7051 (m-80) REVERT: A 218 LEU cc_start: 0.8306 (tp) cc_final: 0.7854 (tt) REVERT: A 265 THR cc_start: 0.7831 (p) cc_final: 0.7563 (p) REVERT: A 344 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 346 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6955 (mp0) REVERT: A 350 GLN cc_start: 0.7397 (mt0) cc_final: 0.7183 (mt0) REVERT: A 382 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6826 (mtm110) REVERT: A 387 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7752 (ttpt) REVERT: A 403 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7191 (m-70) REVERT: A 433 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7961 (p) REVERT: A 439 LYS cc_start: 0.8176 (mptt) cc_final: 0.7930 (mptt) REVERT: A 475 ASP cc_start: 0.7492 (t70) cc_final: 0.6880 (t0) REVERT: A 530 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7145 (ttpp) REVERT: A 574 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6381 (mm-30) REVERT: A 575 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7592 (mtpt) REVERT: B 80 ARG cc_start: 0.7206 (mtt-85) cc_final: 0.6508 (mtt-85) REVERT: B 101 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7935 (pt) REVERT: B 125 ASP cc_start: 0.8376 (m-30) cc_final: 0.7893 (m-30) REVERT: B 142 GLU cc_start: 0.7435 (pt0) cc_final: 0.7060 (pt0) REVERT: B 143 GLN cc_start: 0.7628 (mt0) cc_final: 0.7230 (mt0) REVERT: B 145 ILE cc_start: 0.8149 (mt) cc_final: 0.7776 (mm) REVERT: B 150 LEU cc_start: 0.8157 (tp) cc_final: 0.7876 (tp) REVERT: B 151 LYS cc_start: 0.7983 (mttm) cc_final: 0.7767 (mttm) REVERT: B 174 MET cc_start: 0.6795 (mtp) cc_final: 0.6438 (mtp) REVERT: B 183 MET cc_start: 0.6895 (mmm) cc_final: 0.6353 (mmm) REVERT: B 190 MET cc_start: 0.7847 (tpp) cc_final: 0.7393 (tpp) REVERT: B 198 TYR cc_start: 0.7156 (m-80) cc_final: 0.6556 (m-80) REVERT: B 237 ASP cc_start: 0.7325 (m-30) cc_final: 0.6716 (m-30) REVERT: B 247 GLU cc_start: 0.6269 (mp0) cc_final: 0.6032 (mp0) REVERT: B 266 PHE cc_start: 0.7290 (t80) cc_final: 0.6881 (t80) REVERT: B 377 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6157 (mmm-85) REVERT: B 382 ARG cc_start: 0.7619 (mmt90) cc_final: 0.7055 (mmp80) REVERT: B 383 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7066 (tm-30) REVERT: B 469 ILE cc_start: 0.7975 (mt) cc_final: 0.7540 (mp) REVERT: B 470 TRP cc_start: 0.8123 (p90) cc_final: 0.7917 (p90) REVERT: B 501 LYS cc_start: 0.7854 (tttt) cc_final: 0.7301 (tttt) REVERT: B 509 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6248 (mm-30) REVERT: B 527 PHE cc_start: 0.6889 (p90) cc_final: 0.6475 (p90) REVERT: B 530 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: B 532 LYS cc_start: 0.7256 (tttm) cc_final: 0.6896 (tttm) REVERT: B 533 LEU cc_start: 0.8012 (tp) cc_final: 0.7617 (tp) REVERT: B 551 MET cc_start: 0.5935 (mmt) cc_final: 0.5430 (mmt) REVERT: E 45 PHE cc_start: 0.7433 (t80) cc_final: 0.6837 (t80) REVERT: E 121 PHE cc_start: 0.7757 (m-80) cc_final: 0.7095 (m-10) REVERT: E 166 ASN cc_start: 0.6874 (m110) cc_final: 0.6563 (m110) REVERT: E 190 MET cc_start: 0.5641 (mtm) cc_final: 0.5204 (mtm) REVERT: E 329 THR cc_start: 0.4933 (t) cc_final: 0.4613 (m) REVERT: E 378 TYR cc_start: 0.7207 (m-80) cc_final: 0.6447 (m-80) REVERT: E 398 PHE cc_start: 0.7975 (p90) cc_final: 0.7481 (p90) REVERT: E 400 TYR cc_start: 0.7826 (t80) cc_final: 0.7442 (t80) REVERT: E 455 THR cc_start: 0.4215 (p) cc_final: 0.3662 (t) REVERT: E 527 PHE cc_start: 0.7237 (p90) cc_final: 0.6833 (p90) REVERT: E 528 TRP cc_start: 0.6639 (m100) cc_final: 0.6396 (m100) REVERT: E 561 TYR cc_start: 0.8295 (m-80) cc_final: 0.7655 (m-80) REVERT: E 565 ASN cc_start: 0.8431 (m-40) cc_final: 0.7317 (t0) REVERT: I 47 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7277 (t0) REVERT: I 52 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7504 (ttmm) REVERT: I 87 MET cc_start: 0.6740 (ttp) cc_final: 0.6304 (ttp) REVERT: I 115 ASN cc_start: 0.7770 (t0) cc_final: 0.7111 (t0) REVERT: I 144 GLU cc_start: 0.7339 (pt0) cc_final: 0.7125 (pt0) REVERT: I 174 MET cc_start: 0.6978 (mtp) cc_final: 0.6564 (mtp) REVERT: I 201 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7900 (ttpt) REVERT: I 268 PHE cc_start: 0.7560 (m-80) cc_final: 0.7161 (m-80) REVERT: I 331 MET cc_start: 0.7263 (ttm) cc_final: 0.7005 (ttm) REVERT: I 444 TYR cc_start: 0.7928 (p90) cc_final: 0.7538 (p90) REVERT: I 535 PHE cc_start: 0.8418 (m-80) cc_final: 0.7929 (m-80) REVERT: I 544 THR cc_start: 0.8008 (p) cc_final: 0.7607 (p) REVERT: I 546 ASN cc_start: 0.7925 (p0) cc_final: 0.7609 (p0) REVERT: I 549 GLN cc_start: 0.8033 (tt0) cc_final: 0.7609 (tt0) REVERT: I 550 GLN cc_start: 0.7754 (mm110) cc_final: 0.7290 (mm-40) REVERT: I 570 LYS cc_start: 0.7497 (ptpt) cc_final: 0.7166 (ptpt) REVERT: I 573 TYR cc_start: 0.8229 (p90) cc_final: 0.7751 (p90) REVERT: I 575 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7651 (mtmm) REVERT: I 576 SER cc_start: 0.7963 (t) cc_final: 0.7610 (p) REVERT: F 52 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7555 (ttmm) REVERT: F 60 GLU cc_start: 0.7488 (tt0) cc_final: 0.7179 (tt0) REVERT: F 101 ILE cc_start: 0.8370 (mm) cc_final: 0.8101 (mm) REVERT: F 143 GLN cc_start: 0.7533 (mp10) cc_final: 0.7176 (mp10) REVERT: F 180 ASN cc_start: 0.7516 (t0) cc_final: 0.7154 (t0) REVERT: F 213 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7483 (tm-30) REVERT: F 245 THR cc_start: 0.7846 (t) cc_final: 0.7593 (p) REVERT: F 248 ASN cc_start: 0.7133 (m110) cc_final: 0.6818 (t0) REVERT: F 271 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7995 (mtpp) REVERT: F 276 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7359 (m) REVERT: F 280 GLN cc_start: 0.7830 (mm110) cc_final: 0.7502 (mm-40) REVERT: F 327 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6840 (mm-30) REVERT: F 330 ILE cc_start: 0.8764 (tt) cc_final: 0.8325 (tt) REVERT: F 405 ASP cc_start: 0.6010 (m-30) cc_final: 0.5644 (m-30) REVERT: F 425 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8179 (p) REVERT: F 475 ASP cc_start: 0.7238 (t0) cc_final: 0.6680 (t0) REVERT: F 484 VAL cc_start: 0.8410 (m) cc_final: 0.7988 (p) REVERT: F 551 MET cc_start: 0.6651 (ttt) cc_final: 0.6017 (ttt) REVERT: F 569 MET cc_start: 0.5754 (mmm) cc_final: 0.5511 (mmm) REVERT: C 174 MET cc_start: 0.7152 (mtp) cc_final: 0.6532 (mtp) outliers start: 109 outliers final: 74 residues processed: 804 average time/residue: 0.4226 time to fit residues: 525.4659 Evaluate side-chains 840 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 753 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 179 SER Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 217 THR 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 331 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 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 570 LYS 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 342 TYR 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 92 VAL Chi-restraints excluded: chain B residue 101 ILE 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 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 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 60 GLU 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 525 SER 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 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 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 317 THR Chi-restraints excluded: chain F residue 331 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 216 optimal weight: 0.6980 chunk 297 optimal weight: 0.8980 chunk 313 optimal weight: 0.0170 chunk 64 optimal weight: 10.0000 chunk 287 optimal weight: 0.0970 chunk 226 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN G 497 GLN A 143 GLN A 483 HIS B 386 GLN B 508 ASN B 558 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.222782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.167663 restraints weight = 41015.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173502 restraints weight = 17764.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.177393 restraints weight = 10318.059| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26524 Z= 0.103 Angle : 0.568 8.600 36261 Z= 0.285 Chirality : 0.041 0.167 3973 Planarity : 0.005 0.057 4735 Dihedral : 5.319 62.180 3509 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 16.81 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2990 helix: -0.53 (0.49), residues: 105 sheet: -0.49 (0.19), residues: 755 loop : -0.30 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 545 HIS 0.005 0.001 HIS F 277 PHE 0.027 0.001 PHE B 398 TYR 0.033 0.001 TYR B 464 ARG 0.010 0.001 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 329) hydrogen bonds : angle 5.72300 ( 615) SS BOND : bond 0.00201 ( 5) SS BOND : angle 2.79665 ( 10) covalent geometry : bond 0.00237 (26519) covalent geometry : angle 0.56581 (36251) *********************** 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 852 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 773 time to evaluate : 2.478 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 47 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7960 (t0) REVERT: G 59 VAL cc_start: 0.8800 (t) cc_final: 0.8492 (m) REVERT: G 80 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: G 90 THR cc_start: 0.8380 (t) cc_final: 0.8173 (t) REVERT: G 125 ASP cc_start: 0.6449 (m-30) cc_final: 0.6206 (m-30) REVERT: G 135 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: G 151 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7676 (mtpp) REVERT: G 211 TYR cc_start: 0.8231 (m-80) cc_final: 0.7639 (m-80) REVERT: G 248 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7235 (t0) REVERT: G 271 LYS cc_start: 0.7882 (mtpp) cc_final: 0.7662 (mtpp) REVERT: G 319 MET cc_start: 0.2053 (OUTLIER) cc_final: 0.1701 (ptm) REVERT: G 338 TYR cc_start: 0.8727 (p90) cc_final: 0.8465 (p90) REVERT: G 350 GLN cc_start: 0.7183 (mt0) cc_final: 0.6831 (mt0) REVERT: G 380 PHE cc_start: 0.7763 (p90) cc_final: 0.7333 (p90) REVERT: G 382 ARG cc_start: 0.5669 (mtm180) cc_final: 0.5030 (mtm180) REVERT: G 390 THR cc_start: 0.8591 (t) cc_final: 0.8220 (p) REVERT: G 471 ASP cc_start: 0.7514 (t0) cc_final: 0.7094 (t0) REVERT: G 473 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6532 (tm-30) REVERT: G 536 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8056 (ttpp) REVERT: G 560 ASN cc_start: 0.7768 (m-40) cc_final: 0.7388 (m-40) REVERT: G 561 TYR cc_start: 0.8484 (m-80) cc_final: 0.8219 (m-80) REVERT: G 581 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7909 (ttp-110) REVERT: A 47 ASN cc_start: 0.7950 (t160) cc_final: 0.7623 (t160) REVERT: A 66 SER cc_start: 0.7691 (m) cc_final: 0.7255 (m) REVERT: A 98 LEU cc_start: 0.7578 (mt) cc_final: 0.6948 (tp) REVERT: A 99 ASP cc_start: 0.6931 (t0) cc_final: 0.6463 (t70) REVERT: A 100 ASP cc_start: 0.6717 (m-30) cc_final: 0.6204 (m-30) REVERT: A 115 ASN cc_start: 0.7951 (t0) cc_final: 0.7720 (t0) REVERT: A 183 MET cc_start: 0.7043 (mmm) cc_final: 0.6539 (mmm) REVERT: A 218 LEU cc_start: 0.8268 (tp) cc_final: 0.7799 (tt) REVERT: A 265 THR cc_start: 0.7526 (p) cc_final: 0.7269 (p) REVERT: A 344 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7788 (p) REVERT: A 350 GLN cc_start: 0.7430 (mt0) cc_final: 0.7145 (mt0) REVERT: A 382 ARG cc_start: 0.7073 (mtm110) cc_final: 0.6674 (mtm110) REVERT: A 387 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7626 (ttpt) REVERT: A 397 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7831 (mtt-85) REVERT: A 433 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7952 (p) REVERT: A 439 LYS cc_start: 0.8100 (mptt) cc_final: 0.7840 (mptt) REVERT: A 475 ASP cc_start: 0.7381 (t70) cc_final: 0.6757 (t0) REVERT: A 530 LYS cc_start: 0.7138 (ttmt) cc_final: 0.6780 (ttpp) REVERT: A 575 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7569 (mtpt) REVERT: B 80 ARG cc_start: 0.7217 (mtt-85) cc_final: 0.6496 (mtt-85) REVERT: B 101 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7918 (pt) REVERT: B 125 ASP cc_start: 0.8233 (m-30) cc_final: 0.7816 (m-30) REVERT: B 142 GLU cc_start: 0.7404 (pt0) cc_final: 0.6913 (pt0) REVERT: B 143 GLN cc_start: 0.7626 (mt0) cc_final: 0.7279 (mt0) REVERT: B 145 ILE cc_start: 0.8085 (mt) cc_final: 0.7733 (mm) REVERT: B 174 MET cc_start: 0.6764 (mtp) cc_final: 0.6450 (mtp) REVERT: B 178 ASP cc_start: 0.5959 (t0) cc_final: 0.5668 (t0) REVERT: B 183 MET cc_start: 0.6885 (mmm) cc_final: 0.6493 (mmm) REVERT: B 190 MET cc_start: 0.7817 (tpp) cc_final: 0.7380 (tpp) REVERT: B 198 TYR cc_start: 0.7078 (m-80) cc_final: 0.6580 (m-10) REVERT: B 237 ASP cc_start: 0.7295 (m-30) cc_final: 0.6616 (m-30) REVERT: B 265 THR cc_start: 0.7470 (t) cc_final: 0.7206 (t) REVERT: B 266 PHE cc_start: 0.7323 (t80) cc_final: 0.7022 (t80) REVERT: B 354 LYS cc_start: 0.7537 (mmtp) cc_final: 0.6941 (mmtp) REVERT: B 377 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6134 (mmm-85) REVERT: B 382 ARG cc_start: 0.7595 (mmt90) cc_final: 0.7192 (mmp80) REVERT: B 383 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7462 (tm-30) REVERT: B 469 ILE cc_start: 0.7981 (mt) cc_final: 0.7702 (mp) REVERT: B 501 LYS cc_start: 0.7938 (tttt) cc_final: 0.7444 (tttt) REVERT: B 509 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6247 (mm-30) REVERT: B 527 PHE cc_start: 0.6722 (p90) cc_final: 0.6373 (p90) REVERT: B 530 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: B 533 LEU cc_start: 0.8010 (tp) cc_final: 0.7621 (tp) REVERT: B 536 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7657 (ttpp) REVERT: B 551 MET cc_start: 0.5660 (mmt) cc_final: 0.5114 (mmt) REVERT: E 45 PHE cc_start: 0.7401 (t80) cc_final: 0.6796 (t80) REVERT: E 121 PHE cc_start: 0.7693 (m-80) cc_final: 0.7104 (m-10) REVERT: E 166 ASN cc_start: 0.6627 (m110) cc_final: 0.6378 (m110) REVERT: E 190 MET cc_start: 0.5591 (mtm) cc_final: 0.5146 (mtm) REVERT: E 378 TYR cc_start: 0.7127 (m-80) cc_final: 0.6406 (m-80) REVERT: E 398 PHE cc_start: 0.7875 (p90) cc_final: 0.7454 (p90) REVERT: E 400 TYR cc_start: 0.7806 (t80) cc_final: 0.7532 (t80) REVERT: E 455 THR cc_start: 0.4378 (p) cc_final: 0.4110 (p) REVERT: E 527 PHE cc_start: 0.7245 (p90) cc_final: 0.6819 (p90) REVERT: E 528 TRP cc_start: 0.6438 (m100) cc_final: 0.6220 (m100) REVERT: E 561 TYR cc_start: 0.8277 (m-80) cc_final: 0.7608 (m-80) REVERT: E 565 ASN cc_start: 0.8415 (m-40) cc_final: 0.7281 (t0) REVERT: E 566 ILE cc_start: 0.8316 (pt) cc_final: 0.8002 (pt) REVERT: I 47 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.6980 (t0) REVERT: I 52 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7536 (ttmm) REVERT: I 87 MET cc_start: 0.6829 (ttp) cc_final: 0.6353 (ttp) REVERT: I 115 ASN cc_start: 0.7645 (t0) cc_final: 0.7232 (t0) REVERT: I 174 MET cc_start: 0.7097 (mtp) cc_final: 0.6645 (mtp) REVERT: I 201 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7843 (ttpt) REVERT: I 268 PHE cc_start: 0.7553 (m-80) cc_final: 0.7001 (m-80) REVERT: I 319 MET cc_start: 0.5539 (tpp) cc_final: 0.4498 (tpp) REVERT: I 331 MET cc_start: 0.7197 (ttm) cc_final: 0.6957 (ttm) REVERT: I 444 TYR cc_start: 0.7926 (p90) cc_final: 0.7501 (p90) REVERT: I 468 GLN cc_start: 0.7196 (mm110) cc_final: 0.6901 (mm110) REVERT: I 538 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7836 (ttmm) REVERT: I 544 THR cc_start: 0.7969 (p) cc_final: 0.7587 (p) REVERT: I 546 ASN cc_start: 0.8014 (p0) cc_final: 0.7721 (p0) REVERT: I 550 GLN cc_start: 0.7751 (mm110) cc_final: 0.7288 (mm110) REVERT: I 573 TYR cc_start: 0.8311 (p90) cc_final: 0.7885 (p90) REVERT: I 575 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7647 (mtmm) REVERT: F 52 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7446 (ttmm) REVERT: F 180 ASN cc_start: 0.7518 (t0) cc_final: 0.7109 (t0) REVERT: F 213 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7528 (tm-30) REVERT: F 248 ASN cc_start: 0.7116 (m110) cc_final: 0.6806 (t0) REVERT: F 271 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7924 (mtpp) REVERT: F 280 GLN cc_start: 0.7556 (mm110) cc_final: 0.7138 (mm-40) REVERT: F 283 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.7860 (tpt-90) REVERT: F 327 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6879 (mm-30) REVERT: F 425 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8124 (p) REVERT: F 475 ASP cc_start: 0.7211 (t0) cc_final: 0.6641 (t0) REVERT: F 484 VAL cc_start: 0.8271 (m) cc_final: 0.7899 (p) REVERT: F 485 ASN cc_start: 0.7770 (p0) cc_final: 0.7092 (p0) REVERT: F 551 MET cc_start: 0.6563 (ttt) cc_final: 0.6174 (ttt) REVERT: F 569 MET cc_start: 0.5684 (mmm) cc_final: 0.5455 (mmm) REVERT: C 174 MET cc_start: 0.7135 (mtp) cc_final: 0.6560 (mtp) REVERT: C 236 THR cc_start: 0.4969 (OUTLIER) cc_final: 0.4501 (p) REVERT: C 250 VAL cc_start: 0.7312 (t) cc_final: 0.7079 (t) outliers start: 79 outliers final: 53 residues processed: 802 average time/residue: 0.3977 time to fit residues: 487.6130 Evaluate side-chains 818 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 753 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 248 ASN Chi-restraints excluded: chain G residue 249 SER 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 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 548 ILE Chi-restraints excluded: chain G residue 570 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 203 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS 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 490 CYS Chi-restraints excluded: chain A residue 518 MET 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 194 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 377 ARG 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 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 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 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 276 THR Chi-restraints excluded: chain F residue 331 MET 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 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 269 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 153 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 263 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 ASN G 492 ASN A 48 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN B 558 GLN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.216733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.158588 restraints weight = 40826.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164468 restraints weight = 17956.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.168185 restraints weight = 10621.339| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 26524 Z= 0.299 Angle : 0.644 8.905 36261 Z= 0.329 Chirality : 0.046 0.182 3973 Planarity : 0.005 0.058 4735 Dihedral : 5.673 62.883 3509 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.33 % Allowed : 17.77 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2990 helix: -0.58 (0.50), residues: 101 sheet: -0.59 (0.19), residues: 776 loop : -0.42 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 545 HIS 0.007 0.001 HIS I 384 PHE 0.037 0.002 PHE F 353 TYR 0.038 0.002 TYR G 233 ARG 0.012 0.001 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 329) hydrogen bonds : angle 5.79323 ( 615) SS BOND : bond 0.00265 ( 5) SS BOND : angle 3.21905 ( 10) covalent geometry : bond 0.00642 (26519) covalent geometry : angle 0.64137 (36251) *********************** 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 847 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 756 time to evaluate : 2.829 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: 0.8370 (OUTLIER) cc_final: 0.8118 (t0) REVERT: G 59 VAL cc_start: 0.8798 (t) cc_final: 0.8442 (m) REVERT: G 125 ASP cc_start: 0.6568 (m-30) cc_final: 0.6279 (m-30) REVERT: G 135 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: G 151 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7712 (mtpp) REVERT: G 217 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7753 (p) REVERT: G 271 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7710 (mtpp) REVERT: G 319 MET cc_start: 0.2282 (OUTLIER) cc_final: 0.1948 (ptm) REVERT: G 380 PHE cc_start: 0.7977 (p90) cc_final: 0.7488 (p90) REVERT: G 382 ARG cc_start: 0.5861 (mtm180) cc_final: 0.5288 (mtm180) REVERT: G 471 ASP cc_start: 0.7497 (t0) cc_final: 0.7104 (t0) REVERT: G 473 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6606 (tm-30) REVERT: G 485 ASN cc_start: 0.7795 (p0) cc_final: 0.7093 (p0) REVERT: G 536 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8000 (ttpp) REVERT: G 540 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7531 (ttp-170) REVERT: G 560 ASN cc_start: 0.7758 (m-40) cc_final: 0.7382 (m-40) REVERT: A 47 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7746 (t160) REVERT: A 98 LEU cc_start: 0.7753 (mt) cc_final: 0.7028 (tp) REVERT: A 99 ASP cc_start: 0.6987 (t70) cc_final: 0.6571 (t70) REVERT: A 100 ASP cc_start: 0.6918 (m-30) cc_final: 0.6337 (m-30) REVERT: A 115 ASN cc_start: 0.8140 (t0) cc_final: 0.7724 (t0) REVERT: A 174 MET cc_start: 0.7468 (mtp) cc_final: 0.6933 (mtp) REVERT: A 183 MET cc_start: 0.7206 (mmm) cc_final: 0.6739 (mmm) REVERT: A 211 TYR cc_start: 0.7409 (m-80) cc_final: 0.7111 (m-10) REVERT: A 218 LEU cc_start: 0.8329 (tp) cc_final: 0.7829 (tt) REVERT: A 265 THR cc_start: 0.7755 (p) cc_final: 0.7450 (p) REVERT: A 344 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7582 (p) REVERT: A 382 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6863 (mtm110) REVERT: A 387 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7597 (ttpt) REVERT: A 403 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7148 (m-70) REVERT: A 427 ASP cc_start: 0.7323 (p0) cc_final: 0.7094 (p0) REVERT: A 433 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 475 ASP cc_start: 0.7529 (t70) cc_final: 0.6891 (t0) REVERT: A 530 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7105 (ttpp) REVERT: A 569 MET cc_start: 0.5722 (mmm) cc_final: 0.5455 (mmm) REVERT: A 574 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6372 (mm-30) REVERT: A 575 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7660 (mtpt) REVERT: B 80 ARG cc_start: 0.7204 (mtt-85) cc_final: 0.6464 (mtt-85) REVERT: B 101 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7937 (pt) REVERT: B 117 TRP cc_start: 0.7064 (m100) cc_final: 0.6288 (m100) REVERT: B 125 ASP cc_start: 0.8313 (m-30) cc_final: 0.7890 (m-30) REVERT: B 142 GLU cc_start: 0.7571 (pt0) cc_final: 0.7130 (pt0) REVERT: B 143 GLN cc_start: 0.7627 (mt0) cc_final: 0.7321 (mt0) REVERT: B 145 ILE cc_start: 0.8075 (mt) cc_final: 0.7790 (mm) REVERT: B 151 LYS cc_start: 0.7869 (mttm) cc_final: 0.7630 (mttm) REVERT: B 174 MET cc_start: 0.6836 (mtp) cc_final: 0.6504 (mtp) REVERT: B 183 MET cc_start: 0.6942 (mmm) cc_final: 0.6396 (mmm) REVERT: B 190 MET cc_start: 0.7841 (tpp) cc_final: 0.7404 (tpp) REVERT: B 198 TYR cc_start: 0.7213 (m-80) cc_final: 0.6746 (m-80) REVERT: B 237 ASP cc_start: 0.7378 (m-30) cc_final: 0.6833 (m-30) REVERT: B 265 THR cc_start: 0.7634 (t) cc_final: 0.7311 (t) REVERT: B 266 PHE cc_start: 0.7369 (t80) cc_final: 0.6909 (t80) REVERT: B 354 LYS cc_start: 0.7559 (mmtp) cc_final: 0.6944 (mmtp) REVERT: B 377 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6096 (tpp80) REVERT: B 380 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5685 (p90) REVERT: B 383 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7534 (tm-30) REVERT: B 501 LYS cc_start: 0.7923 (tttt) cc_final: 0.7425 (tttt) REVERT: B 527 PHE cc_start: 0.6983 (p90) cc_final: 0.6562 (p90) REVERT: B 530 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: B 532 LYS cc_start: 0.7379 (tttm) cc_final: 0.6931 (tttm) REVERT: B 533 LEU cc_start: 0.7963 (tp) cc_final: 0.7642 (tp) REVERT: B 536 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7634 (ttpp) REVERT: B 551 MET cc_start: 0.5728 (mmt) cc_final: 0.5148 (mmt) REVERT: E 45 PHE cc_start: 0.7537 (t80) cc_final: 0.6862 (t80) REVERT: E 121 PHE cc_start: 0.7726 (m-80) cc_final: 0.7115 (m-10) REVERT: E 166 ASN cc_start: 0.6883 (m110) cc_final: 0.6597 (m110) REVERT: E 190 MET cc_start: 0.5661 (mtm) cc_final: 0.5183 (mtm) REVERT: E 378 TYR cc_start: 0.7224 (m-80) cc_final: 0.6461 (m-80) REVERT: E 398 PHE cc_start: 0.7952 (p90) cc_final: 0.7463 (p90) REVERT: E 400 TYR cc_start: 0.7803 (t80) cc_final: 0.7426 (t80) REVERT: E 455 THR cc_start: 0.4482 (p) cc_final: 0.4244 (p) REVERT: E 527 PHE cc_start: 0.7426 (p90) cc_final: 0.6939 (p90) REVERT: E 528 TRP cc_start: 0.6684 (m100) cc_final: 0.6421 (m100) REVERT: E 561 TYR cc_start: 0.8306 (m-80) cc_final: 0.7675 (m-80) REVERT: E 565 ASN cc_start: 0.8423 (m-40) cc_final: 0.7217 (t0) REVERT: E 566 ILE cc_start: 0.8362 (pt) cc_final: 0.8045 (pt) REVERT: I 47 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7362 (t0) REVERT: I 52 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7472 (ttmm) REVERT: I 87 MET cc_start: 0.6920 (ttp) cc_final: 0.6468 (ttp) REVERT: I 115 ASN cc_start: 0.7704 (t0) cc_final: 0.7054 (t0) REVERT: I 174 MET cc_start: 0.7069 (mtp) cc_final: 0.6622 (mtp) REVERT: I 201 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7898 (ttpt) REVERT: I 268 PHE cc_start: 0.7597 (m-80) cc_final: 0.7237 (m-80) REVERT: I 319 MET cc_start: 0.5298 (tpp) cc_final: 0.4438 (tpp) REVERT: I 331 MET cc_start: 0.7202 (ttm) cc_final: 0.6972 (ttm) REVERT: I 383 GLN cc_start: 0.7680 (mt0) cc_final: 0.7360 (mt0) REVERT: I 444 TYR cc_start: 0.8001 (p90) cc_final: 0.7651 (p90) REVERT: I 535 PHE cc_start: 0.8480 (m-80) cc_final: 0.8021 (m-80) REVERT: I 538 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7798 (ttpp) REVERT: I 539 LEU cc_start: 0.8514 (mt) cc_final: 0.8248 (mp) REVERT: I 544 THR cc_start: 0.8002 (p) cc_final: 0.7587 (p) REVERT: I 546 ASN cc_start: 0.7927 (p0) cc_final: 0.7651 (p0) REVERT: I 550 GLN cc_start: 0.7780 (mm110) cc_final: 0.7260 (mm-40) REVERT: I 570 LYS cc_start: 0.7505 (ptpt) cc_final: 0.7176 (ptpt) REVERT: I 573 TYR cc_start: 0.8231 (p90) cc_final: 0.7755 (p90) REVERT: I 575 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7730 (mtmm) REVERT: F 52 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7585 (ttmm) REVERT: F 60 GLU cc_start: 0.7427 (tt0) cc_final: 0.7112 (tt0) REVERT: F 143 GLN cc_start: 0.7583 (mp10) cc_final: 0.6980 (mp10) REVERT: F 213 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7532 (tm-30) REVERT: F 245 THR cc_start: 0.7812 (t) cc_final: 0.7604 (p) REVERT: F 248 ASN cc_start: 0.7184 (m110) cc_final: 0.6838 (t0) REVERT: F 271 LYS cc_start: 0.8231 (mtpp) cc_final: 0.8003 (mtpp) REVERT: F 276 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7363 (m) REVERT: F 327 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7028 (mm-30) REVERT: F 350 GLN cc_start: 0.7678 (mp10) cc_final: 0.7305 (mp10) REVERT: F 425 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8124 (p) REVERT: F 475 ASP cc_start: 0.7242 (t0) cc_final: 0.6570 (t0) REVERT: F 484 VAL cc_start: 0.8393 (m) cc_final: 0.7992 (p) REVERT: F 485 ASN cc_start: 0.7788 (p0) cc_final: 0.7188 (p0) REVERT: F 551 MET cc_start: 0.6573 (ttt) cc_final: 0.6209 (ttt) REVERT: F 569 MET cc_start: 0.5704 (mmm) cc_final: 0.5427 (mmm) REVERT: C 174 MET cc_start: 0.7149 (mtp) cc_final: 0.6580 (mtp) REVERT: C 250 VAL cc_start: 0.7408 (t) cc_final: 0.7176 (t) outliers start: 91 outliers final: 59 residues processed: 786 average time/residue: 0.3986 time to fit residues: 480.0496 Evaluate side-chains 823 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 749 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 179 SER Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 217 THR 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 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 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 518 MET 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 62 THR Chi-restraints excluded: chain A residue 73 MET 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 457 LEU 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 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 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 E residue 47 ASN 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 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 558 GLN Chi-restraints excluded: chain I residue 571 ILE 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 276 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 331 MET 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 448 PHE Chi-restraints excluded: chain F residue 582 LYS 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 212 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 273 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 chunk 301 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 267 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 181 ASN A 48 GLN A 143 GLN A 350 GLN B 48 GLN B 558 GLN I 248 ASN ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 497 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 = 0.4470 r_free = 0.4470 target = 0.219757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.162211 restraints weight = 41003.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.168148 restraints weight = 18026.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171984 restraints weight = 10626.497| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26524 Z= 0.105 Angle : 0.567 10.904 36261 Z= 0.286 Chirality : 0.042 0.178 3973 Planarity : 0.005 0.051 4735 Dihedral : 5.208 62.670 3509 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.89 % Allowed : 18.79 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2990 helix: -0.65 (0.48), residues: 106 sheet: -0.44 (0.19), residues: 737 loop : -0.35 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 545 HIS 0.006 0.001 HIS F 277 PHE 0.031 0.002 PHE F 353 TYR 0.035 0.001 TYR B 464 ARG 0.010 0.001 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 329) hydrogen bonds : angle 5.69049 ( 615) SS BOND : bond 0.00199 ( 5) SS BOND : angle 4.22291 ( 10) covalent geometry : bond 0.00240 (26519) covalent geometry : angle 0.56247 (36251) *********************** 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 859 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 780 time to evaluate : 2.715 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: 0.8329 (OUTLIER) cc_final: 0.7957 (t0) REVERT: G 59 VAL cc_start: 0.8722 (t) cc_final: 0.8365 (m) REVERT: G 135 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: G 185 PHE cc_start: 0.8005 (t80) cc_final: 0.7711 (t80) REVERT: G 211 TYR cc_start: 0.8276 (m-80) cc_final: 0.7681 (m-80) REVERT: G 271 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7666 (mtpp) REVERT: G 319 MET cc_start: 0.2128 (OUTLIER) cc_final: 0.1814 (ptm) REVERT: G 338 TYR cc_start: 0.8733 (p90) cc_final: 0.8445 (p90) REVERT: G 350 GLN cc_start: 0.7197 (mt0) cc_final: 0.6812 (mt0) REVERT: G 380 PHE cc_start: 0.7811 (p90) cc_final: 0.7440 (p90) REVERT: G 382 ARG cc_start: 0.5705 (mtm180) cc_final: 0.5066 (mtm180) REVERT: G 471 ASP cc_start: 0.7502 (t0) cc_final: 0.7095 (t0) REVERT: G 473 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6560 (tm-30) REVERT: G 536 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8020 (ttpp) REVERT: G 540 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7486 (ttp80) REVERT: G 559 PHE cc_start: 0.7910 (m-80) cc_final: 0.7619 (m-80) REVERT: G 560 ASN cc_start: 0.7818 (m-40) cc_final: 0.7398 (m-40) REVERT: G 561 TYR cc_start: 0.8470 (m-80) cc_final: 0.8228 (m-80) REVERT: A 47 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7696 (t160) REVERT: A 62 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8039 (m) REVERT: A 66 SER cc_start: 0.7696 (m) cc_final: 0.7261 (m) REVERT: A 98 LEU cc_start: 0.7678 (mt) cc_final: 0.7049 (tp) REVERT: A 99 ASP cc_start: 0.6903 (t70) cc_final: 0.6489 (t70) REVERT: A 100 ASP cc_start: 0.6489 (m-30) cc_final: 0.6025 (m-30) REVERT: A 115 ASN cc_start: 0.8027 (t0) cc_final: 0.7623 (t0) REVERT: A 174 MET cc_start: 0.7375 (mtp) cc_final: 0.6950 (mtp) REVERT: A 183 MET cc_start: 0.7078 (mmm) cc_final: 0.6571 (mmm) REVERT: A 197 PHE cc_start: 0.8113 (m-10) cc_final: 0.7874 (m-80) REVERT: A 211 TYR cc_start: 0.7199 (m-80) cc_final: 0.6996 (m-10) REVERT: A 265 THR cc_start: 0.7395 (p) cc_final: 0.7157 (p) REVERT: A 344 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7863 (p) REVERT: A 382 ARG cc_start: 0.7091 (mtm110) cc_final: 0.6674 (mtm110) REVERT: A 387 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7525 (ttpt) REVERT: A 397 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7793 (mtt-85) REVERT: A 433 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7946 (p) REVERT: A 439 LYS cc_start: 0.8077 (mptt) cc_final: 0.7808 (mptt) REVERT: A 475 ASP cc_start: 0.7366 (t70) cc_final: 0.6731 (t0) REVERT: A 530 LYS cc_start: 0.7261 (ttmt) cc_final: 0.6838 (ttpp) REVERT: A 569 MET cc_start: 0.5667 (mmm) cc_final: 0.5408 (mmm) REVERT: A 574 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6252 (mm-30) REVERT: A 575 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7581 (mtpt) REVERT: B 80 ARG cc_start: 0.7170 (mtt-85) cc_final: 0.6447 (mtt-85) REVERT: B 101 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7895 (pt) REVERT: B 104 GLN cc_start: 0.7971 (pt0) cc_final: 0.7456 (pt0) REVERT: B 117 TRP cc_start: 0.6857 (m100) cc_final: 0.6241 (m100) REVERT: B 125 ASP cc_start: 0.8301 (m-30) cc_final: 0.7935 (m-30) REVERT: B 142 GLU cc_start: 0.7505 (pt0) cc_final: 0.7104 (pt0) REVERT: B 143 GLN cc_start: 0.7616 (mt0) cc_final: 0.7336 (mt0) REVERT: B 145 ILE cc_start: 0.8058 (mt) cc_final: 0.7857 (mm) REVERT: B 151 LYS cc_start: 0.7809 (mttm) cc_final: 0.7566 (mttm) REVERT: B 174 MET cc_start: 0.6803 (mtp) cc_final: 0.6434 (mtp) REVERT: B 183 MET cc_start: 0.6931 (mmm) cc_final: 0.6416 (mmm) REVERT: B 190 MET cc_start: 0.7764 (tpp) cc_final: 0.7349 (tpp) REVERT: B 197 PHE cc_start: 0.6946 (m-10) cc_final: 0.6288 (m-10) REVERT: B 198 TYR cc_start: 0.7163 (m-80) cc_final: 0.6599 (m-80) REVERT: B 237 ASP cc_start: 0.7319 (m-30) cc_final: 0.6651 (m-30) REVERT: B 265 THR cc_start: 0.7648 (t) cc_final: 0.7372 (t) REVERT: B 266 PHE cc_start: 0.7374 (t80) cc_final: 0.7013 (t80) REVERT: B 354 LYS cc_start: 0.7570 (mmtp) cc_final: 0.6924 (mmtp) REVERT: B 377 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6122 (tpp80) REVERT: B 380 PHE cc_start: 0.6382 (p90) cc_final: 0.5352 (p90) REVERT: B 382 ARG cc_start: 0.7797 (mmp80) cc_final: 0.7033 (mmt180) REVERT: B 383 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7248 (tm-30) REVERT: B 501 LYS cc_start: 0.7879 (tttt) cc_final: 0.7352 (tttt) REVERT: B 509 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6235 (mm-30) REVERT: B 527 PHE cc_start: 0.6860 (p90) cc_final: 0.6530 (p90) REVERT: B 530 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8078 (ttmt) REVERT: B 533 LEU cc_start: 0.7926 (tp) cc_final: 0.7642 (tp) REVERT: B 536 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7601 (ttpp) REVERT: B 551 MET cc_start: 0.5710 (mmt) cc_final: 0.5108 (mmt) REVERT: E 45 PHE cc_start: 0.7415 (t80) cc_final: 0.6724 (t80) REVERT: E 46 ASN cc_start: 0.7656 (t0) cc_final: 0.7231 (t0) REVERT: E 64 ASN cc_start: 0.7143 (p0) cc_final: 0.6896 (p0) REVERT: E 121 PHE cc_start: 0.7675 (m-80) cc_final: 0.6908 (m-10) REVERT: E 166 ASN cc_start: 0.6781 (m110) cc_final: 0.6509 (m110) REVERT: E 190 MET cc_start: 0.5805 (mtm) cc_final: 0.5349 (mtm) REVERT: E 197 PHE cc_start: 0.7702 (m-10) cc_final: 0.7458 (m-10) REVERT: E 378 TYR cc_start: 0.7189 (m-80) cc_final: 0.6436 (m-80) REVERT: E 398 PHE cc_start: 0.7897 (p90) cc_final: 0.7405 (p90) REVERT: E 400 TYR cc_start: 0.7862 (t80) cc_final: 0.7411 (t80) REVERT: E 527 PHE cc_start: 0.7355 (p90) cc_final: 0.6953 (p90) REVERT: E 528 TRP cc_start: 0.6584 (m100) cc_final: 0.6344 (m100) REVERT: E 529 TRP cc_start: 0.7759 (t60) cc_final: 0.7440 (t60) REVERT: E 535 PHE cc_start: 0.7611 (m-80) cc_final: 0.7185 (m-80) REVERT: E 559 PHE cc_start: 0.7121 (m-80) cc_final: 0.6889 (m-80) REVERT: E 560 ASN cc_start: 0.8142 (p0) cc_final: 0.7698 (p0) REVERT: E 561 TYR cc_start: 0.8336 (m-80) cc_final: 0.7639 (m-80) REVERT: E 565 ASN cc_start: 0.8384 (m-40) cc_final: 0.8157 (m-40) REVERT: I 47 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.6999 (t0) REVERT: I 52 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7443 (ttmm) REVERT: I 67 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7913 (mtt90) REVERT: I 73 MET cc_start: 0.6489 (ptt) cc_final: 0.6107 (ptt) REVERT: I 87 MET cc_start: 0.6831 (ttp) cc_final: 0.6392 (ttp) REVERT: I 115 ASN cc_start: 0.7653 (t0) cc_final: 0.7212 (t0) REVERT: I 174 MET cc_start: 0.7079 (mtp) cc_final: 0.6703 (mtp) REVERT: I 201 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7856 (ttpt) REVERT: I 268 PHE cc_start: 0.7515 (m-80) cc_final: 0.7162 (m-80) REVERT: I 319 MET cc_start: 0.5303 (tpp) cc_final: 0.4555 (tpp) REVERT: I 331 MET cc_start: 0.7208 (ttm) cc_final: 0.6969 (ttm) REVERT: I 383 GLN cc_start: 0.7589 (mt0) cc_final: 0.7340 (mt0) REVERT: I 444 TYR cc_start: 0.7958 (p90) cc_final: 0.7583 (p90) REVERT: I 468 GLN cc_start: 0.7305 (mm110) cc_final: 0.6998 (mm110) REVERT: I 535 PHE cc_start: 0.8460 (m-80) cc_final: 0.7988 (m-80) REVERT: I 538 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7868 (ttmm) REVERT: I 544 THR cc_start: 0.7969 (p) cc_final: 0.7625 (p) REVERT: I 546 ASN cc_start: 0.8032 (p0) cc_final: 0.7749 (p0) REVERT: I 550 GLN cc_start: 0.7709 (mm110) cc_final: 0.7210 (mm-40) REVERT: I 561 TYR cc_start: 0.7903 (m-80) cc_final: 0.7664 (m-80) REVERT: I 570 LYS cc_start: 0.7414 (ptpt) cc_final: 0.7051 (ptpt) REVERT: I 573 TYR cc_start: 0.8269 (p90) cc_final: 0.7858 (p90) REVERT: I 575 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7657 (mtmm) REVERT: F 52 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7461 (ttmm) REVERT: F 143 GLN cc_start: 0.7412 (mp10) cc_final: 0.7178 (mp10) REVERT: F 213 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7641 (tm-30) REVERT: F 248 ASN cc_start: 0.7193 (m110) cc_final: 0.6804 (t0) REVERT: F 271 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7929 (mtpp) REVERT: F 283 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7716 (tpt-90) REVERT: F 327 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6855 (mm-30) REVERT: F 425 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8083 (p) REVERT: F 450 THR cc_start: 0.8808 (p) cc_final: 0.8431 (t) REVERT: F 475 ASP cc_start: 0.7207 (t0) cc_final: 0.6516 (t0) REVERT: F 484 VAL cc_start: 0.8139 (m) cc_final: 0.7696 (p) REVERT: F 485 ASN cc_start: 0.7808 (p0) cc_final: 0.7538 (p0) REVERT: F 551 MET cc_start: 0.6455 (ttt) cc_final: 0.6072 (ttt) REVERT: F 569 MET cc_start: 0.5676 (mmm) cc_final: 0.5410 (mmm) REVERT: C 174 MET cc_start: 0.7160 (mtp) cc_final: 0.6602 (mtp) REVERT: C 236 THR cc_start: 0.4948 (OUTLIER) cc_final: 0.4506 (p) REVERT: C 250 VAL cc_start: 0.7333 (t) cc_final: 0.7108 (t) outliers start: 79 outliers final: 53 residues processed: 805 average time/residue: 0.4056 time to fit residues: 502.3878 Evaluate side-chains 820 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 754 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 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 442 ILE Chi-restraints excluded: chain G residue 447 ILE 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 A residue 47 ASN Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 140 SER 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 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 538 LYS 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 150 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 240 ASP 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 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 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 182 THR Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 331 MET 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 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 183 optimal weight: 40.0000 chunk 154 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 230 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 237 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 161 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 386 GLN G 468 GLN G 497 GLN G 505 ASN A 546 ASN F 497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.219330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.162814 restraints weight = 41420.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.168623 restraints weight = 17923.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172179 restraints weight = 10472.238| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26524 Z= 0.105 Angle : 0.559 11.637 36261 Z= 0.280 Chirality : 0.042 0.178 3973 Planarity : 0.005 0.066 4735 Dihedral : 4.967 61.177 3507 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.89 % Allowed : 19.19 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 2990 helix: -0.86 (0.45), residues: 107 sheet: -0.45 (0.19), residues: 762 loop : -0.32 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 545 HIS 0.006 0.001 HIS F 277 PHE 0.029 0.002 PHE F 353 TYR 0.032 0.001 TYR B 464 ARG 0.010 0.001 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 329) hydrogen bonds : angle 5.52413 ( 615) SS BOND : bond 0.00217 ( 5) SS BOND : angle 3.32528 ( 10) covalent geometry : bond 0.00243 (26519) covalent geometry : angle 0.55598 (36251) *********************** 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 847 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 768 time to evaluate : 2.715 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: 0.8317 (OUTLIER) cc_final: 0.7916 (t0) REVERT: G 59 VAL cc_start: 0.8711 (t) cc_final: 0.8347 (m) REVERT: G 99 ASP cc_start: 0.7561 (t0) cc_final: 0.7352 (t0) REVERT: G 100 ASP cc_start: 0.6258 (t70) cc_final: 0.5977 (t70) REVERT: G 130 VAL cc_start: 0.8460 (t) cc_final: 0.8231 (t) REVERT: G 135 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: G 151 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7670 (mtpp) REVERT: G 268 PHE cc_start: 0.8364 (m-80) cc_final: 0.7997 (m-80) REVERT: G 271 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7611 (mtpp) REVERT: G 319 MET cc_start: 0.2096 (OUTLIER) cc_final: 0.1631 (ptm) REVERT: G 348 SER cc_start: 0.8705 (t) cc_final: 0.8326 (p) REVERT: G 380 PHE cc_start: 0.7789 (p90) cc_final: 0.7424 (p90) REVERT: G 382 ARG cc_start: 0.5689 (mtm180) cc_final: 0.5047 (mtm180) REVERT: G 471 ASP cc_start: 0.7521 (t0) cc_final: 0.7215 (t0) REVERT: G 473 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6566 (tm-30) REVERT: G 492 ASN cc_start: 0.7808 (m-40) cc_final: 0.7595 (p0) REVERT: G 536 LYS cc_start: 0.8459 (ttpp) cc_final: 0.7994 (ttpp) REVERT: G 560 ASN cc_start: 0.7870 (m-40) cc_final: 0.7401 (m-40) REVERT: A 47 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7650 (t160) REVERT: A 62 THR cc_start: 0.8297 (m) cc_final: 0.8058 (m) REVERT: A 66 SER cc_start: 0.7720 (m) cc_final: 0.7269 (m) REVERT: A 92 VAL cc_start: 0.8296 (t) cc_final: 0.8027 (p) REVERT: A 98 LEU cc_start: 0.7650 (mt) cc_final: 0.7072 (tp) REVERT: A 99 ASP cc_start: 0.6964 (t70) cc_final: 0.6025 (t0) REVERT: A 100 ASP cc_start: 0.6571 (m-30) cc_final: 0.6240 (m-30) REVERT: A 115 ASN cc_start: 0.8085 (t0) cc_final: 0.7693 (t0) REVERT: A 174 MET cc_start: 0.7387 (mtp) cc_final: 0.6941 (mtp) REVERT: A 183 MET cc_start: 0.7061 (mmm) cc_final: 0.6535 (mmm) REVERT: A 218 LEU cc_start: 0.8287 (tp) cc_final: 0.7979 (tt) REVERT: A 344 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.7954 (p) REVERT: A 387 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7480 (ttpt) REVERT: A 433 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7960 (p) REVERT: A 475 ASP cc_start: 0.7381 (t70) cc_final: 0.6792 (t0) REVERT: A 530 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6852 (ttpp) REVERT: A 569 MET cc_start: 0.5694 (mmm) cc_final: 0.5440 (mmm) REVERT: A 574 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6152 (mm-30) REVERT: A 575 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7618 (mtpt) REVERT: B 80 ARG cc_start: 0.7162 (mtt-85) cc_final: 0.6459 (mtt-85) REVERT: B 101 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7943 (pt) REVERT: B 104 GLN cc_start: 0.7989 (pt0) cc_final: 0.7523 (pt0) REVERT: B 117 TRP cc_start: 0.6900 (m100) cc_final: 0.6309 (m100) REVERT: B 125 ASP cc_start: 0.8289 (m-30) cc_final: 0.7925 (m-30) REVERT: B 142 GLU cc_start: 0.7493 (pt0) cc_final: 0.7086 (pt0) REVERT: B 143 GLN cc_start: 0.7558 (mt0) cc_final: 0.7297 (mt0) REVERT: B 151 LYS cc_start: 0.7851 (mttm) cc_final: 0.7591 (mttm) REVERT: B 174 MET cc_start: 0.6820 (mtp) cc_final: 0.6487 (mtp) REVERT: B 178 ASP cc_start: 0.5897 (t0) cc_final: 0.5593 (t0) REVERT: B 183 MET cc_start: 0.6935 (mmm) cc_final: 0.6556 (mmm) REVERT: B 190 MET cc_start: 0.7773 (tpp) cc_final: 0.7348 (tpp) REVERT: B 198 TYR cc_start: 0.7210 (m-80) cc_final: 0.6741 (m-80) REVERT: B 237 ASP cc_start: 0.7299 (m-30) cc_final: 0.6880 (m-30) REVERT: B 265 THR cc_start: 0.7678 (t) cc_final: 0.7448 (t) REVERT: B 266 PHE cc_start: 0.7388 (t80) cc_final: 0.7011 (t80) REVERT: B 354 LYS cc_start: 0.7556 (mmtp) cc_final: 0.6887 (mmtp) REVERT: B 377 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6020 (mmm-85) REVERT: B 380 PHE cc_start: 0.6483 (p90) cc_final: 0.5411 (p90) REVERT: B 382 ARG cc_start: 0.7829 (mmp80) cc_final: 0.6820 (mmt180) REVERT: B 383 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7273 (tm-30) REVERT: B 501 LYS cc_start: 0.7926 (tttt) cc_final: 0.7439 (tttt) REVERT: B 527 PHE cc_start: 0.6878 (p90) cc_final: 0.6512 (p90) REVERT: B 530 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8040 (ttmt) REVERT: B 533 LEU cc_start: 0.7911 (tp) cc_final: 0.7661 (tp) REVERT: B 536 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7605 (ttpp) REVERT: B 551 MET cc_start: 0.5565 (mmt) cc_final: 0.5093 (mmt) REVERT: E 45 PHE cc_start: 0.7427 (t80) cc_final: 0.6720 (t80) REVERT: E 46 ASN cc_start: 0.7657 (t0) cc_final: 0.7312 (t0) REVERT: E 64 ASN cc_start: 0.7150 (p0) cc_final: 0.6839 (p0) REVERT: E 127 GLN cc_start: 0.7640 (tp40) cc_final: 0.7390 (tp-100) REVERT: E 166 ASN cc_start: 0.6861 (m110) cc_final: 0.6584 (m110) REVERT: E 190 MET cc_start: 0.5801 (mtm) cc_final: 0.5337 (mtm) REVERT: E 378 TYR cc_start: 0.7138 (m-80) cc_final: 0.6402 (m-80) REVERT: E 398 PHE cc_start: 0.7882 (p90) cc_final: 0.7396 (p90) REVERT: E 400 TYR cc_start: 0.7826 (t80) cc_final: 0.7397 (t80) REVERT: E 527 PHE cc_start: 0.7379 (p90) cc_final: 0.7022 (p90) REVERT: E 528 TRP cc_start: 0.6550 (m100) cc_final: 0.6341 (m100) REVERT: E 530 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7586 (tmtt) REVERT: E 535 PHE cc_start: 0.7571 (m-80) cc_final: 0.7235 (m-80) REVERT: E 560 ASN cc_start: 0.8136 (p0) cc_final: 0.7710 (p0) REVERT: E 561 TYR cc_start: 0.8310 (m-80) cc_final: 0.7629 (m-80) REVERT: E 565 ASN cc_start: 0.8392 (m-40) cc_final: 0.8187 (m-40) REVERT: I 47 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7088 (t0) REVERT: I 52 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7393 (ttmm) REVERT: I 87 MET cc_start: 0.6910 (ttp) cc_final: 0.6461 (ttp) REVERT: I 115 ASN cc_start: 0.7700 (t0) cc_final: 0.7232 (t0) REVERT: I 174 MET cc_start: 0.7114 (mtp) cc_final: 0.6721 (mtp) REVERT: I 201 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7908 (ttpt) REVERT: I 268 PHE cc_start: 0.7449 (m-80) cc_final: 0.7177 (m-80) REVERT: I 319 MET cc_start: 0.5527 (tpp) cc_final: 0.4814 (tpp) REVERT: I 331 MET cc_start: 0.7209 (ttm) cc_final: 0.6943 (ttm) REVERT: I 444 TYR cc_start: 0.8027 (p90) cc_final: 0.7686 (p90) REVERT: I 468 GLN cc_start: 0.7305 (mm110) cc_final: 0.7009 (mm110) REVERT: I 535 PHE cc_start: 0.8477 (m-80) cc_final: 0.8014 (m-80) REVERT: I 539 LEU cc_start: 0.8556 (mt) cc_final: 0.8299 (mp) REVERT: I 544 THR cc_start: 0.7985 (p) cc_final: 0.7617 (p) REVERT: I 546 ASN cc_start: 0.8023 (p0) cc_final: 0.7788 (p0) REVERT: I 550 GLN cc_start: 0.7675 (mm110) cc_final: 0.7174 (mm-40) REVERT: I 561 TYR cc_start: 0.7918 (m-80) cc_final: 0.7668 (m-80) REVERT: I 573 TYR cc_start: 0.8255 (p90) cc_final: 0.7833 (p90) REVERT: I 575 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7696 (mtmm) REVERT: F 52 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7463 (ttmm) REVERT: F 123 PRO cc_start: 0.8670 (Cg_exo) cc_final: 0.8456 (Cg_endo) REVERT: F 143 GLN cc_start: 0.7446 (mp10) cc_final: 0.7066 (mp10) REVERT: F 213 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 248 ASN cc_start: 0.7173 (m110) cc_final: 0.6757 (t0) REVERT: F 271 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7903 (mtpp) REVERT: F 327 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6889 (mm-30) REVERT: F 405 ASP cc_start: 0.5667 (m-30) cc_final: 0.5409 (m-30) REVERT: F 425 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8073 (p) REVERT: F 450 THR cc_start: 0.8792 (p) cc_final: 0.8402 (t) REVERT: F 475 ASP cc_start: 0.7211 (t0) cc_final: 0.6544 (t0) REVERT: F 485 ASN cc_start: 0.8031 (p0) cc_final: 0.7501 (p0) REVERT: F 551 MET cc_start: 0.6429 (ttt) cc_final: 0.6088 (ttt) REVERT: F 569 MET cc_start: 0.5667 (mmm) cc_final: 0.5385 (mmm) REVERT: C 174 MET cc_start: 0.7210 (mtp) cc_final: 0.6686 (mtp) REVERT: C 236 THR cc_start: 0.4966 (OUTLIER) cc_final: 0.4510 (p) REVERT: C 250 VAL cc_start: 0.7380 (t) cc_final: 0.7156 (t) outliers start: 79 outliers final: 52 residues processed: 794 average time/residue: 0.4089 time to fit residues: 503.6758 Evaluate side-chains 820 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 756 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 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 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU 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 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 538 LYS 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 204 ILE Chi-restraints excluded: chain B residue 240 ASP 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 47 ASN 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 399 THR 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 142 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 331 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 131 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 197 optimal weight: 40.0000 chunk 148 optimal weight: 50.0000 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 GLN G 497 GLN A 48 GLN A 143 GLN A 231 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.216987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159089 restraints weight = 41022.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.164801 restraints weight = 18019.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.168455 restraints weight = 10683.187| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 26524 Z= 0.268 Angle : 0.654 16.845 36261 Z= 0.330 Chirality : 0.045 0.183 3973 Planarity : 0.006 0.140 4735 Dihedral : 5.374 61.532 3507 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.49 % Allowed : 20.29 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 2990 helix: -0.63 (0.48), residues: 100 sheet: -0.49 (0.19), residues: 754 loop : -0.42 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 470 HIS 0.007 0.001 HIS F 277 PHE 0.034 0.002 PHE G 353 TYR 0.049 0.002 TYR A 211 ARG 0.016 0.001 ARG I 67 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 329) hydrogen bonds : angle 5.67179 ( 615) SS BOND : bond 0.00339 ( 5) SS BOND : angle 3.92975 ( 10) covalent geometry : bond 0.00580 (26519) covalent geometry : angle 0.65046 (36251) ********************** 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 814 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 746 time to evaluate : 2.684 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: G 47 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8037 (t0) REVERT: G 59 VAL cc_start: 0.8799 (t) cc_final: 0.8418 (m) REVERT: G 100 ASP cc_start: 0.6542 (t70) cc_final: 0.6243 (t70) REVERT: G 135 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: G 217 THR cc_start: 0.7931 (p) cc_final: 0.7536 (p) REVERT: G 263 THR cc_start: 0.8385 (m) cc_final: 0.7867 (p) REVERT: G 271 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7728 (mtpp) REVERT: G 319 MET cc_start: 0.2292 (OUTLIER) cc_final: 0.2006 (ptm) REVERT: G 380 PHE cc_start: 0.7978 (p90) cc_final: 0.7526 (p90) REVERT: G 382 ARG cc_start: 0.5857 (mtm180) cc_final: 0.5257 (mtm180) REVERT: G 471 ASP cc_start: 0.7653 (t0) cc_final: 0.7390 (t0) REVERT: G 473 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6605 (tm-30) REVERT: G 536 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7961 (ttpp) REVERT: G 559 PHE cc_start: 0.8121 (m-80) cc_final: 0.7751 (m-80) REVERT: G 560 ASN cc_start: 0.7795 (m-40) cc_final: 0.7394 (m-40) REVERT: A 47 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7782 (t160) REVERT: A 92 VAL cc_start: 0.8435 (t) cc_final: 0.8137 (p) REVERT: A 98 LEU cc_start: 0.7604 (mt) cc_final: 0.6964 (mt) REVERT: A 115 ASN cc_start: 0.8122 (t0) cc_final: 0.7752 (t0) REVERT: A 143 GLN cc_start: 0.7554 (mt0) cc_final: 0.7288 (mt0) REVERT: A 174 MET cc_start: 0.7373 (mtp) cc_final: 0.6881 (mtp) REVERT: A 183 MET cc_start: 0.7231 (mmm) cc_final: 0.6786 (mmm) REVERT: A 218 LEU cc_start: 0.8462 (tp) cc_final: 0.8001 (tt) REVERT: A 293 SER cc_start: 0.8188 (m) cc_final: 0.7883 (p) REVERT: A 344 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7774 (p) REVERT: A 382 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6839 (mtm110) REVERT: A 387 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7489 (ttpt) REVERT: A 403 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7098 (m-70) REVERT: A 427 ASP cc_start: 0.7294 (p0) cc_final: 0.7037 (p0) REVERT: A 433 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8022 (p) REVERT: A 475 ASP cc_start: 0.7437 (t70) cc_final: 0.6851 (t0) REVERT: A 530 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7216 (ttpp) REVERT: A 569 MET cc_start: 0.5726 (mmm) cc_final: 0.5469 (mmm) REVERT: A 574 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6322 (mm-30) REVERT: A 575 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7602 (mtpt) REVERT: B 80 ARG cc_start: 0.7204 (mtt-85) cc_final: 0.6483 (mtt-85) REVERT: B 101 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7921 (pt) REVERT: B 104 GLN cc_start: 0.7837 (pt0) cc_final: 0.7381 (pt0) REVERT: B 117 TRP cc_start: 0.6896 (m100) cc_final: 0.6431 (m100) REVERT: B 125 ASP cc_start: 0.8321 (m-30) cc_final: 0.7961 (m-30) REVERT: B 142 GLU cc_start: 0.7498 (pt0) cc_final: 0.7090 (pt0) REVERT: B 143 GLN cc_start: 0.7551 (mt0) cc_final: 0.7280 (mt0) REVERT: B 145 ILE cc_start: 0.8015 (mt) cc_final: 0.7779 (mm) REVERT: B 151 LYS cc_start: 0.7901 (mttm) cc_final: 0.7641 (mttm) REVERT: B 174 MET cc_start: 0.6818 (mtp) cc_final: 0.6482 (mtp) REVERT: B 183 MET cc_start: 0.6976 (mmm) cc_final: 0.6469 (mmm) REVERT: B 190 MET cc_start: 0.7751 (tpp) cc_final: 0.7331 (tpp) REVERT: B 197 PHE cc_start: 0.7093 (m-10) cc_final: 0.6490 (m-10) REVERT: B 198 TYR cc_start: 0.7325 (m-80) cc_final: 0.6933 (m-80) REVERT: B 237 ASP cc_start: 0.7524 (m-30) cc_final: 0.7005 (m-30) REVERT: B 265 THR cc_start: 0.7767 (t) cc_final: 0.7519 (t) REVERT: B 266 PHE cc_start: 0.7427 (t80) cc_final: 0.6954 (t80) REVERT: B 306 ILE cc_start: 0.7929 (pt) cc_final: 0.7590 (mp) REVERT: B 354 LYS cc_start: 0.7484 (mmtp) cc_final: 0.6836 (mmtp) REVERT: B 377 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5986 (mmm-85) REVERT: B 380 PHE cc_start: 0.6500 (p90) cc_final: 0.5387 (p90) REVERT: B 382 ARG cc_start: 0.7841 (mmp80) cc_final: 0.6824 (mmt180) REVERT: B 383 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7417 (tm-30) REVERT: B 501 LYS cc_start: 0.7909 (tttt) cc_final: 0.7418 (tttt) REVERT: B 527 PHE cc_start: 0.6914 (p90) cc_final: 0.6525 (p90) REVERT: B 530 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8085 (ttmt) REVERT: B 532 LYS cc_start: 0.7282 (tttm) cc_final: 0.6893 (tttm) REVERT: B 533 LEU cc_start: 0.7860 (tp) cc_final: 0.7618 (tp) REVERT: B 536 LYS cc_start: 0.7887 (ttpp) cc_final: 0.7665 (ttpp) REVERT: B 551 MET cc_start: 0.5573 (mmt) cc_final: 0.5102 (mmt) REVERT: E 45 PHE cc_start: 0.7548 (t80) cc_final: 0.6848 (t80) REVERT: E 46 ASN cc_start: 0.7567 (t0) cc_final: 0.7031 (t0) REVERT: E 64 ASN cc_start: 0.7021 (p0) cc_final: 0.6681 (p0) REVERT: E 166 ASN cc_start: 0.6996 (m110) cc_final: 0.6711 (m110) REVERT: E 190 MET cc_start: 0.5864 (mtm) cc_final: 0.5389 (mtm) REVERT: E 378 TYR cc_start: 0.7200 (m-80) cc_final: 0.6437 (m-80) REVERT: E 398 PHE cc_start: 0.7932 (p90) cc_final: 0.7419 (p90) REVERT: E 400 TYR cc_start: 0.7804 (t80) cc_final: 0.7435 (t80) REVERT: E 527 PHE cc_start: 0.7467 (p90) cc_final: 0.7066 (p90) REVERT: E 528 TRP cc_start: 0.6637 (m100) cc_final: 0.6426 (m100) REVERT: E 530 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7629 (tmtt) REVERT: E 535 PHE cc_start: 0.7588 (m-80) cc_final: 0.7253 (m-80) REVERT: E 561 TYR cc_start: 0.8318 (m-80) cc_final: 0.7736 (m-80) REVERT: E 565 ASN cc_start: 0.8432 (m-40) cc_final: 0.8220 (m-40) REVERT: I 47 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7166 (t0) REVERT: I 52 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7390 (ttmm) REVERT: I 115 ASN cc_start: 0.7739 (t0) cc_final: 0.7047 (t0) REVERT: I 174 MET cc_start: 0.7110 (mtp) cc_final: 0.6734 (mtp) REVERT: I 268 PHE cc_start: 0.7521 (m-80) cc_final: 0.7205 (m-80) REVERT: I 319 MET cc_start: 0.5576 (tpp) cc_final: 0.4836 (tpp) REVERT: I 331 MET cc_start: 0.7189 (ttm) cc_final: 0.6948 (ttm) REVERT: I 382 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7019 (mpt-90) REVERT: I 383 GLN cc_start: 0.7264 (mt0) cc_final: 0.6998 (mp10) REVERT: I 444 TYR cc_start: 0.7935 (p90) cc_final: 0.7618 (p90) REVERT: I 535 PHE cc_start: 0.8491 (m-80) cc_final: 0.7989 (m-80) REVERT: I 538 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7964 (ttmm) REVERT: I 539 LEU cc_start: 0.8622 (mt) cc_final: 0.8391 (mp) REVERT: I 544 THR cc_start: 0.8041 (p) cc_final: 0.7682 (p) REVERT: I 546 ASN cc_start: 0.7950 (p0) cc_final: 0.7693 (p0) REVERT: I 550 GLN cc_start: 0.7723 (mm110) cc_final: 0.7106 (mm-40) REVERT: I 560 ASN cc_start: 0.7954 (m-40) cc_final: 0.7673 (m-40) REVERT: I 561 TYR cc_start: 0.7986 (m-80) cc_final: 0.7772 (m-80) REVERT: I 570 LYS cc_start: 0.7441 (ptpt) cc_final: 0.7091 (ptpt) REVERT: I 573 TYR cc_start: 0.8239 (p90) cc_final: 0.7798 (p90) REVERT: I 575 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7748 (mtmm) REVERT: F 52 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7499 (ttmm) REVERT: F 60 GLU cc_start: 0.7399 (tt0) cc_final: 0.7062 (tt0) REVERT: F 143 GLN cc_start: 0.7596 (mp10) cc_final: 0.7248 (mp10) REVERT: F 190 MET cc_start: 0.5788 (mmt) cc_final: 0.5349 (mmt) REVERT: F 213 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7501 (tm-30) REVERT: F 245 THR cc_start: 0.7838 (t) cc_final: 0.7638 (p) REVERT: F 248 ASN cc_start: 0.7224 (m110) cc_final: 0.6848 (t0) REVERT: F 271 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7998 (mtpp) REVERT: F 276 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7243 (m) REVERT: F 280 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7507 (mm110) REVERT: F 310 GLN cc_start: 0.7236 (tt0) cc_final: 0.7018 (tt0) REVERT: F 312 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8320 (mtmm) REVERT: F 327 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7046 (mm-30) REVERT: F 350 GLN cc_start: 0.7672 (mp10) cc_final: 0.7346 (mp10) REVERT: F 405 ASP cc_start: 0.5775 (m-30) cc_final: 0.5493 (m-30) REVERT: F 425 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8095 (p) REVERT: F 473 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6758 (mm-30) REVERT: F 475 ASP cc_start: 0.7258 (t0) cc_final: 0.6594 (t0) REVERT: F 485 ASN cc_start: 0.7924 (p0) cc_final: 0.7602 (p0) REVERT: F 551 MET cc_start: 0.6532 (ttt) cc_final: 0.6137 (ttt) REVERT: C 174 MET cc_start: 0.7287 (mtp) cc_final: 0.6762 (mtp) REVERT: C 250 VAL cc_start: 0.7442 (t) cc_final: 0.7215 (t) outliers start: 68 outliers final: 49 residues processed: 771 average time/residue: 0.3840 time to fit residues: 457.1393 Evaluate side-chains 800 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 738 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 47 ASN 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 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 447 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 497 GLN 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 203 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 518 MET 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 502 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 538 LYS 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 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 87 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 276 THR Chi-restraints excluded: chain F residue 331 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 255 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.218491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161412 restraints weight = 40956.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167138 restraints weight = 17929.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170822 restraints weight = 10590.836| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3557 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= 0.133 Angle : 0.600 15.614 36261 Z= 0.298 Chirality : 0.042 0.173 3973 Planarity : 0.005 0.059 4735 Dihedral : 5.098 61.365 3507 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.49 % Allowed : 20.51 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 2990 helix: -0.65 (0.47), residues: 101 sheet: -0.50 (0.19), residues: 775 loop : -0.37 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 528 HIS 0.007 0.001 HIS F 277 PHE 0.034 0.002 PHE F 353 TYR 0.036 0.002 TYR B 464 ARG 0.013 0.001 ARG I 67 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 329) hydrogen bonds : angle 5.62583 ( 615) SS BOND : bond 0.00216 ( 5) SS BOND : angle 3.01747 ( 10) covalent geometry : bond 0.00302 (26519) covalent geometry : angle 0.59773 (36251) =============================================================================== Job complete usr+sys time: 11758.73 seconds wall clock time: 204 minutes 33.21 seconds (12273.21 seconds total)