Starting phenix.real_space_refine on Fri Sep 11 18:03:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vtk_21380/09_2026/6vtk_21380.cif" } resolution = 2.82 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= 0.066 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 81 5.16 5 C 6846 2.51 5 N 1725 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3534 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, B Time building chain proxies: 3.25, per 1000 atoms: 0.30 Number of scatterers: 10686 At special positions: 0 Unit cell: (97.544, 94.256, 132.616, 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 81 16.00 O 2034 8.00 N 1725 7.00 C 6846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 195 " distance=2.02 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 195 " distance=2.02 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 366 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 366 " distance=2.05 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 362 " distance=2.04 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 362 " distance=2.04 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 360 " distance=2.04 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.04 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.04 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 336 " 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 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 437.5 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 42.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.754A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.570A pdb=" N ARG A 103 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.762A pdb=" N LYS A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.719A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.548A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.520A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.753A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.571A pdb=" N ARG C 103 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 104 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 134 through 142 removed outlier: 3.761A pdb=" N LYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 214 through 217 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.718A pdb=" N LYS C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.549A pdb=" N GLU C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 removed outlier: 3.521A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.753A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.571A pdb=" N ARG B 103 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 104 " --> pdb=" O PHE B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 104' Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.762A pdb=" N LYS B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.718A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.548A pdb=" N GLU B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.521A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU A 278 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU A 414 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ARG A 280 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR A 416 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE A 282 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N THR A 418 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.085A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU C 278 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU C 414 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ARG C 280 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR C 416 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 12.556A pdb=" N ILE C 282 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N THR C 418 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 190 removed outlier: 7.085A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 81 Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU B 278 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU B 414 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ARG B 280 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR B 416 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE B 282 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N THR B 418 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'B' and resid 185 through 190 removed outlier: 7.086A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1350 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: 1.57 Time building geometry restraints manager: 1.09 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: 3398 1.34 - 1.46: 2101 1.46 - 1.58: 5325 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10935 Sorted by residual: bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 10930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14253 1.90 - 3.81: 501 3.81 - 5.71: 48 5.71 - 7.61: 15 7.61 - 9.52: 6 Bond angle restraints: 14823 Sorted by residual: angle pdb=" C GLN B 202 " pdb=" N ASP B 203 " pdb=" CA ASP B 203 " ideal model delta sigma weight residual 122.40 127.24 -4.84 1.45e+00 4.76e-01 1.11e+01 angle pdb=" C GLN A 202 " pdb=" N ASP A 203 " pdb=" CA ASP A 203 " ideal model delta sigma weight residual 122.40 127.19 -4.79 1.45e+00 4.76e-01 1.09e+01 angle pdb=" C GLN C 202 " pdb=" N ASP C 203 " pdb=" CA ASP C 203 " ideal model delta sigma weight residual 122.40 127.17 -4.77 1.45e+00 4.76e-01 1.08e+01 angle pdb=" N ILE A 442 " pdb=" CA ILE A 442 " pdb=" C ILE A 442 " ideal model delta sigma weight residual 113.53 110.62 2.91 9.80e-01 1.04e+00 8.82e+00 angle pdb=" N ILE C 442 " pdb=" CA ILE C 442 " pdb=" C ILE C 442 " ideal model delta sigma weight residual 113.53 110.66 2.87 9.80e-01 1.04e+00 8.55e+00 ... (remaining 14818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 6188 15.13 - 30.27: 292 30.27 - 45.40: 42 45.40 - 60.54: 6 60.54 - 75.67: 9 Dihedral angle restraints: 6537 sinusoidal: 2622 harmonic: 3915 Sorted by residual: dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 360 " pdb=" CB CYS B 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.90 71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.87 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " pdb=" SG CYS C 360 " pdb=" CB CYS C 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.84 71.84 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 6534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 962 0.035 - 0.070: 461 0.070 - 0.106: 138 0.106 - 0.141: 61 0.141 - 0.176: 13 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CA CYS B 366 " pdb=" N CYS B 366 " pdb=" C CYS B 366 " pdb=" CB CYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA CYS A 366 " pdb=" N CYS A 366 " pdb=" C CYS A 366 " pdb=" CB CYS A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA CYS C 366 " pdb=" N CYS C 366 " pdb=" C CYS C 366 " pdb=" CB CYS C 366 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 1632 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 230 " -0.016 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR B 230 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 230 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 230 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 230 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " -0.016 2.00e-02 2.50e+03 1.44e-02 4.12e+00 pdb=" CG TYR A 230 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 230 " 0.015 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR C 230 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 230 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 230 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 230 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 230 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 230 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 230 " 0.003 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3132 2.81 - 3.33: 8418 3.33 - 3.85: 17081 3.85 - 4.38: 20621 4.38 - 4.90: 35915 Nonbonded interactions: 85167 Sorted by model distance: nonbonded pdb=" OG SER C 241 " pdb=" OE1 GLU C 243 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 241 " pdb=" OE1 GLU A 243 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C 283 " pdb=" O GLU B 80 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 241 " pdb=" OE1 GLU B 243 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 283 " pdb=" O GLU C 80 " model vdw 2.290 3.040 ... (remaining 85162 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.005 0.055 10962 Z= 0.232 Angle : 0.829 9.518 14883 Z= 0.458 Chirality : 0.048 0.176 1635 Planarity : 0.005 0.049 1920 Dihedral : 8.887 75.671 3966 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.44 (0.18), residues: 1332 helix: -4.97 (0.06), residues: 456 sheet: -1.42 (0.31), residues: 279 loop : -1.80 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 65 TYR 0.033 0.002 TYR B 230 PHE 0.020 0.002 PHE A 264 TRP 0.008 0.002 TRP A 47 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (10935) covalent geometry : angle 0.81802 / 0.45 (14823) SS BOND : bond 0.01075 / 0.69 ( 21) SS BOND : angle 2.32077 / 1.53 ( 42) hydrogen bonds : bond 0.28204 / 18.38 ( 462) hydrogen bonds : angle 11.01404 / 7.61 ( 1350) link_NAG-ASN : bond 0.01053 / 0.61 ( 6) link_NAG-ASN : angle 2.16923 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.398 Fit side-chains REVERT: A 106 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8161 (ttmm) REVERT: A 124 GLU cc_start: 0.7165 (pt0) cc_final: 0.6453 (pm20) REVERT: C 124 GLU cc_start: 0.7189 (pt0) cc_final: 0.6648 (pm20) REVERT: B 106 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8210 (ttmm) REVERT: B 108 ASP cc_start: 0.7926 (m-30) cc_final: 0.7523 (m-30) REVERT: B 124 GLU cc_start: 0.6984 (pt0) cc_final: 0.6296 (pm20) REVERT: B 453 PHE cc_start: 0.7296 (m-10) cc_final: 0.7075 (m-10) outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 0.6291 time to fit residues: 135.5902 Evaluate side-chains 103 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A 421 GLN C 120 ASN C 421 GLN B 202 GLN B 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111066 restraints weight = 13441.546| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.65 r_work: 0.3342 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10962 Z= 0.155 Angle : 0.634 6.870 14883 Z= 0.334 Chirality : 0.042 0.220 1635 Planarity : 0.005 0.056 1920 Dihedral : 5.594 31.003 1460 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.93 % Allowed : 8.18 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.84 (0.20), residues: 1332 helix: -2.78 (0.17), residues: 489 sheet: -1.05 (0.30), residues: 273 loop : -1.24 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 122 TYR 0.014 0.002 TYR A 230 PHE 0.012 0.001 PHE C 158 TRP 0.003 0.001 TRP B 234 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10935) covalent geometry : angle 0.62574 / 0.33 (14823) SS BOND : bond 0.00426 / 0.27 ( 21) SS BOND : angle 1.90379 / 1.38 ( 42) hydrogen bonds : bond 0.04505 / 2.99 ( 462) hydrogen bonds : angle 5.79235 / 3.97 ( 1350) link_NAG-ASN : bond 0.00343 / 0.20 ( 6) link_NAG-ASN : angle 1.31993 / 0.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.345 Fit side-chains REVERT: A 122 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7538 (mtp-110) REVERT: A 322 CYS cc_start: 0.5981 (p) cc_final: 0.5263 (t) REVERT: C 124 GLU cc_start: 0.7228 (pt0) cc_final: 0.6244 (pm20) REVERT: C 322 CYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5387 (t) REVERT: B 124 GLU cc_start: 0.7054 (pt0) cc_final: 0.6153 (pm20) REVERT: B 137 GLU cc_start: 0.6832 (tp30) cc_final: 0.6580 (tp30) REVERT: B 322 CYS cc_start: 0.5586 (OUTLIER) cc_final: 0.4979 (t) REVERT: B 391 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8195 (tttm) outliers start: 22 outliers final: 4 residues processed: 127 average time/residue: 0.6125 time to fit residues: 83.3920 Evaluate side-chains 96 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain B residue 322 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 97 optimal weight: 0.0170 chunk 18 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115660 restraints weight = 13599.092| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.56 r_work: 0.3341 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10962 Z= 0.137 Angle : 0.577 6.304 14883 Z= 0.302 Chirality : 0.042 0.192 1635 Planarity : 0.004 0.051 1920 Dihedral : 5.175 27.709 1458 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.58 % Allowed : 10.29 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.73 (0.22), residues: 1332 helix: -1.21 (0.22), residues: 489 sheet: -0.92 (0.30), residues: 273 loop : -1.01 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 122 TYR 0.015 0.001 TYR C 457 PHE 0.011 0.001 PHE B 158 TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10935) covalent geometry : angle 0.56588 / 0.30 (14823) SS BOND : bond 0.00395 / 0.26 ( 21) SS BOND : angle 2.08485 / 1.49 ( 42) hydrogen bonds : bond 0.03737 / 2.51 ( 462) hydrogen bonds : angle 5.13122 / 3.51 ( 1350) link_NAG-ASN : bond 0.00295 / 0.17 ( 6) link_NAG-ASN : angle 1.20959 / 0.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.436 Fit side-chains REVERT: A 122 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7087 (ptt90) REVERT: A 137 GLU cc_start: 0.6789 (tp30) cc_final: 0.6551 (tp30) REVERT: A 280 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8151 (ttp-110) REVERT: A 322 CYS cc_start: 0.5177 (OUTLIER) cc_final: 0.4435 (t) REVERT: C 124 GLU cc_start: 0.7168 (pt0) cc_final: 0.6320 (pm20) REVERT: C 450 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7554 (tt) REVERT: C 458 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6371 (tm-30) REVERT: B 124 GLU cc_start: 0.7013 (pt0) cc_final: 0.6080 (pm20) REVERT: B 137 GLU cc_start: 0.6796 (tp30) cc_final: 0.6342 (tp30) REVERT: B 322 CYS cc_start: 0.5384 (OUTLIER) cc_final: 0.4250 (t) REVERT: B 391 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8200 (tttm) REVERT: B 438 MET cc_start: 0.8313 (mtm) cc_final: 0.8070 (mtp) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 0.6648 time to fit residues: 75.3508 Evaluate side-chains 94 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115620 restraints weight = 13733.134| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.55 r_work: 0.3333 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10962 Z= 0.138 Angle : 0.565 7.011 14883 Z= 0.293 Chirality : 0.041 0.174 1635 Planarity : 0.004 0.072 1920 Dihedral : 5.015 26.902 1458 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.20 % Allowed : 11.08 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.15 (0.22), residues: 1332 helix: -0.49 (0.23), residues: 489 sheet: -0.71 (0.30), residues: 273 loop : -0.86 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 122 TYR 0.013 0.001 TYR C 457 PHE 0.009 0.001 PHE A 93 TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (10935) covalent geometry : angle 0.55439 / 0.29 (14823) SS BOND : bond 0.00363 / 0.23 ( 21) SS BOND : angle 1.99606 / 1.41 ( 42) hydrogen bonds : bond 0.03329 / 2.23 ( 462) hydrogen bonds : angle 4.87525 / 3.32 ( 1350) link_NAG-ASN : bond 0.00248 / 0.14 ( 6) link_NAG-ASN : angle 1.14910 / 0.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.363 Fit side-chains REVERT: A 137 GLU cc_start: 0.6861 (tp30) cc_final: 0.6593 (tp30) REVERT: A 280 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8154 (ttp-110) REVERT: A 458 GLU cc_start: 0.6483 (tm-30) cc_final: 0.6253 (tm-30) REVERT: C 124 GLU cc_start: 0.7150 (pt0) cc_final: 0.6166 (pm20) REVERT: B 124 GLU cc_start: 0.6911 (pt0) cc_final: 0.5964 (pm20) REVERT: B 137 GLU cc_start: 0.6795 (tp30) cc_final: 0.6308 (tp30) outliers start: 25 outliers final: 10 residues processed: 106 average time/residue: 0.6229 time to fit residues: 70.7161 Evaluate side-chains 90 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 93 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.147070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117116 restraints weight = 13498.001| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.54 r_work: 0.3353 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10962 Z= 0.106 Angle : 0.537 8.378 14883 Z= 0.279 Chirality : 0.040 0.162 1635 Planarity : 0.004 0.058 1920 Dihedral : 4.815 26.279 1458 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 11.17 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.71 (0.23), residues: 1332 helix: -0.04 (0.24), residues: 492 sheet: -0.55 (0.30), residues: 273 loop : -0.65 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 122 TYR 0.013 0.001 TYR C 457 PHE 0.008 0.001 PHE C 93 TRP 0.005 0.001 TRP A 47 HIS 0.001 0.000 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10935) covalent geometry : angle 0.52536 / 0.27 (14823) SS BOND : bond 0.00305 / 0.19 ( 21) SS BOND : angle 2.09961 / 1.56 ( 42) hydrogen bonds : bond 0.03080 / 2.09 ( 462) hydrogen bonds : angle 4.71775 / 3.22 ( 1350) link_NAG-ASN : bond 0.00309 / 0.18 ( 6) link_NAG-ASN : angle 1.07012 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.404 Fit side-chains REVERT: A 137 GLU cc_start: 0.6857 (tp30) cc_final: 0.6565 (tp30) REVERT: A 280 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8151 (ttp-110) REVERT: A 458 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6317 (tm-30) REVERT: C 124 GLU cc_start: 0.6989 (pt0) cc_final: 0.6319 (pm20) REVERT: B 124 GLU cc_start: 0.6870 (pt0) cc_final: 0.5910 (pm20) REVERT: B 137 GLU cc_start: 0.6786 (tp30) cc_final: 0.6276 (tp30) REVERT: B 202 GLN cc_start: 0.7619 (mt0) cc_final: 0.7381 (pt0) REVERT: B 391 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8158 (tttm) outliers start: 20 outliers final: 9 residues processed: 106 average time/residue: 0.6712 time to fit residues: 75.7784 Evaluate side-chains 89 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116075 restraints weight = 13631.176| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.54 r_work: 0.3339 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10962 Z= 0.134 Angle : 0.565 7.971 14883 Z= 0.290 Chirality : 0.041 0.166 1635 Planarity : 0.004 0.071 1920 Dihedral : 4.844 26.722 1458 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.67 % Allowed : 12.40 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.48 (0.23), residues: 1332 helix: 0.22 (0.24), residues: 489 sheet: -0.45 (0.30), residues: 273 loop : -0.59 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 122 TYR 0.011 0.001 TYR C 457 PHE 0.009 0.001 PHE A 93 TRP 0.003 0.001 TRP C 234 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (10935) covalent geometry : angle 0.55103 / 0.28 (14823) SS BOND : bond 0.00353 / 0.23 ( 21) SS BOND : angle 2.30424 / 1.67 ( 42) hydrogen bonds : bond 0.03148 / 2.12 ( 462) hydrogen bonds : angle 4.69805 / 3.20 ( 1350) link_NAG-ASN : bond 0.00273 / 0.16 ( 6) link_NAG-ASN : angle 1.10983 / 0.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.417 Fit side-chains REVERT: A 137 GLU cc_start: 0.6872 (tp30) cc_final: 0.6565 (tp30) REVERT: A 222 MET cc_start: 0.9315 (ttm) cc_final: 0.8998 (ttm) REVERT: A 280 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8127 (ttp-110) REVERT: C 124 GLU cc_start: 0.7081 (pt0) cc_final: 0.6237 (pm20) REVERT: B 124 GLU cc_start: 0.6830 (pt0) cc_final: 0.5955 (pm20) REVERT: B 137 GLU cc_start: 0.6781 (tp30) cc_final: 0.6269 (tp30) REVERT: B 391 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8229 (tttm) outliers start: 19 outliers final: 9 residues processed: 99 average time/residue: 0.7047 time to fit residues: 74.4177 Evaluate side-chains 93 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115873 restraints weight = 13598.369| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.54 r_work: 0.3335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10962 Z= 0.142 Angle : 0.570 7.491 14883 Z= 0.294 Chirality : 0.041 0.164 1635 Planarity : 0.004 0.057 1920 Dihedral : 4.868 26.255 1458 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.50 % Allowed : 12.49 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.33 (0.23), residues: 1332 helix: 0.41 (0.25), residues: 489 sheet: -0.41 (0.30), residues: 273 loop : -0.52 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 122 TYR 0.011 0.001 TYR C 457 PHE 0.009 0.001 PHE A 264 TRP 0.003 0.001 TRP C 234 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (10935) covalent geometry : angle 0.55688 / 0.29 (14823) SS BOND : bond 0.00337 / 0.21 ( 21) SS BOND : angle 2.31533 / 1.72 ( 42) hydrogen bonds : bond 0.03173 / 2.14 ( 462) hydrogen bonds : angle 4.68032 / 3.20 ( 1350) link_NAG-ASN : bond 0.00279 / 0.16 ( 6) link_NAG-ASN : angle 1.08052 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.425 Fit side-chains REVERT: A 137 GLU cc_start: 0.6887 (tp30) cc_final: 0.6558 (tp30) REVERT: A 280 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8126 (ttp-110) REVERT: C 124 GLU cc_start: 0.7011 (pt0) cc_final: 0.6350 (pm20) REVERT: B 124 GLU cc_start: 0.6873 (pt0) cc_final: 0.5943 (pm20) REVERT: B 137 GLU cc_start: 0.6862 (tp30) cc_final: 0.6459 (tp30) REVERT: B 391 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8247 (tttm) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.7228 time to fit residues: 75.4512 Evaluate side-chains 89 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115790 restraints weight = 13609.564| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.55 r_work: 0.3335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10962 Z= 0.140 Angle : 0.570 7.601 14883 Z= 0.293 Chirality : 0.041 0.151 1635 Planarity : 0.004 0.085 1920 Dihedral : 4.853 26.191 1458 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.67 % Allowed : 12.40 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.24 (0.23), residues: 1332 helix: 0.51 (0.25), residues: 489 sheet: -0.38 (0.30), residues: 273 loop : -0.50 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 122 TYR 0.010 0.001 TYR C 457 PHE 0.009 0.001 PHE A 264 TRP 0.003 0.001 TRP B 234 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (10935) covalent geometry : angle 0.55724 / 0.29 (14823) SS BOND : bond 0.00324 / 0.21 ( 21) SS BOND : angle 2.21355 / 1.64 ( 42) hydrogen bonds : bond 0.03127 / 2.11 ( 462) hydrogen bonds : angle 4.66892 / 3.19 ( 1350) link_NAG-ASN : bond 0.00270 / 0.16 ( 6) link_NAG-ASN : angle 1.07366 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.458 Fit side-chains REVERT: A 137 GLU cc_start: 0.6880 (tp30) cc_final: 0.6549 (tp30) REVERT: A 280 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8123 (ttp-110) REVERT: A 460 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7808 (mp) REVERT: C 124 GLU cc_start: 0.7084 (pt0) cc_final: 0.6214 (pm20) REVERT: B 124 GLU cc_start: 0.6827 (pt0) cc_final: 0.5987 (pm20) REVERT: B 137 GLU cc_start: 0.6835 (tp30) cc_final: 0.6391 (tp30) REVERT: B 202 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: B 271 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 391 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8247 (tttm) outliers start: 19 outliers final: 11 residues processed: 98 average time/residue: 0.7239 time to fit residues: 75.7084 Evaluate side-chains 93 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115326 restraints weight = 13572.605| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.54 r_work: 0.3328 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10962 Z= 0.162 Angle : 0.586 7.761 14883 Z= 0.302 Chirality : 0.042 0.152 1635 Planarity : 0.004 0.058 1920 Dihedral : 4.903 26.022 1458 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.58 % Allowed : 12.58 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.27 (0.23), residues: 1332 helix: 0.48 (0.25), residues: 489 sheet: -0.36 (0.30), residues: 273 loop : -0.52 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 122 TYR 0.011 0.001 TYR C 457 PHE 0.009 0.001 PHE A 264 TRP 0.003 0.001 TRP B 47 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (10935) covalent geometry : angle 0.57371 / 0.30 (14823) SS BOND : bond 0.00329 / 0.21 ( 21) SS BOND : angle 2.23531 / 1.64 ( 42) hydrogen bonds : bond 0.03250 / 2.19 ( 462) hydrogen bonds : angle 4.70204 / 3.21 ( 1350) link_NAG-ASN : bond 0.00256 / 0.15 ( 6) link_NAG-ASN : angle 1.09327 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.427 Fit side-chains REVERT: A 134 LYS cc_start: 0.7587 (tppt) cc_final: 0.6846 (tmmt) REVERT: A 137 GLU cc_start: 0.6891 (tp30) cc_final: 0.6551 (tp30) REVERT: A 280 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8117 (ttp-110) REVERT: A 460 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7784 (mp) REVERT: C 124 GLU cc_start: 0.6986 (pt0) cc_final: 0.6359 (pm20) REVERT: B 124 GLU cc_start: 0.6861 (pt0) cc_final: 0.5882 (pm20) REVERT: B 137 GLU cc_start: 0.6838 (tp30) cc_final: 0.6395 (tp30) REVERT: B 202 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: B 271 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: B 391 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8249 (tttm) outliers start: 18 outliers final: 12 residues processed: 97 average time/residue: 0.7053 time to fit residues: 72.9706 Evaluate side-chains 97 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115812 restraints weight = 13573.729| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.54 r_work: 0.3336 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10962 Z= 0.134 Angle : 0.569 7.099 14883 Z= 0.294 Chirality : 0.041 0.156 1635 Planarity : 0.004 0.055 1920 Dihedral : 4.843 25.681 1458 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.58 % Allowed : 12.84 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.20 (0.23), residues: 1332 helix: 0.56 (0.25), residues: 489 sheet: -0.34 (0.30), residues: 273 loop : -0.50 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 122 TYR 0.011 0.001 TYR C 457 PHE 0.009 0.001 PHE A 264 TRP 0.003 0.001 TRP A 234 HIS 0.002 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (10935) covalent geometry : angle 0.55833 / 0.29 (14823) SS BOND : bond 0.00313 / 0.20 ( 21) SS BOND : angle 2.09994 / 1.54 ( 42) hydrogen bonds : bond 0.03124 / 2.11 ( 462) hydrogen bonds : angle 4.67023 / 3.19 ( 1350) link_NAG-ASN : bond 0.00275 / 0.16 ( 6) link_NAG-ASN : angle 1.04032 / 0.64 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.340 Fit side-chains REVERT: A 134 LYS cc_start: 0.7579 (tppt) cc_final: 0.6852 (tmmt) REVERT: A 137 GLU cc_start: 0.6886 (tp30) cc_final: 0.6546 (tp30) REVERT: A 280 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8121 (ttp-110) REVERT: A 460 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7782 (mp) REVERT: C 124 GLU cc_start: 0.6961 (pt0) cc_final: 0.6363 (pm20) REVERT: B 124 GLU cc_start: 0.6820 (pt0) cc_final: 0.6003 (pm20) REVERT: B 137 GLU cc_start: 0.6839 (tp30) cc_final: 0.6394 (tp30) REVERT: B 202 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: B 271 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: B 391 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8256 (tttm) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.7149 time to fit residues: 73.1058 Evaluate side-chains 95 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 101 optimal weight: 0.0020 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116795 restraints weight = 13508.478| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.55 r_work: 0.3348 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10962 Z= 0.119 Angle : 0.554 6.801 14883 Z= 0.287 Chirality : 0.041 0.151 1635 Planarity : 0.004 0.055 1920 Dihedral : 4.772 25.390 1458 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.67 % Allowed : 13.10 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.12 (0.23), residues: 1332 helix: 0.65 (0.25), residues: 489 sheet: -0.32 (0.30), residues: 273 loop : -0.47 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 122 TYR 0.011 0.001 TYR C 457 PHE 0.009 0.001 PHE C 93 TRP 0.002 0.001 TRP A 234 HIS 0.002 0.000 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10935) covalent geometry : angle 0.54378 / 0.28 (14823) SS BOND : bond 0.00303 / 0.19 ( 21) SS BOND : angle 2.01727 / 1.48 ( 42) hydrogen bonds : bond 0.03025 / 2.04 ( 462) hydrogen bonds : angle 4.62259 / 3.16 ( 1350) link_NAG-ASN : bond 0.00288 / 0.16 ( 6) link_NAG-ASN : angle 1.01486 / 0.63 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3533.71 seconds wall clock time: 60 minutes 55.82 seconds (3655.82 seconds total)