Starting phenix.real_space_refine on Sat Aug 23 12:39:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jn0_61617/08_2025/9jn0_61617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jn0_61617/08_2025/9jn0_61617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jn0_61617/08_2025/9jn0_61617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jn0_61617/08_2025/9jn0_61617.map" model { file = "/net/cci-nas-00/data/ceres_data/9jn0_61617/08_2025/9jn0_61617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jn0_61617/08_2025/9jn0_61617.cif" } resolution = 2.84 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= 0.028 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 69 5.16 5 C 7520 2.51 5 N 2054 2.21 5 O 2358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12001 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3897 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 19, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3892 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 19, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3892 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 19, 'TRANS': 466} Chain breaks: 1 Chain: "D" 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 Chain: "E" 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 Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 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 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.38, per 1000 atoms: 0.20 Number of scatterers: 12001 At special positions: 0 Unit cell: (89.7, 86.25, 153.18, 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 69 16.00 O 2358 8.00 N 2054 7.00 C 7520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " GAL F 2 " " NAG K 1 " - " GAL K 2 " " NAG L 1 " - " GAL L 2 " BETA2-6 " GAL F 2 " - " SIA F 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL K 2 " - " SIA K 3 " " GAL L 2 " - " SIA L 3 " NAG-ASN " NAG A 601 " - " ASN A 165 " " NAG A 602 " - " ASN A 11 " " NAG A 603 " - " ASN A 23 " " NAG A 604 " - " ASN A 286 " " NAG B 601 " - " ASN B 11 " " NAG B 602 " - " ASN B 286 " " NAG C 601 " - " ASN C 165 " " NAG C 602 " - " ASN C 23 " " NAG C 603 " - " ASN C 286 " " NAG D 1 " - " ASN B 165 " " NAG E 1 " - " ASN B 23 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 400.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 33 sheets defined 26.7% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.527A pdb=" N TRP A 122 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 366 through 387 removed outlier: 3.622A pdb=" N THR A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 452 removed outlier: 3.512A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.867A pdb=" N TYR A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.553A pdb=" N TRP B 122 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.721A pdb=" N GLU B 340 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 366 through 387 removed outlier: 3.566A pdb=" N THR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 456 removed outlier: 3.597A pdb=" N ASP B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.128A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.738A pdb=" N TRP C 122 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 366 through 387 removed outlier: 3.759A pdb=" N LYS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 452 removed outlier: 3.595A pdb=" N GLU C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 491 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.582A pdb=" N SER A 356 " --> pdb=" O GLN A 2 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.999A pdb=" N GLU A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.761A pdb=" N LEU A 41 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N CYS A 274 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.731A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 79 " --> pdb=" O MET A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.935A pdb=" N SER A 94 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N TRP A 230 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 225 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 171 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU A 175 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR A 252 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 110 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.935A pdb=" N SER A 94 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N TRP A 230 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 225 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A 175 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 177 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.775A pdb=" N CYS A 135 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 160 through 165 Processing sheet with id=AB2, first strand: chain 'A' and resid 283 through 285 removed outlier: 4.113A pdb=" N CYS A 278 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 393 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.690A pdb=" N GLY B 352 " --> pdb=" O GLY B 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 6 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 356 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 3 " --> pdb=" O PHE B 467 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.044A pdb=" N LEU B 41 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS B 274 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.524A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 79 " --> pdb=" O MET B 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.923A pdb=" N SER B 94 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N TRP B 230 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 225 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 171 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 175 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR B 252 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 257 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N HIS B 110 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.923A pdb=" N SER B 94 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N TRP B 230 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 225 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU B 175 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 137 removed outlier: 4.887A pdb=" N CYS B 135 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.775A pdb=" N CYS B 278 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 393 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.698A pdb=" N GLY C 352 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS C 4 " --> pdb=" O HIS C 354 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 356 " --> pdb=" O GLN C 2 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.093A pdb=" N GLU C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC8, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.960A pdb=" N LEU C 41 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N CYS C 274 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.545A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.921A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 225 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 171 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU C 175 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C 252 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.921A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 225 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU C 175 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 132 through 137 removed outlier: 4.722A pdb=" N CYS C 135 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 160 through 165 removed outlier: 3.553A pdb=" N ILE C 162 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 283 through 285 removed outlier: 4.062A pdb=" N CYS C 278 " --> pdb=" O ILE C 285 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1380 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: 2.24 Time building geometry restraints manager: 1.22 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: 3952 1.34 - 1.46: 2873 1.46 - 1.58: 5338 1.58 - 1.70: 3 1.70 - 1.82: 102 Bond restraints: 12268 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 16515 3.10 - 6.19: 86 6.19 - 9.29: 9 9.29 - 12.39: 5 12.39 - 15.48: 1 Bond angle restraints: 16616 Sorted by residual: angle pdb=" CA LEU A 453 " pdb=" CB LEU A 453 " pdb=" CG LEU A 453 " ideal model delta sigma weight residual 116.30 131.78 -15.48 3.50e+00 8.16e-02 1.96e+01 angle pdb=" C ASN A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta sigma weight residual 122.67 129.35 -6.68 1.59e+00 3.96e-01 1.77e+01 angle pdb=" CB MET A 388 " pdb=" CG MET A 388 " pdb=" SD MET A 388 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ARG C 72 " pdb=" CB ARG C 72 " pdb=" CG ARG C 72 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CB MET A 66 " pdb=" CG MET A 66 " pdb=" SD MET A 66 " ideal model delta sigma weight residual 112.70 122.63 -9.93 3.00e+00 1.11e-01 1.10e+01 ... (remaining 16611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6958 17.91 - 35.82: 562 35.82 - 53.74: 118 53.74 - 71.65: 46 71.65 - 89.56: 11 Dihedral angle restraints: 7695 sinusoidal: 3456 harmonic: 4239 Sorted by residual: dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual 93.00 145.52 -52.52 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CA ASN B 23 " pdb=" C ASN B 23 " pdb=" N VAL B 24 " pdb=" CA VAL B 24 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LYS A 255 " pdb=" C LYS A 255 " pdb=" N ILE A 256 " pdb=" CA ILE A 256 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1822 0.136 - 0.272: 8 0.272 - 0.408: 2 0.408 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 1833 Sorted by residual: chirality pdb=" C2 SIA F 3 " pdb=" O6 GAL F 2 " pdb=" C1 SIA F 3 " pdb=" O6 SIA F 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.73 0.23 2.00e-02 2.50e+03 1.34e+02 chirality pdb=" C2 SIA L 3 " pdb=" O6 GAL L 2 " pdb=" C1 SIA L 3 " pdb=" O6 SIA L 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C2 SIA K 3 " pdb=" O6 GAL K 2 " pdb=" C1 SIA K 3 " pdb=" O6 SIA K 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-02 2.50e+03 1.08e+02 ... (remaining 1830 not shown) Planarity restraints: 2155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 11 " 0.034 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" CG ASN A 11 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 11 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 11 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG A 602 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 23 " 0.021 2.00e-02 2.50e+03 1.90e-02 4.53e+00 pdb=" CG ASN C 23 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 23 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 23 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 70 " -0.013 2.00e-02 2.50e+03 1.45e-02 3.69e+00 pdb=" CG PHE A 70 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 70 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 70 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 70 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 70 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 70 " -0.001 2.00e-02 2.50e+03 ... (remaining 2152 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 884 2.74 - 3.28: 11161 3.28 - 3.82: 18947 3.82 - 4.36: 22066 4.36 - 4.90: 39207 Nonbonded interactions: 92265 Sorted by model distance: nonbonded pdb=" N GLU C 270 " pdb=" OE1 GLU C 270 " model vdw 2.199 3.120 nonbonded pdb=" N GLU B 270 " pdb=" OE1 GLU B 270 " model vdw 2.230 3.120 nonbonded pdb=" NZ LYS B 258 " pdb=" O GLY B 260 " model vdw 2.280 3.120 nonbonded pdb=" OE2 GLU C 126 " pdb=" OG SER C 128 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR B 280 " pdb=" O GLY B 283 " model vdw 2.287 3.040 ... (remaining 92260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 320 or resid 335 through 602)) selection = chain 'B' selection = (chain 'C' and resid 1 through 602) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.850 Find NCS groups from input model: 0.260 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 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 : 0.003 0.051 12305 Z= 0.145 Angle : 0.714 21.904 16709 Z= 0.315 Chirality : 0.047 0.681 1833 Planarity : 0.003 0.039 2144 Dihedral : 14.138 89.559 4921 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.70 % Allowed : 14.80 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.44 (0.22), residues: 1447 helix: 2.30 (0.27), residues: 370 sheet: 0.64 (0.32), residues: 228 loop : -0.76 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.010 0.001 TYR C 164 PHE 0.034 0.001 PHE A 70 TRP 0.005 0.000 TRP B 343 HIS 0.002 0.000 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00293 (12268) covalent geometry : angle 0.61487 (16616) SS BOND : bond 0.00113 ( 18) SS BOND : angle 0.71382 ( 36) hydrogen bonds : bond 0.18549 ( 458) hydrogen bonds : angle 6.89190 ( 1380) glycosidic custom : bond 0.00574 ( 3) glycosidic custom : angle 9.42988 ( 9) link_BETA1-4 : bond 0.00397 ( 5) link_BETA1-4 : angle 1.78157 ( 15) link_NAG-ASN : bond 0.00897 ( 11) link_NAG-ASN : angle 6.44810 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.4736 time to fit residues: 38.8954 Evaluate side-chains 71 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.043526 restraints weight = 37385.679| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 4.14 r_work: 0.2418 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12305 Z= 0.133 Angle : 0.596 18.181 16709 Z= 0.291 Chirality : 0.043 0.298 1833 Planarity : 0.003 0.037 2144 Dihedral : 8.150 84.062 2086 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 12.77 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.45 (0.22), residues: 1447 helix: 2.44 (0.28), residues: 373 sheet: 0.63 (0.31), residues: 248 loop : -0.86 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 435 TYR 0.011 0.001 TYR C 353 PHE 0.014 0.001 PHE B 70 TRP 0.004 0.001 TRP A 176 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00299 (12268) covalent geometry : angle 0.55564 (16616) SS BOND : bond 0.00185 ( 18) SS BOND : angle 0.84622 ( 36) hydrogen bonds : bond 0.05675 ( 458) hydrogen bonds : angle 5.17782 ( 1380) glycosidic custom : bond 0.00770 ( 3) glycosidic custom : angle 1.55043 ( 9) link_BETA1-4 : bond 0.00315 ( 5) link_BETA1-4 : angle 1.27013 ( 15) link_NAG-ASN : bond 0.00622 ( 11) link_NAG-ASN : angle 4.72444 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.520 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 81 average time/residue: 0.5340 time to fit residues: 48.0505 Evaluate side-chains 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 367 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 0.0060 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN B 440 HIS C 355 HIS C 440 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.062828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.043864 restraints weight = 37475.459| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 4.10 r_work: 0.2426 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12305 Z= 0.116 Angle : 0.565 17.297 16709 Z= 0.272 Chirality : 0.042 0.246 1833 Planarity : 0.003 0.033 2144 Dihedral : 7.447 82.723 2077 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.34 % Allowed : 12.23 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.56 (0.22), residues: 1447 helix: 2.50 (0.28), residues: 373 sheet: 1.08 (0.33), residues: 228 loop : -0.87 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 435 TYR 0.009 0.001 TYR B 271 PHE 0.017 0.001 PHE A 70 TRP 0.003 0.000 TRP B 343 HIS 0.004 0.000 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00258 (12268) covalent geometry : angle 0.53050 (16616) SS BOND : bond 0.00180 ( 18) SS BOND : angle 0.78367 ( 36) hydrogen bonds : bond 0.05283 ( 458) hydrogen bonds : angle 4.85186 ( 1380) glycosidic custom : bond 0.00443 ( 3) glycosidic custom : angle 1.24748 ( 9) link_BETA1-4 : bond 0.00351 ( 5) link_BETA1-4 : angle 1.31025 ( 15) link_NAG-ASN : bond 0.00452 ( 11) link_NAG-ASN : angle 4.22405 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9080 (m-80) cc_final: 0.8510 (m-80) REVERT: C 449 ASP cc_start: 0.9557 (OUTLIER) cc_final: 0.8859 (p0) REVERT: C 450 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9085 (tptp) outliers start: 30 outliers final: 9 residues processed: 94 average time/residue: 0.5124 time to fit residues: 53.4954 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 450 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.041220 restraints weight = 36869.777| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 3.99 r_work: 0.2340 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12305 Z= 0.252 Angle : 0.629 17.364 16709 Z= 0.314 Chirality : 0.044 0.262 1833 Planarity : 0.003 0.035 2144 Dihedral : 7.295 82.463 2077 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.79 % Allowed : 13.32 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.29 (0.22), residues: 1447 helix: 2.34 (0.27), residues: 377 sheet: 0.86 (0.33), residues: 238 loop : -1.10 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 435 TYR 0.011 0.001 TYR C 353 PHE 0.018 0.002 PHE A 439 TRP 0.005 0.001 TRP C 421 HIS 0.018 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00601 (12268) covalent geometry : angle 0.60027 (16616) SS BOND : bond 0.00309 ( 18) SS BOND : angle 0.91708 ( 36) hydrogen bonds : bond 0.06280 ( 458) hydrogen bonds : angle 4.94531 ( 1380) glycosidic custom : bond 0.00272 ( 3) glycosidic custom : angle 0.95692 ( 9) link_BETA1-4 : bond 0.00231 ( 5) link_BETA1-4 : angle 1.29913 ( 15) link_NAG-ASN : bond 0.00478 ( 11) link_NAG-ASN : angle 4.13176 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9083 (m-80) cc_final: 0.8510 (m-80) REVERT: C 449 ASP cc_start: 0.9596 (m-30) cc_final: 0.8939 (p0) REVERT: C 450 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9297 (ttpp) outliers start: 23 outliers final: 13 residues processed: 85 average time/residue: 0.5309 time to fit residues: 49.8173 Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 450 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 108 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.043078 restraints weight = 37082.976| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 4.09 r_work: 0.2400 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12305 Z= 0.102 Angle : 0.568 16.504 16709 Z= 0.272 Chirality : 0.042 0.231 1833 Planarity : 0.003 0.033 2144 Dihedral : 6.740 79.988 2077 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.79 % Allowed : 13.08 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.49 (0.22), residues: 1447 helix: 2.49 (0.27), residues: 377 sheet: 1.01 (0.33), residues: 238 loop : -0.97 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 452 TYR 0.010 0.001 TYR B 271 PHE 0.015 0.001 PHE B 338 TRP 0.004 0.000 TRP B 343 HIS 0.002 0.000 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00211 (12268) covalent geometry : angle 0.53888 (16616) SS BOND : bond 0.00161 ( 18) SS BOND : angle 0.75860 ( 36) hydrogen bonds : bond 0.05245 ( 458) hydrogen bonds : angle 4.66533 ( 1380) glycosidic custom : bond 0.00405 ( 3) glycosidic custom : angle 0.92019 ( 9) link_BETA1-4 : bond 0.00336 ( 5) link_BETA1-4 : angle 1.18462 ( 15) link_NAG-ASN : bond 0.00457 ( 11) link_NAG-ASN : angle 3.95591 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9092 (m-80) cc_final: 0.8530 (m-80) REVERT: C 449 ASP cc_start: 0.9553 (m-30) cc_final: 0.8874 (p0) REVERT: C 450 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9110 (tptp) outliers start: 23 outliers final: 13 residues processed: 86 average time/residue: 0.5313 time to fit residues: 50.8495 Evaluate side-chains 79 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 450 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.060282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.041056 restraints weight = 37479.568| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 4.06 r_work: 0.2335 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12305 Z= 0.215 Angle : 0.612 18.924 16709 Z= 0.299 Chirality : 0.044 0.294 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.859 82.167 2077 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.71 % Allowed : 13.71 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.37 (0.22), residues: 1447 helix: 2.41 (0.27), residues: 377 sheet: 0.88 (0.32), residues: 258 loop : -1.09 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 169 TYR 0.014 0.001 TYR B 491 PHE 0.020 0.002 PHE A 70 TRP 0.005 0.001 TRP C 421 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00512 (12268) covalent geometry : angle 0.57934 (16616) SS BOND : bond 0.00287 ( 18) SS BOND : angle 0.83201 ( 36) hydrogen bonds : bond 0.06045 ( 458) hydrogen bonds : angle 4.76069 ( 1380) glycosidic custom : bond 0.00122 ( 3) glycosidic custom : angle 0.72757 ( 9) link_BETA1-4 : bond 0.00366 ( 5) link_BETA1-4 : angle 1.34167 ( 15) link_NAG-ASN : bond 0.00542 ( 11) link_NAG-ASN : angle 4.35841 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9203 (m-80) cc_final: 0.8591 (m-80) REVERT: C 20 MET cc_start: 0.9164 (mmm) cc_final: 0.8933 (mmt) REVERT: C 346 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8594 (ptm) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.4481 time to fit residues: 42.3195 Evaluate side-chains 80 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 355 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN A 354 HIS C 218 GLN C 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.041893 restraints weight = 37083.144| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 4.06 r_work: 0.2360 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12305 Z= 0.138 Angle : 0.596 18.392 16709 Z= 0.287 Chirality : 0.043 0.297 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.740 81.504 2077 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.56 % Allowed : 14.49 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.39 (0.22), residues: 1447 helix: 2.46 (0.27), residues: 377 sheet: 0.65 (0.31), residues: 278 loop : -1.04 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.012 0.001 TYR B 491 PHE 0.017 0.001 PHE A 469 TRP 0.004 0.000 TRP C 421 HIS 0.007 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00318 (12268) covalent geometry : angle 0.56528 (16616) SS BOND : bond 0.00187 ( 18) SS BOND : angle 0.77548 ( 36) hydrogen bonds : bond 0.05590 ( 458) hydrogen bonds : angle 4.69179 ( 1380) glycosidic custom : bond 0.00240 ( 3) glycosidic custom : angle 0.74535 ( 9) link_BETA1-4 : bond 0.00302 ( 5) link_BETA1-4 : angle 1.17133 ( 15) link_NAG-ASN : bond 0.00469 ( 11) link_NAG-ASN : angle 4.20028 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8630 (mp) REVERT: B 469 PHE cc_start: 0.9200 (m-80) cc_final: 0.8593 (m-80) outliers start: 20 outliers final: 15 residues processed: 82 average time/residue: 0.4078 time to fit residues: 37.2890 Evaluate side-chains 80 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 355 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 10.0000 chunk 50 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.041989 restraints weight = 37096.932| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 4.04 r_work: 0.2367 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12305 Z= 0.149 Angle : 0.597 17.595 16709 Z= 0.287 Chirality : 0.043 0.261 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.699 81.654 2077 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.48 % Allowed : 14.49 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.39 (0.22), residues: 1447 helix: 2.45 (0.27), residues: 377 sheet: 0.68 (0.31), residues: 278 loop : -1.04 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 435 TYR 0.011 0.001 TYR B 491 PHE 0.020 0.001 PHE A 70 TRP 0.003 0.000 TRP C 421 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00348 (12268) covalent geometry : angle 0.56706 (16616) SS BOND : bond 0.00199 ( 18) SS BOND : angle 0.82261 ( 36) hydrogen bonds : bond 0.05536 ( 458) hydrogen bonds : angle 4.62788 ( 1380) glycosidic custom : bond 0.00184 ( 3) glycosidic custom : angle 0.69522 ( 9) link_BETA1-4 : bond 0.00305 ( 5) link_BETA1-4 : angle 1.17183 ( 15) link_NAG-ASN : bond 0.00465 ( 11) link_NAG-ASN : angle 4.09810 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9215 (m-80) cc_final: 0.8603 (m-80) outliers start: 19 outliers final: 16 residues processed: 85 average time/residue: 0.4947 time to fit residues: 46.9568 Evaluate side-chains 81 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 355 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.041095 restraints weight = 37004.709| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 3.99 r_work: 0.2334 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12305 Z= 0.217 Angle : 0.643 17.975 16709 Z= 0.312 Chirality : 0.044 0.270 1833 Planarity : 0.003 0.035 2144 Dihedral : 6.756 82.852 2077 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.48 % Allowed : 14.72 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.29 (0.22), residues: 1447 helix: 2.34 (0.27), residues: 377 sheet: 0.83 (0.32), residues: 268 loop : -1.17 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.011 0.001 TYR B 491 PHE 0.019 0.001 PHE A 469 TRP 0.005 0.001 TRP C 421 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00518 (12268) covalent geometry : angle 0.61469 (16616) SS BOND : bond 0.00266 ( 18) SS BOND : angle 0.88297 ( 36) hydrogen bonds : bond 0.06012 ( 458) hydrogen bonds : angle 4.73074 ( 1380) glycosidic custom : bond 0.00085 ( 3) glycosidic custom : angle 0.65669 ( 9) link_BETA1-4 : bond 0.00240 ( 5) link_BETA1-4 : angle 1.16883 ( 15) link_NAG-ASN : bond 0.00465 ( 11) link_NAG-ASN : angle 4.15568 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9231 (m-80) cc_final: 0.8595 (m-80) outliers start: 19 outliers final: 16 residues processed: 84 average time/residue: 0.4998 time to fit residues: 46.9456 Evaluate side-chains 80 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 355 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.041789 restraints weight = 36831.600| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 4.02 r_work: 0.2355 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12305 Z= 0.140 Angle : 0.608 17.474 16709 Z= 0.293 Chirality : 0.043 0.252 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.623 81.955 2077 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.25 % Allowed : 15.03 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.37 (0.22), residues: 1447 helix: 2.39 (0.27), residues: 377 sheet: 0.88 (0.31), residues: 268 loop : -1.11 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.011 0.001 TYR B 491 PHE 0.022 0.001 PHE A 70 TRP 0.003 0.000 TRP C 421 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00323 (12268) covalent geometry : angle 0.57799 (16616) SS BOND : bond 0.00211 ( 18) SS BOND : angle 1.07319 ( 36) hydrogen bonds : bond 0.05602 ( 458) hydrogen bonds : angle 4.63056 ( 1380) glycosidic custom : bond 0.00179 ( 3) glycosidic custom : angle 0.67572 ( 9) link_BETA1-4 : bond 0.00297 ( 5) link_BETA1-4 : angle 1.15967 ( 15) link_NAG-ASN : bond 0.00466 ( 11) link_NAG-ASN : angle 4.11038 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9252 (m-80) cc_final: 0.8614 (m-80) outliers start: 16 outliers final: 15 residues processed: 81 average time/residue: 0.5227 time to fit residues: 47.0228 Evaluate side-chains 79 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 355 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.042796 restraints weight = 36743.295| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 4.01 r_work: 0.2383 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12305 Z= 0.116 Angle : 0.602 16.981 16709 Z= 0.287 Chirality : 0.043 0.237 1833 Planarity : 0.003 0.032 2144 Dihedral : 6.416 80.887 2076 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.25 % Allowed : 15.03 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.40 (0.22), residues: 1447 helix: 2.42 (0.27), residues: 373 sheet: 0.68 (0.30), residues: 288 loop : -1.01 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.011 0.001 TYR B 491 PHE 0.022 0.001 PHE B 70 TRP 0.004 0.000 TRP B 343 HIS 0.002 0.000 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00259 (12268) covalent geometry : angle 0.57305 (16616) SS BOND : bond 0.00176 ( 18) SS BOND : angle 0.99629 ( 36) hydrogen bonds : bond 0.05164 ( 458) hydrogen bonds : angle 4.53479 ( 1380) glycosidic custom : bond 0.00241 ( 3) glycosidic custom : angle 0.69488 ( 9) link_BETA1-4 : bond 0.00372 ( 5) link_BETA1-4 : angle 1.14924 ( 15) link_NAG-ASN : bond 0.00460 ( 11) link_NAG-ASN : angle 4.03116 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3133.12 seconds wall clock time: 54 minutes 38.90 seconds (3278.90 seconds total)