Starting phenix.real_space_refine on Mon Jul 28 23:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vtk_21380/07_2025/6vtk_21380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtk_21380/07_2025/6vtk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vtk_21380/07_2025/6vtk_21380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtk_21380/07_2025/6vtk_21380.map" model { file = "/net/cci-nas-00/data/ceres_data/6vtk_21380/07_2025/6vtk_21380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtk_21380/07_2025/6vtk_21380.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU: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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, B Time building chain proxies: 7.02, per 1000 atoms: 0.66 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.24 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: 3.24 Time building geometry restraints manager: 3.02 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: 6296 15.13 - 30.27: 298 30.27 - 45.40: 48 45.40 - 60.54: 12 60.54 - 75.67: 9 Dihedral angle restraints: 6663 sinusoidal: 2748 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 6660 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: 0.07 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: 2.780 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.800 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 9.132 75.671 4092 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.002 TRP A 47 HIS 0.004 0.001 HIS B 164 PHE 0.020 0.002 PHE A 264 TYR 0.033 0.002 TYR B 230 ARG 0.003 0.001 ARG C 65 Details of bonding type rmsd link_NAG-ASN : bond 0.01053 ( 6) link_NAG-ASN : angle 2.16923 ( 18) hydrogen bonds : bond 0.28204 ( 462) hydrogen bonds : angle 11.01404 ( 1350) SS BOND : bond 0.01075 ( 21) SS BOND : angle 2.32077 ( 42) covalent geometry : bond 0.00528 (10935) covalent geometry : angle 0.81802 (14823) *********************** 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 : 1.127 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: 1.4505 time to fit residues: 312.9672 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 : 1.286 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3785 r_free = 0.3785 target = 0.140317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110690 restraints weight = 13395.582| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.64 r_work: 0.3338 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10962 Z= 0.164 Angle : 0.642 6.966 14883 Z= 0.338 Chirality : 0.043 0.221 1635 Planarity : 0.005 0.056 1920 Dihedral : 6.338 51.889 1586 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.11 % Allowed : 8.00 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.20), residues: 1332 helix: -2.74 (0.18), residues: 489 sheet: -1.05 (0.30), residues: 273 loop : -1.25 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 234 HIS 0.002 0.001 HIS B 111 PHE 0.013 0.002 PHE C 158 TYR 0.015 0.002 TYR B 230 ARG 0.009 0.001 ARG C 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 1.36528 ( 18) hydrogen bonds : bond 0.04453 ( 462) hydrogen bonds : angle 5.76761 ( 1350) SS BOND : bond 0.00427 ( 21) SS BOND : angle 1.90174 ( 42) covalent geometry : bond 0.00383 (10935) covalent geometry : angle 0.63348 (14823) *********************** 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 138 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.764 Fit side-chains REVERT: A 122 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7574 (mtp-110) REVERT: A 322 CYS cc_start: 0.5960 (p) cc_final: 0.5263 (t) REVERT: C 124 GLU cc_start: 0.7258 (pt0) cc_final: 0.6274 (pm20) REVERT: C 322 CYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5382 (t) REVERT: B 122 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7559 (mtm110) REVERT: B 137 GLU cc_start: 0.6845 (tp30) cc_final: 0.6595 (tp30) REVERT: B 322 CYS cc_start: 0.5572 (OUTLIER) cc_final: 0.4990 (t) REVERT: B 391 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8199 (tttm) outliers start: 24 outliers final: 5 residues processed: 130 average time/residue: 1.9527 time to fit residues: 274.5497 Evaluate side-chains 98 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 C residue 376 SER 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 69 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115631 restraints weight = 13691.399| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.55 r_work: 0.3339 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2212 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= 0.143 Angle : 0.583 6.644 14883 Z= 0.304 Chirality : 0.042 0.196 1635 Planarity : 0.004 0.052 1920 Dihedral : 5.917 50.833 1584 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.76 % Allowed : 10.20 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1332 helix: -1.21 (0.22), residues: 489 sheet: -0.90 (0.30), residues: 273 loop : -1.01 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS C 33 PHE 0.010 0.001 PHE B 158 TYR 0.016 0.001 TYR C 457 ARG 0.009 0.001 ARG C 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 1.30342 ( 18) hydrogen bonds : bond 0.03817 ( 462) hydrogen bonds : angle 5.14706 ( 1350) SS BOND : bond 0.00413 ( 21) SS BOND : angle 2.03363 ( 42) covalent geometry : bond 0.00340 (10935) covalent geometry : angle 0.57214 (14823) *********************** 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 111 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.197 Fit side-chains REVERT: A 122 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7196 (ptt90) REVERT: A 134 LYS cc_start: 0.7622 (tppt) cc_final: 0.7352 (tppt) REVERT: A 137 GLU cc_start: 0.6836 (tp30) cc_final: 0.6562 (tp30) REVERT: A 280 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8177 (ttp-110) REVERT: A 322 CYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4394 (t) REVERT: C 124 GLU cc_start: 0.7205 (pt0) cc_final: 0.6280 (pm20) REVERT: C 450 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7596 (tt) REVERT: C 458 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6398 (tm-30) REVERT: B 137 GLU cc_start: 0.6806 (tp30) cc_final: 0.6349 (tp30) REVERT: B 322 CYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4305 (t) REVERT: B 391 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8204 (tttm) outliers start: 20 outliers final: 6 residues processed: 106 average time/residue: 1.6111 time to fit residues: 183.2491 Evaluate side-chains 91 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3839 r_free = 0.3839 target = 0.144929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115227 restraints weight = 13556.914| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.55 r_work: 0.3327 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: 0.8005 moved from start: 0.2462 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= 0.143 Angle : 0.568 7.116 14883 Z= 0.295 Chirality : 0.042 0.177 1635 Planarity : 0.004 0.065 1920 Dihedral : 5.773 50.928 1584 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 10.82 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1332 helix: -0.56 (0.23), residues: 492 sheet: -0.75 (0.30), residues: 273 loop : -0.87 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 47 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE B 93 TYR 0.013 0.001 TYR C 457 ARG 0.011 0.001 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 6) link_NAG-ASN : angle 1.19537 ( 18) hydrogen bonds : bond 0.03359 ( 462) hydrogen bonds : angle 4.90000 ( 1350) SS BOND : bond 0.00389 ( 21) SS BOND : angle 2.01150 ( 42) covalent geometry : bond 0.00343 (10935) covalent geometry : angle 0.55710 (14823) *********************** 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 109 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 2.127 Fit side-chains REVERT: A 137 GLU cc_start: 0.6952 (tp30) cc_final: 0.6618 (tp30) REVERT: A 280 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8148 (ttp-110) REVERT: A 458 GLU cc_start: 0.6399 (tm-30) cc_final: 0.6149 (tm-30) REVERT: C 124 GLU cc_start: 0.7064 (pt0) cc_final: 0.6130 (pm20) REVERT: C 450 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7586 (tt) REVERT: B 137 GLU cc_start: 0.6810 (tp30) cc_final: 0.6458 (tp30) outliers start: 25 outliers final: 9 residues processed: 101 average time/residue: 1.7336 time to fit residues: 189.3675 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 : 1.197 ------------------------------------------------------------------------------- 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 C residue 450 LEU 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 107 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3827 r_free = 0.3827 target = 0.143997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114219 restraints weight = 13659.286| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.54 r_work: 0.3309 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10962 Z= 0.181 Angle : 0.609 8.954 14883 Z= 0.314 Chirality : 0.043 0.181 1635 Planarity : 0.004 0.056 1920 Dihedral : 5.813 49.928 1584 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.20 % Allowed : 10.99 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1332 helix: -0.25 (0.24), residues: 489 sheet: -0.57 (0.30), residues: 273 loop : -0.81 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS C 33 PHE 0.010 0.001 PHE B 93 TYR 0.013 0.001 TYR B 425 ARG 0.011 0.000 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 1.24645 ( 18) hydrogen bonds : bond 0.03520 ( 462) hydrogen bonds : angle 4.89480 ( 1350) SS BOND : bond 0.00375 ( 21) SS BOND : angle 2.62628 ( 42) covalent geometry : bond 0.00438 (10935) covalent geometry : angle 0.59212 (14823) *********************** 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 110 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.307 Fit side-chains REVERT: A 137 GLU cc_start: 0.6959 (tp30) cc_final: 0.6602 (tp30) REVERT: A 280 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8129 (ttp-110) REVERT: C 124 GLU cc_start: 0.7079 (pt0) cc_final: 0.6275 (pm20) REVERT: C 450 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7673 (tt) REVERT: B 137 GLU cc_start: 0.6822 (tp30) cc_final: 0.6460 (tp30) REVERT: B 391 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8198 (tttm) REVERT: B 458 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6246 (tm-30) outliers start: 25 outliers final: 11 residues processed: 103 average time/residue: 1.7504 time to fit residues: 193.0288 Evaluate side-chains 93 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET 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 C residue 450 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 112 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3811 r_free = 0.3811 target = 0.142588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112887 restraints weight = 13818.180| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.55 r_work: 0.3292 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2756 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= 0.224 Angle : 0.650 9.308 14883 Z= 0.333 Chirality : 0.044 0.168 1635 Planarity : 0.004 0.082 1920 Dihedral : 5.904 49.136 1584 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 11.43 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1332 helix: -0.26 (0.24), residues: 492 sheet: -0.54 (0.30), residues: 273 loop : -0.81 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 HIS 0.003 0.001 HIS C 33 PHE 0.010 0.002 PHE A 264 TYR 0.015 0.002 TYR B 425 ARG 0.014 0.001 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 1.27916 ( 18) hydrogen bonds : bond 0.03681 ( 462) hydrogen bonds : angle 4.94811 ( 1350) SS BOND : bond 0.00402 ( 21) SS BOND : angle 2.80277 ( 42) covalent geometry : bond 0.00548 (10935) covalent geometry : angle 0.63197 (14823) *********************** 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 108 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.208 Fit side-chains REVERT: A 137 GLU cc_start: 0.7000 (tp30) cc_final: 0.6635 (tp30) REVERT: A 458 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6177 (tm-30) REVERT: C 124 GLU cc_start: 0.7129 (pt0) cc_final: 0.6258 (pm20) REVERT: C 450 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7737 (tt) REVERT: B 137 GLU cc_start: 0.6878 (tp30) cc_final: 0.6515 (tp30) REVERT: B 391 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8232 (tttm) outliers start: 22 outliers final: 14 residues processed: 102 average time/residue: 1.4389 time to fit residues: 157.1701 Evaluate side-chains 100 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 155 MET 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 C residue 450 LEU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3835 r_free = 0.3835 target = 0.144579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114837 restraints weight = 13846.485| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.56 r_work: 0.3320 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10962 Z= 0.138 Angle : 0.569 7.429 14883 Z= 0.295 Chirality : 0.041 0.156 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.724 49.855 1584 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1332 helix: 0.02 (0.24), residues: 492 sheet: -0.53 (0.30), residues: 273 loop : -0.67 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 288 HIS 0.002 0.001 HIS B 111 PHE 0.010 0.001 PHE A 264 TYR 0.015 0.001 TYR C 457 ARG 0.007 0.000 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 1.10577 ( 18) hydrogen bonds : bond 0.03239 ( 462) hydrogen bonds : angle 4.79154 ( 1350) SS BOND : bond 0.00324 ( 21) SS BOND : angle 2.38963 ( 42) covalent geometry : bond 0.00335 (10935) covalent geometry : angle 0.55478 (14823) *********************** 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 105 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.143 Fit side-chains REVERT: A 134 LYS cc_start: 0.7630 (tppt) cc_final: 0.6939 (tmmt) REVERT: A 137 GLU cc_start: 0.6913 (tp30) cc_final: 0.6554 (tp30) REVERT: A 280 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8119 (ttp-110) REVERT: A 458 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6277 (tm-30) REVERT: C 124 GLU cc_start: 0.7023 (pt0) cc_final: 0.6208 (pm20) REVERT: B 137 GLU cc_start: 0.6838 (tp30) cc_final: 0.6423 (tp30) REVERT: B 202 GLN cc_start: 0.7639 (mt0) cc_final: 0.7422 (pt0) REVERT: B 391 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8229 (tttm) REVERT: B 458 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6499 (tm-30) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 1.8337 time to fit residues: 200.3914 Evaluate side-chains 92 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 366 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114925 restraints weight = 13587.209| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.57 r_work: 0.3318 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2904 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= 0.141 Angle : 0.571 7.711 14883 Z= 0.295 Chirality : 0.041 0.157 1635 Planarity : 0.004 0.072 1920 Dihedral : 5.682 50.211 1584 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.76 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1332 helix: 0.20 (0.24), residues: 489 sheet: -0.44 (0.30), residues: 273 loop : -0.61 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 234 HIS 0.002 0.001 HIS B 111 PHE 0.010 0.001 PHE A 264 TYR 0.014 0.001 TYR C 457 ARG 0.017 0.000 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 6) link_NAG-ASN : angle 1.14996 ( 18) hydrogen bonds : bond 0.03192 ( 462) hydrogen bonds : angle 4.73370 ( 1350) SS BOND : bond 0.00323 ( 21) SS BOND : angle 2.24761 ( 42) covalent geometry : bond 0.00343 (10935) covalent geometry : angle 0.55811 (14823) *********************** 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 102 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.157 Fit side-chains REVERT: A 134 LYS cc_start: 0.7607 (tppt) cc_final: 0.6905 (tmmt) REVERT: A 137 GLU cc_start: 0.6940 (tp30) cc_final: 0.6553 (tp30) REVERT: A 280 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8138 (ttp-110) REVERT: A 460 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7677 (mp) REVERT: C 124 GLU cc_start: 0.7090 (pt0) cc_final: 0.6191 (pm20) REVERT: B 137 GLU cc_start: 0.6816 (tp30) cc_final: 0.6396 (tp30) REVERT: B 391 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8208 (tttm) REVERT: B 458 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6524 (tm-30) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 1.9320 time to fit residues: 200.3739 Evaluate side-chains 93 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 3.199 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN B 121 ASN B 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114672 restraints weight = 13729.240| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.56 r_work: 0.3317 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10962 Z= 0.157 Angle : 0.583 8.032 14883 Z= 0.301 Chirality : 0.042 0.159 1635 Planarity : 0.004 0.067 1920 Dihedral : 5.688 50.048 1584 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.67 % Allowed : 13.02 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1332 helix: 0.27 (0.24), residues: 489 sheet: -0.40 (0.30), residues: 273 loop : -0.57 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE A 264 TYR 0.014 0.001 TYR C 457 ARG 0.019 0.001 ARG C 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 1.15852 ( 18) hydrogen bonds : bond 0.03244 ( 462) hydrogen bonds : angle 4.75306 ( 1350) SS BOND : bond 0.00331 ( 21) SS BOND : angle 2.30012 ( 42) covalent geometry : bond 0.00382 (10935) covalent geometry : angle 0.56954 (14823) *********************** 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 99 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.380 Fit side-chains REVERT: A 134 LYS cc_start: 0.7602 (tppt) cc_final: 0.6909 (tmmt) REVERT: A 137 GLU cc_start: 0.6951 (tp30) cc_final: 0.6558 (tp30) REVERT: A 280 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8168 (ttp-110) REVERT: A 460 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7754 (mp) REVERT: C 124 GLU cc_start: 0.6980 (pt0) cc_final: 0.6103 (pm20) REVERT: B 137 GLU cc_start: 0.6859 (tp30) cc_final: 0.6437 (tp30) REVERT: B 391 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8243 (tttm) REVERT: B 426 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: B 458 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6534 (tm-30) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 2.0931 time to fit residues: 209.3902 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 : 2.589 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115760 restraints weight = 13511.122| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.57 r_work: 0.3328 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10962 Z= 0.127 Angle : 0.558 7.160 14883 Z= 0.289 Chirality : 0.041 0.153 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.595 50.433 1584 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.41 % Allowed : 13.46 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1332 helix: 0.37 (0.24), residues: 498 sheet: -0.36 (0.30), residues: 273 loop : -0.45 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE C 93 TYR 0.013 0.001 TYR C 457 ARG 0.009 0.000 ARG C 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 1.09282 ( 18) hydrogen bonds : bond 0.03073 ( 462) hydrogen bonds : angle 4.66982 ( 1350) SS BOND : bond 0.00302 ( 21) SS BOND : angle 2.08683 ( 42) covalent geometry : bond 0.00306 (10935) covalent geometry : angle 0.54644 (14823) ********************** 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 102 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 2.045 Fit side-chains REVERT: A 134 LYS cc_start: 0.7556 (tppt) cc_final: 0.6899 (tmmt) REVERT: A 137 GLU cc_start: 0.6927 (tp30) cc_final: 0.6532 (tp30) REVERT: A 280 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8124 (ttp-110) REVERT: A 460 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7476 (mp) REVERT: C 124 GLU cc_start: 0.6909 (pt0) cc_final: 0.6235 (pm20) REVERT: B 137 GLU cc_start: 0.6789 (tp30) cc_final: 0.6366 (tp30) REVERT: B 391 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8222 (tttm) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 2.2256 time to fit residues: 237.5177 Evaluate side-chains 95 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3835 r_free = 0.3835 target = 0.144623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114660 restraints weight = 13605.863| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.55 r_work: 0.3314 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10962 Z= 0.163 Angle : 0.590 8.619 14883 Z= 0.304 Chirality : 0.042 0.160 1635 Planarity : 0.004 0.056 1920 Dihedral : 5.649 50.123 1584 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.50 % Allowed : 13.72 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1332 helix: 0.49 (0.25), residues: 489 sheet: -0.37 (0.30), residues: 273 loop : -0.50 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.010 0.001 PHE A 264 TYR 0.015 0.001 TYR C 457 ARG 0.008 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 1.17812 ( 18) hydrogen bonds : bond 0.03231 ( 462) hydrogen bonds : angle 4.72870 ( 1350) SS BOND : bond 0.00335 ( 21) SS BOND : angle 2.17774 ( 42) covalent geometry : bond 0.00397 (10935) covalent geometry : angle 0.57790 (14823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9555.21 seconds wall clock time: 176 minutes 16.13 seconds (10576.13 seconds total)