Starting phenix.real_space_refine on Thu Aug 6 22:51:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zvl_74879/08_2026/9zvl_74879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zvl_74879/08_2026/9zvl_74879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zvl_74879/08_2026/9zvl_74879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zvl_74879/08_2026/9zvl_74879.map" model { file = "/net/cci-nas-00/data/ceres_data/9zvl_74879/08_2026/9zvl_74879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zvl_74879/08_2026/9zvl_74879.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 93 5.16 5 C 10928 2.51 5 N 3000 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17372 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3926 Classifications: {'peptide': 491} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.28, per 1000 atoms: 0.25 Number of scatterers: 17372 At special positions: 0 Unit cell: (128.7, 134.475, 174.075, 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 93 16.00 O 3351 8.00 N 3000 7.00 C 10928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 482 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 314 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 314 " distance=2.03 Simple disulfide: pdb=" SG CYS C 486 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 27 " " NAG A 602 " - " ASN A 290 " " NAG A 603 " - " ASN A 14 " " NAG A 604 " - " ASN A 488 " " NAG B 601 " - " ASN B 27 " " NAG B 602 " - " ASN B 298 " " NAG B 603 " - " ASN B 14 " " NAG B 604 " - " ASN B 496 " " NAG C 601 " - " ASN C 27 " " NAG C 602 " - " ASN C 298 " " NAG C 603 " - " ASN C 14 " " NAG C 604 " - " ASN C 496 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 749.6 milliseconds 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3988 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 52 sheets defined 20.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.847A pdb=" N PHE A 74 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 75' Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.057A pdb=" N TRP A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 374 through 393 removed outlier: 3.868A pdb=" N MET A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 408 through 460 removed outlier: 3.740A pdb=" N GLU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.945A pdb=" N TYR A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.807A pdb=" N PHE B 74 " --> pdb=" O CYS B 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 75' Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.064A pdb=" N TRP B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.908A pdb=" N MET B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 469 Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.847A pdb=" N SER B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.748A pdb=" N TYR B 504 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 4.063A pdb=" N LEU B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.897A pdb=" N PHE C 74 " --> pdb=" O CYS C 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 75' Processing helix chain 'C' and resid 101 through 109 removed outlier: 3.565A pdb=" N HIS C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.590A pdb=" N GLN C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 401 Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 416 through 469 removed outlier: 3.629A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 500 through 512 removed outlier: 4.111A pdb=" N TYR C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU C 506 " --> pdb=" O PRO C 502 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.070A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.594A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.904A pdb=" N LYS D 64 " --> pdb=" O ASP D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.696A pdb=" N ASP D 86 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.945A pdb=" N LYS E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.672A pdb=" N ASP E 86 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.712A pdb=" N CYS A 8 " --> pdb=" O HIS A 359 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 357 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.210A pdb=" N GLU A 18 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 6.731A pdb=" N LEU A 45 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 47 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 7.125A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 83 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 6.403A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 261 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 118 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 119 removed outlier: 6.403A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 261 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 118 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.706A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 11 removed outlier: 3.846A pdb=" N GLY B 365 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 373 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.173A pdb=" N GLU B 18 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AB7, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55 removed outlier: 7.009A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 83 " --> pdb=" O MET B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 99 removed outlier: 5.273A pdb=" N LEU B 179 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B 264 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 118 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 269 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS B 114 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 271 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 112 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 removed outlier: 7.914A pdb=" N LEU B 179 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AC3, first strand: chain 'B' and resid 136 through 141 removed outlier: 3.537A pdb=" N SER B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA B 138 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ALA B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AC6, first strand: chain 'B' and resid 472 through 474 Processing sheet with id=AC7, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.749A pdb=" N GLY C 365 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC9, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AD1, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AD2, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.742A pdb=" N LEU C 45 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N CYS C 286 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C 47 " --> pdb=" O CYS C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 54 through 55 removed outlier: 7.096A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 83 " --> pdb=" O MET C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 112 through 118 removed outlier: 6.418A pdb=" N ILE C 112 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS C 271 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS C 114 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 269 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD6, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AD7, first strand: chain 'C' and resid 229 through 232 Processing sheet with id=AD8, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AD9, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AE1, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AE2, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.663A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 49 through 50 Processing sheet with id=AE5, first strand: chain 'H' and resid 67 through 72 removed outlier: 3.537A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.585A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.848A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AF1, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.544A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.790A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AF4, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.845A pdb=" N ALA E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AF6, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.510A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.238A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1296 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: 3.20 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5688 1.34 - 1.46: 4273 1.46 - 1.58: 7675 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 17774 Sorted by residual: bond pdb=" CB GLU F 81 " pdb=" CG GLU F 81 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.55e+00 bond pdb=" CB ASP E 53 " pdb=" CG ASP E 53 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.84e+00 bond pdb=" CB ASP D 53 " pdb=" CG ASP D 53 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.80e+00 bond pdb=" CB ASP H 53 " pdb=" CG ASP H 53 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.65e+00 bond pdb=" CA ASN C 477 " pdb=" CB ASN C 477 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.66e-02 3.63e+03 2.61e+00 ... (remaining 17769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 23661 2.85 - 5.70: 323 5.70 - 8.55: 68 8.55 - 11.40: 19 11.40 - 14.25: 2 Bond angle restraints: 24073 Sorted by residual: angle pdb=" C SER G 91 " pdb=" N TYR G 92 " pdb=" CA TYR G 92 " ideal model delta sigma weight residual 121.54 133.35 -11.81 1.91e+00 2.74e-01 3.83e+01 angle pdb=" C SER F 91 " pdb=" N TYR F 92 " pdb=" CA TYR F 92 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.68e+01 angle pdb=" C SER L 91 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" CA TYR G 92 " pdb=" CB TYR G 92 " pdb=" CG TYR G 92 " ideal model delta sigma weight residual 113.90 122.53 -8.63 1.80e+00 3.09e-01 2.30e+01 angle pdb=" C ASN E 100C" pdb=" N TYR E 100D" pdb=" CA TYR E 100D" ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 ... (remaining 24068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 9120 17.79 - 35.57: 1208 35.57 - 53.36: 326 53.36 - 71.14: 63 71.14 - 88.93: 18 Dihedral angle restraints: 10735 sinusoidal: 4488 harmonic: 6247 Sorted by residual: dihedral pdb=" CB CYS C 486 " pdb=" SG CYS C 486 " pdb=" SG CYS C 490 " pdb=" CB CYS C 490 " ideal model delta sinusoidal sigma weight residual 93.00 173.88 -80.88 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 490 " pdb=" CB CYS B 490 " ideal model delta sinusoidal sigma weight residual 93.00 165.65 -72.65 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS A 478 " pdb=" SG CYS A 478 " pdb=" SG CYS A 482 " pdb=" CB CYS A 482 " ideal model delta sinusoidal sigma weight residual 93.00 158.21 -65.21 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 10732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2048 0.060 - 0.120: 469 0.120 - 0.180: 63 0.180 - 0.240: 15 0.240 - 0.300: 5 Chirality restraints: 2600 Sorted by residual: chirality pdb=" C1 NAG C 603 " pdb=" ND2 ASN C 14 " pdb=" C2 NAG C 603 " pdb=" O5 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE B 7 " pdb=" CA ILE B 7 " pdb=" CG1 ILE B 7 " pdb=" CG2 ILE B 7 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE A 243 " pdb=" CA ILE A 243 " pdb=" CG1 ILE A 243 " pdb=" CG2 ILE A 243 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2597 not shown) Planarity restraints: 3129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 92 " -0.025 2.00e-02 2.50e+03 3.24e-02 2.10e+01 pdb=" CG TYR G 92 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR G 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR G 92 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR G 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 92 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 92 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 91 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER G 91 " -0.062 2.00e-02 2.50e+03 pdb=" O SER G 91 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR G 92 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 79 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.82e+00 pdb=" N PRO F 80 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 80 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 80 " -0.043 5.00e-02 4.00e+02 ... (remaining 3126 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 8687 3.01 - 3.48: 16464 3.48 - 3.95: 28333 3.95 - 4.43: 32057 4.43 - 4.90: 53363 Nonbonded interactions: 138904 Sorted by model distance: nonbonded pdb=" N THR H 23 " pdb=" OG1 THR H 23 " model vdw 2.536 2.496 nonbonded pdb=" O5 NAG A 604 " pdb=" O6 NAG A 604 " model vdw 2.563 2.432 nonbonded pdb=" N THR E 28 " pdb=" OG1 THR E 28 " model vdw 2.595 2.496 nonbonded pdb=" N THR D 28 " pdb=" OG1 THR D 28 " model vdw 2.597 2.496 nonbonded pdb=" N ILE C 155 " pdb=" O ILE C 155 " model vdw 2.608 2.496 ... (remaining 138899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 604)) selection = (chain 'C' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 604)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.220 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 : 0.004 0.056 17807 Z= 0.186 Angle : 0.905 14.246 24151 Z= 0.467 Chirality : 0.054 0.300 2600 Planarity : 0.006 0.078 3117 Dihedral : 17.075 88.927 6684 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.32 % Favored : 92.17 % Rotamer: Outliers : 2.55 % Allowed : 23.07 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2145 helix: -0.28 (0.24), residues: 389 sheet: -2.00 (0.25), residues: 443 loop : -1.86 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 61 TYR 0.079 0.002 TYR G 92 PHE 0.018 0.002 PHE E 27 TRP 0.015 0.001 TRP G 35 HIS 0.009 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17774) covalent geometry : angle 0.88777 / 0.46 (24073) SS BOND : bond 0.00301 / 0.18 ( 21) SS BOND : angle 1.32055 / 0.81 ( 42) hydrogen bonds : bond 0.19504 / 13.73 ( 472) hydrogen bonds : angle 8.00564 / 5.65 ( 1296) link_NAG-ASN : bond 0.00955 / 0.63 ( 12) link_NAG-ASN : angle 4.54517 / 3.18 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7482 (tp40) cc_final: 0.7120 (tm-30) REVERT: A 37 LEU cc_start: 0.8252 (tp) cc_final: 0.8028 (tp) REVERT: A 393 MET cc_start: 0.8192 (tpp) cc_final: 0.7596 (mmm) REVERT: A 412 GLU cc_start: 0.8021 (tt0) cc_final: 0.7679 (tm-30) REVERT: A 440 ARG cc_start: 0.4439 (tpt170) cc_final: 0.3055 (mmm160) REVERT: B 37 LEU cc_start: 0.8262 (tp) cc_final: 0.7991 (tp) REVERT: B 82 TYR cc_start: 0.8910 (p90) cc_final: 0.8624 (p90) REVERT: B 111 ARG cc_start: 0.7433 (mpt180) cc_final: 0.7157 (mtm110) REVERT: B 174 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: B 230 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7428 (mtt) REVERT: B 491 MET cc_start: 0.0273 (OUTLIER) cc_final: 0.0059 (ptt) REVERT: B 504 TYR cc_start: 0.3268 (OUTLIER) cc_final: 0.0790 (m-80) REVERT: C 174 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: C 230 MET cc_start: 0.7637 (ttm) cc_final: 0.7351 (ttm) REVERT: C 447 GLU cc_start: 0.3356 (OUTLIER) cc_final: 0.2396 (mm-30) REVERT: L 92 TYR cc_start: 0.7027 (p90) cc_final: 0.6761 (p90) REVERT: E 77 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (m) outliers start: 48 outliers final: 31 residues processed: 251 average time/residue: 0.1661 time to fit residues: 61.6563 Evaluate side-chains 246 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 210 ASN B 423 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100FHIS ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.191683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.152522 restraints weight = 28330.193| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.48 r_work: 0.3879 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17807 Z= 0.132 Angle : 0.593 8.411 24151 Z= 0.303 Chirality : 0.045 0.225 2600 Planarity : 0.004 0.058 3117 Dihedral : 7.218 59.903 2677 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.85 % Favored : 92.87 % Rotamer: Outliers : 3.88 % Allowed : 20.52 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.18), residues: 2145 helix: 0.63 (0.27), residues: 389 sheet: -1.94 (0.26), residues: 419 loop : -1.78 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 16 TYR 0.034 0.001 TYR L 92 PHE 0.010 0.001 PHE B 351 TRP 0.008 0.001 TRP A 80 HIS 0.010 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17774) covalent geometry : angle 0.57997 / 0.30 (24073) SS BOND : bond 0.00257 / 0.17 ( 21) SS BOND : angle 1.17494 / 0.71 ( 42) hydrogen bonds : bond 0.03524 / 2.37 ( 472) hydrogen bonds : angle 5.70159 / 4.00 ( 1296) link_NAG-ASN : bond 0.00537 / 0.32 ( 12) link_NAG-ASN : angle 3.10539 / 2.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 218 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8077 (tp) cc_final: 0.7805 (tp) REVERT: A 58 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 420 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7973 (t0) REVERT: A 424 ASP cc_start: 0.8470 (m-30) cc_final: 0.8186 (m-30) REVERT: A 440 ARG cc_start: 0.4204 (tpt170) cc_final: 0.3070 (mmm160) REVERT: B 37 LEU cc_start: 0.8086 (tp) cc_final: 0.7842 (tp) REVERT: B 491 MET cc_start: -0.1238 (OUTLIER) cc_final: -0.1497 (ptt) REVERT: B 504 TYR cc_start: 0.3306 (OUTLIER) cc_final: 0.1775 (m-80) REVERT: C 411 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7348 (mt-10) outliers start: 73 outliers final: 40 residues processed: 268 average time/residue: 0.1575 time to fit residues: 62.6511 Evaluate side-chains 245 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 124 optimal weight: 0.0870 chunk 96 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 210 ASN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 158 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN C 423 ASN C 484 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 100FHIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.188165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.146648 restraints weight = 28690.752| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.60 r_work: 0.3733 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17807 Z= 0.320 Angle : 0.757 7.979 24151 Z= 0.390 Chirality : 0.050 0.278 2600 Planarity : 0.005 0.057 3117 Dihedral : 7.325 59.475 2641 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.70 % Favored : 90.02 % Rotamer: Outliers : 6.06 % Allowed : 20.68 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.18), residues: 2145 helix: 0.52 (0.27), residues: 389 sheet: -2.26 (0.25), residues: 429 loop : -1.91 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 16 TYR 0.045 0.002 TYR L 92 PHE 0.018 0.002 PHE A 404 TRP 0.018 0.002 TRP B 80 HIS 0.013 0.002 HIS E 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.32 (17774) covalent geometry : angle 0.74408 / 0.39 (24073) SS BOND : bond 0.00425 / 0.28 ( 21) SS BOND : angle 1.93034 / 1.26 ( 42) hydrogen bonds : bond 0.03950 / 2.64 ( 472) hydrogen bonds : angle 5.91015 / 4.16 ( 1296) link_NAG-ASN : bond 0.00449 / 0.27 ( 12) link_NAG-ASN : angle 3.17368 / 2.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 203 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8327 (tp) cc_final: 0.8061 (tp) REVERT: A 58 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (t0) REVERT: A 393 MET cc_start: 0.8178 (mmm) cc_final: 0.7566 (mmm) REVERT: A 416 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8400 (ttmm) REVERT: A 440 ARG cc_start: 0.4172 (tpt170) cc_final: 0.2956 (mmt180) REVERT: B 37 LEU cc_start: 0.8321 (tp) cc_final: 0.8118 (tp) REVERT: B 400 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8417 (ttpt) REVERT: B 504 TYR cc_start: 0.3392 (OUTLIER) cc_final: 0.1984 (m-80) REVERT: C 116 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: C 411 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: C 458 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6317 (pttt) REVERT: C 503 GLN cc_start: 0.3329 (OUTLIER) cc_final: 0.2948 (tt0) REVERT: H 95 ASP cc_start: 0.8007 (p0) cc_final: 0.7766 (p0) REVERT: E 2 GLU cc_start: 0.7581 (pt0) cc_final: 0.7243 (mt-10) REVERT: E 83 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7944 (mtm-85) REVERT: G 55 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7627 (tm-30) REVERT: G 62 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6908 (m-80) outliers start: 114 outliers final: 62 residues processed: 294 average time/residue: 0.1523 time to fit residues: 67.0166 Evaluate side-chains 265 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 194 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 160 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 210 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS E 100FHIS ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.190580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.150970 restraints weight = 28368.553| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.86 r_work: 0.3807 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17807 Z= 0.153 Angle : 0.620 8.577 24151 Z= 0.315 Chirality : 0.046 0.229 2600 Planarity : 0.004 0.053 3117 Dihedral : 6.810 59.754 2641 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.88 % Favored : 91.89 % Rotamer: Outliers : 5.00 % Allowed : 21.58 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 2145 helix: 0.83 (0.27), residues: 389 sheet: -2.11 (0.25), residues: 423 loop : -1.82 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 16 TYR 0.036 0.001 TYR L 92 PHE 0.011 0.001 PHE B 351 TRP 0.009 0.001 TRP B 80 HIS 0.009 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17774) covalent geometry : angle 0.60699 / 0.31 (24073) SS BOND : bond 0.00260 / 0.17 ( 21) SS BOND : angle 1.28900 / 0.80 ( 42) hydrogen bonds : bond 0.03330 / 2.23 ( 472) hydrogen bonds : angle 5.53207 / 3.88 ( 1296) link_NAG-ASN : bond 0.00519 / 0.32 ( 12) link_NAG-ASN : angle 3.15122 / 2.18 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 205 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8274 (t0) REVERT: A 109 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 393 MET cc_start: 0.8118 (mmm) cc_final: 0.7504 (mmm) REVERT: A 420 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8159 (t0) REVERT: A 440 ARG cc_start: 0.4029 (tpt170) cc_final: 0.2872 (mmm160) REVERT: B 37 LEU cc_start: 0.8163 (tp) cc_final: 0.7853 (tp) REVERT: B 400 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (ttpt) REVERT: B 504 TYR cc_start: 0.3313 (OUTLIER) cc_final: 0.2051 (m-80) REVERT: C 116 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8837 (tt0) REVERT: C 174 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: C 411 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: C 458 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6273 (pttt) REVERT: H 82 MET cc_start: 0.7574 (mmt) cc_final: 0.7328 (mmt) REVERT: H 95 ASP cc_start: 0.7939 (p0) cc_final: 0.7656 (p0) REVERT: E 2 GLU cc_start: 0.7490 (pt0) cc_final: 0.7202 (mt-10) REVERT: G 49 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.5212 (t80) REVERT: G 55 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 94 outliers final: 62 residues processed: 271 average time/residue: 0.1514 time to fit residues: 61.2465 Evaluate side-chains 267 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 63 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 165 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 151 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.192075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.150982 restraints weight = 28043.062| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.96 r_work: 0.3858 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17807 Z= 0.136 Angle : 0.603 9.711 24151 Z= 0.305 Chirality : 0.045 0.221 2600 Planarity : 0.004 0.052 3117 Dihedral : 6.592 59.275 2637 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.88 % Favored : 91.93 % Rotamer: Outliers : 4.47 % Allowed : 22.70 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 2145 helix: 1.01 (0.27), residues: 387 sheet: -2.05 (0.25), residues: 423 loop : -1.72 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 16 TYR 0.039 0.001 TYR L 92 PHE 0.010 0.001 PHE B 351 TRP 0.024 0.001 TRP F 35 HIS 0.012 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17774) covalent geometry : angle 0.58779 / 0.30 (24073) SS BOND : bond 0.00269 / 0.17 ( 21) SS BOND : angle 1.37297 / 0.77 ( 42) hydrogen bonds : bond 0.03214 / 2.15 ( 472) hydrogen bonds : angle 5.36544 / 3.76 ( 1296) link_NAG-ASN : bond 0.00565 / 0.36 ( 12) link_NAG-ASN : angle 3.31710 / 2.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 393 MET cc_start: 0.8023 (mmm) cc_final: 0.7434 (mmm) REVERT: A 416 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8309 (ttmm) REVERT: A 420 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8064 (t0) REVERT: A 424 ASP cc_start: 0.8509 (m-30) cc_final: 0.8183 (t0) REVERT: A 440 ARG cc_start: 0.4219 (tpt170) cc_final: 0.3067 (mmm160) REVERT: B 37 LEU cc_start: 0.8103 (tp) cc_final: 0.7801 (tp) REVERT: B 400 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8297 (ttpt) REVERT: B 403 THR cc_start: 0.8368 (p) cc_final: 0.6732 (p) REVERT: B 432 ASP cc_start: 0.8772 (t0) cc_final: 0.8527 (t0) REVERT: B 504 TYR cc_start: 0.3437 (OUTLIER) cc_final: 0.2131 (m-80) REVERT: C 116 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (tt0) REVERT: C 174 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: C 403 THR cc_start: 0.8619 (p) cc_final: 0.8219 (p) REVERT: C 411 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: C 458 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6262 (pttt) REVERT: H 82 MET cc_start: 0.7543 (mmt) cc_final: 0.7272 (mmt) REVERT: H 95 ASP cc_start: 0.7888 (p0) cc_final: 0.7614 (p0) REVERT: E 2 GLU cc_start: 0.7387 (pt0) cc_final: 0.7150 (mt-10) REVERT: G 49 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5261 (t80) REVERT: G 55 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7444 (tm-30) outliers start: 84 outliers final: 57 residues processed: 268 average time/residue: 0.1489 time to fit residues: 59.3961 Evaluate side-chains 264 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 152 optimal weight: 0.0070 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 74 optimal weight: 0.0050 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100FHIS D 35 HIS E 100FHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.188444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.147714 restraints weight = 27868.156| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.53 r_work: 0.3837 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17807 Z= 0.139 Angle : 0.594 9.230 24151 Z= 0.301 Chirality : 0.045 0.218 2600 Planarity : 0.004 0.052 3117 Dihedral : 6.362 59.979 2633 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.03 % Rotamer: Outliers : 5.53 % Allowed : 21.90 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.18), residues: 2145 helix: 1.07 (0.27), residues: 387 sheet: -1.99 (0.25), residues: 423 loop : -1.68 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 16 TYR 0.037 0.001 TYR L 92 PHE 0.011 0.001 PHE B 351 TRP 0.025 0.001 TRP L 35 HIS 0.011 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17774) covalent geometry : angle 0.58271 / 0.30 (24073) SS BOND : bond 0.00259 / 0.17 ( 21) SS BOND : angle 1.25681 / 0.73 ( 42) hydrogen bonds : bond 0.03166 / 2.12 ( 472) hydrogen bonds : angle 5.28166 / 3.71 ( 1296) link_NAG-ASN : bond 0.00562 / 0.37 ( 12) link_NAG-ASN : angle 2.83104 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 211 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 109 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 393 MET cc_start: 0.8023 (mmm) cc_final: 0.7433 (mmm) REVERT: A 416 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8329 (ttmm) REVERT: A 420 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8086 (t0) REVERT: A 424 ASP cc_start: 0.8567 (m-30) cc_final: 0.8365 (t0) REVERT: A 440 ARG cc_start: 0.4161 (tpt170) cc_final: 0.3069 (mmm160) REVERT: B 37 LEU cc_start: 0.8072 (tp) cc_final: 0.7771 (tp) REVERT: B 213 LEU cc_start: 0.8783 (mt) cc_final: 0.8567 (mt) REVERT: B 504 TYR cc_start: 0.3620 (OUTLIER) cc_final: 0.2478 (m-80) REVERT: C 116 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: C 174 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: C 403 THR cc_start: 0.8736 (p) cc_final: 0.8419 (p) REVERT: C 411 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: C 458 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6211 (pttt) REVERT: H 95 ASP cc_start: 0.7895 (p0) cc_final: 0.7664 (p0) REVERT: D 100 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.7983 (m-70) REVERT: E 2 GLU cc_start: 0.7413 (pt0) cc_final: 0.7172 (mt-10) REVERT: E 83 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7930 (mtm-85) REVERT: G 49 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5335 (t80) REVERT: G 55 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7505 (tm-30) REVERT: G 62 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6694 (m-80) outliers start: 104 outliers final: 73 residues processed: 288 average time/residue: 0.1459 time to fit residues: 62.7868 Evaluate side-chains 287 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 202 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 160 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 211 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN A 360 HIS ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 100FHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.185711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.145354 restraints weight = 27953.110| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.74 r_work: 0.3855 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17807 Z= 0.140 Angle : 0.608 13.892 24151 Z= 0.305 Chirality : 0.045 0.216 2600 Planarity : 0.004 0.051 3117 Dihedral : 6.185 59.584 2631 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.03 % Rotamer: Outliers : 5.37 % Allowed : 22.01 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.18), residues: 2145 helix: 1.12 (0.27), residues: 387 sheet: -1.94 (0.26), residues: 423 loop : -1.65 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 16 TYR 0.037 0.001 TYR L 92 PHE 0.011 0.001 PHE B 351 TRP 0.024 0.001 TRP L 35 HIS 0.009 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17774) covalent geometry : angle 0.59708 / 0.30 (24073) SS BOND : bond 0.00231 / 0.15 ( 21) SS BOND : angle 1.35228 / 0.74 ( 42) hydrogen bonds : bond 0.03116 / 2.09 ( 472) hydrogen bonds : angle 5.25676 / 3.70 ( 1296) link_NAG-ASN : bond 0.00530 / 0.34 ( 12) link_NAG-ASN : angle 2.74993 / 1.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 203 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8126 (t0) REVERT: A 109 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 393 MET cc_start: 0.8018 (mmm) cc_final: 0.7406 (mmm) REVERT: A 416 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8297 (ttmm) REVERT: A 420 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (t0) REVERT: A 440 ARG cc_start: 0.4126 (tpt170) cc_final: 0.3033 (mmm160) REVERT: B 37 LEU cc_start: 0.8037 (tp) cc_final: 0.7782 (tp) REVERT: B 504 TYR cc_start: 0.3732 (OUTLIER) cc_final: 0.2461 (m-80) REVERT: C 116 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8718 (tt0) REVERT: C 174 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: C 403 THR cc_start: 0.8683 (p) cc_final: 0.8445 (p) REVERT: C 411 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: C 458 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6212 (pttt) REVERT: C 503 GLN cc_start: 0.3129 (OUTLIER) cc_final: 0.2788 (tt0) REVERT: E 2 GLU cc_start: 0.7447 (pt0) cc_final: 0.7166 (mt-10) REVERT: E 83 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7909 (mtm-85) REVERT: G 49 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5293 (t80) REVERT: G 62 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6744 (m-80) outliers start: 101 outliers final: 74 residues processed: 274 average time/residue: 0.1432 time to fit residues: 58.1336 Evaluate side-chains 284 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 198 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 99 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100FHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.186343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.145414 restraints weight = 28059.676| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.57 r_work: 0.3835 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17807 Z= 0.146 Angle : 0.602 9.769 24151 Z= 0.304 Chirality : 0.045 0.217 2600 Planarity : 0.004 0.051 3117 Dihedral : 6.158 58.930 2631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.93 % Favored : 91.84 % Rotamer: Outliers : 5.00 % Allowed : 22.38 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 2145 helix: 1.17 (0.27), residues: 387 sheet: -2.03 (0.24), residues: 447 loop : -1.65 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 16 TYR 0.036 0.001 TYR L 92 PHE 0.011 0.001 PHE B 351 TRP 0.037 0.001 TRP F 35 HIS 0.009 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17774) covalent geometry : angle 0.59104 / 0.30 (24073) SS BOND : bond 0.00318 / 0.20 ( 21) SS BOND : angle 1.36903 / 0.76 ( 42) hydrogen bonds : bond 0.03141 / 2.11 ( 472) hydrogen bonds : angle 5.23138 / 3.69 ( 1296) link_NAG-ASN : bond 0.00528 / 0.34 ( 12) link_NAG-ASN : angle 2.72233 / 1.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 201 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8138 (t0) REVERT: A 109 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 393 MET cc_start: 0.8060 (mmm) cc_final: 0.7445 (mmm) REVERT: A 416 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8310 (ttmm) REVERT: A 420 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8077 (t0) REVERT: A 440 ARG cc_start: 0.4109 (tpt170) cc_final: 0.3072 (mmm160) REVERT: A 483 MET cc_start: -0.0085 (ttm) cc_final: -0.0302 (mmm) REVERT: B 37 LEU cc_start: 0.8070 (tp) cc_final: 0.7850 (tp) REVERT: B 504 TYR cc_start: 0.3742 (OUTLIER) cc_final: 0.2447 (m-80) REVERT: C 116 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8761 (tt0) REVERT: C 174 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: C 329 LEU cc_start: 0.7616 (mm) cc_final: 0.7410 (tp) REVERT: C 403 THR cc_start: 0.8638 (p) cc_final: 0.8412 (p) REVERT: C 411 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: C 428 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8378 (t0) REVERT: C 458 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6184 (pttt) REVERT: C 503 GLN cc_start: 0.3139 (OUTLIER) cc_final: 0.2780 (tt0) REVERT: D 100 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7508 (m90) REVERT: E 2 GLU cc_start: 0.7462 (pt0) cc_final: 0.7147 (mt-10) REVERT: E 83 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7902 (mtm-85) REVERT: G 49 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.5272 (t80) REVERT: G 55 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7688 (tm-30) REVERT: G 62 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6702 (m-80) outliers start: 94 outliers final: 76 residues processed: 264 average time/residue: 0.1550 time to fit residues: 60.4004 Evaluate side-chains 286 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 209 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.181002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.131791 restraints weight = 28147.618| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.86 r_work: 0.3745 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17807 Z= 0.256 Angle : 0.698 10.122 24151 Z= 0.355 Chirality : 0.048 0.256 2600 Planarity : 0.004 0.053 3117 Dihedral : 6.580 59.670 2631 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.98 % Favored : 89.79 % Rotamer: Outliers : 5.05 % Allowed : 22.33 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 2145 helix: 0.91 (0.27), residues: 387 sheet: -2.29 (0.24), residues: 447 loop : -1.80 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 16 TYR 0.040 0.002 TYR L 92 PHE 0.016 0.002 PHE D 29 TRP 0.040 0.002 TRP F 35 HIS 0.008 0.002 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (17774) covalent geometry : angle 0.68681 / 0.35 (24073) SS BOND : bond 0.00437 / 0.29 ( 21) SS BOND : angle 1.75071 / 0.99 ( 42) hydrogen bonds : bond 0.03526 / 2.36 ( 472) hydrogen bonds : angle 5.55505 / 3.91 ( 1296) link_NAG-ASN : bond 0.00495 / 0.31 ( 12) link_NAG-ASN : angle 2.83266 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 203 time to evaluate : 0.672 Fit side-chains REVERT: A 58 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8282 (t0) REVERT: A 109 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 393 MET cc_start: 0.8292 (mmm) cc_final: 0.7437 (mmm) REVERT: A 416 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8332 (ttmm) REVERT: A 440 ARG cc_start: 0.4137 (tpt170) cc_final: 0.2993 (mmm160) REVERT: A 483 MET cc_start: -0.0166 (ttm) cc_final: -0.0391 (mmm) REVERT: B 37 LEU cc_start: 0.8253 (tp) cc_final: 0.8041 (tp) REVERT: B 504 TYR cc_start: 0.3772 (OUTLIER) cc_final: 0.2602 (m-80) REVERT: C 116 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8954 (tt0) REVERT: C 202 ILE cc_start: 0.8703 (mp) cc_final: 0.8455 (mt) REVERT: C 403 THR cc_start: 0.8664 (p) cc_final: 0.8445 (p) REVERT: C 411 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: C 448 ARG cc_start: 0.4217 (tpt170) cc_final: 0.3121 (tpp80) REVERT: C 458 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6230 (pttt) REVERT: C 503 GLN cc_start: 0.3114 (OUTLIER) cc_final: 0.2798 (tt0) REVERT: E 2 GLU cc_start: 0.7712 (pt0) cc_final: 0.7002 (mt-10) REVERT: E 27 PHE cc_start: 0.6930 (m-80) cc_final: 0.6694 (m-80) REVERT: E 83 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7948 (mtm-85) REVERT: G 49 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5432 (t80) REVERT: G 55 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7501 (tm-30) REVERT: G 62 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6932 (m-80) outliers start: 95 outliers final: 74 residues processed: 268 average time/residue: 0.1371 time to fit residues: 54.2507 Evaluate side-chains 285 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 201 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 142 optimal weight: 0.0670 chunk 48 optimal weight: 8.9990 chunk 100 optimal weight: 0.4980 chunk 43 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100FHIS E 100FHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.184634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.144187 restraints weight = 28111.479| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.46 r_work: 0.3905 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17807 Z= 0.146 Angle : 0.629 15.074 24151 Z= 0.314 Chirality : 0.045 0.217 2600 Planarity : 0.004 0.051 3117 Dihedral : 6.234 59.384 2631 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.02 % Favored : 91.75 % Rotamer: Outliers : 4.57 % Allowed : 23.07 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.18), residues: 2145 helix: 1.05 (0.27), residues: 389 sheet: -2.28 (0.23), residues: 471 loop : -1.73 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 16 TYR 0.035 0.001 TYR F 92 PHE 0.012 0.001 PHE D 29 TRP 0.044 0.002 TRP L 35 HIS 0.009 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17774) covalent geometry : angle 0.61808 / 0.31 (24073) SS BOND : bond 0.00331 / 0.22 ( 21) SS BOND : angle 1.44204 / 0.80 ( 42) hydrogen bonds : bond 0.03152 / 2.12 ( 472) hydrogen bonds : angle 5.33489 / 3.75 ( 1296) link_NAG-ASN : bond 0.00521 / 0.33 ( 12) link_NAG-ASN : angle 2.75052 / 1.93 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 202 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8212 (t0) REVERT: A 109 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 393 MET cc_start: 0.8142 (mmm) cc_final: 0.7337 (mmm) REVERT: A 416 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8266 (ttmm) REVERT: A 420 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8134 (t0) REVERT: A 440 ARG cc_start: 0.4150 (tpt170) cc_final: 0.3073 (mmm160) REVERT: A 483 MET cc_start: -0.0097 (ttm) cc_final: -0.0332 (mmm) REVERT: B 37 LEU cc_start: 0.8097 (tp) cc_final: 0.7818 (tp) REVERT: B 411 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: B 448 ARG cc_start: 0.4741 (tpt170) cc_final: 0.3310 (tpp80) REVERT: B 504 TYR cc_start: 0.3834 (OUTLIER) cc_final: 0.2402 (m-80) REVERT: C 24 MET cc_start: 0.3499 (mtm) cc_final: 0.2667 (pmm) REVERT: C 116 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8869 (tt0) REVERT: C 403 THR cc_start: 0.8619 (p) cc_final: 0.8393 (p) REVERT: C 411 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: C 448 ARG cc_start: 0.4303 (tpt170) cc_final: 0.3200 (tpp80) REVERT: C 458 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6177 (pttt) REVERT: C 503 GLN cc_start: 0.3018 (OUTLIER) cc_final: 0.2657 (tt0) REVERT: D 100 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.7442 (m90) REVERT: E 2 GLU cc_start: 0.7577 (pt0) cc_final: 0.6933 (mt-10) REVERT: E 83 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: G 49 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5289 (t80) REVERT: G 55 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7446 (tm-30) REVERT: G 62 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6738 (m-80) outliers start: 86 outliers final: 65 residues processed: 262 average time/residue: 0.1555 time to fit residues: 60.3358 Evaluate side-chains 277 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 199 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain H residue 2 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 71 PHE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain G residue 49 TYR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100CASN E 100FHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.189890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.148736 restraints weight = 28287.665| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.68 r_work: 0.3824 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17807 Z= 0.237 Angle : 0.692 15.003 24151 Z= 0.348 Chirality : 0.048 0.248 2600 Planarity : 0.004 0.053 3117 Dihedral : 6.456 58.938 2631 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.02 % Favored : 89.74 % Rotamer: Outliers : 4.41 % Allowed : 23.29 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 2145 helix: 1.02 (0.27), residues: 387 sheet: -2.32 (0.24), residues: 447 loop : -1.82 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 16 TYR 0.042 0.002 TYR L 92 PHE 0.022 0.002 PHE D 29 TRP 0.050 0.002 TRP L 35 HIS 0.009 0.002 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (17774) covalent geometry : angle 0.68113 / 0.35 (24073) SS BOND : bond 0.00403 / 0.27 ( 21) SS BOND : angle 1.56371 / 0.89 ( 42) hydrogen bonds : bond 0.03377 / 2.26 ( 472) hydrogen bonds : angle 5.48080 / 3.86 ( 1296) link_NAG-ASN : bond 0.00490 / 0.31 ( 12) link_NAG-ASN : angle 2.82374 / 1.97 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6037.98 seconds wall clock time: 104 minutes 5.32 seconds (6245.32 seconds total)