Starting phenix.real_space_refine on Tue Jun 10 22:14:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jn0_61617/06_2025/9jn0_61617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jn0_61617/06_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_61617/06_2025/9jn0_61617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jn0_61617/06_2025/9jn0_61617.map" model { file = "/net/cci-nas-00/data/ceres_data/9jn0_61617/06_2025/9jn0_61617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jn0_61617/06_2025/9jn0_61617.cif" } resolution = 2.84 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= 0.028 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.59, per 1000 atoms: 0.80 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: 3.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.01 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: 4.19 Time building geometry restraints manager: 4.12 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 500 or resid 601 throug \ h 602)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 500 or resid 601 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.790 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 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:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.280 ------------------------------------------------------------------------------- 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 (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: 0.44 (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 TRP 0.005 0.000 TRP B 343 HIS 0.002 0.000 HIS B 355 PHE 0.034 0.001 PHE A 70 TYR 0.010 0.001 TYR C 164 ARG 0.003 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00897 ( 11) link_NAG-ASN : angle 6.44810 ( 33) link_BETA1-4 : bond 0.00397 ( 5) link_BETA1-4 : angle 1.78157 ( 15) hydrogen bonds : bond 0.18549 ( 458) hydrogen bonds : angle 6.89190 ( 1380) SS BOND : bond 0.00113 ( 18) SS BOND : angle 0.71382 ( 36) glycosidic custom : bond 0.00574 ( 3) glycosidic custom : angle 9.42988 ( 9) covalent geometry : bond 0.00293 (12268) covalent geometry : angle 0.61487 (16616) *********************** 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 : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 1.1240 time to fit residues: 92.7146 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 : 1.392 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 0.0670 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.044257 restraints weight = 36962.791| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 4.09 r_work: 0.2437 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12305 Z= 0.116 Angle : 0.587 18.174 16709 Z= 0.285 Chirality : 0.043 0.315 1833 Planarity : 0.003 0.037 2144 Dihedral : 8.090 83.314 2086 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.40 % Allowed : 12.93 % 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 (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: 0.50 (0.22), residues: 1447 helix: 2.46 (0.28), residues: 373 sheet: 0.67 (0.31), residues: 248 loop : -0.82 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.004 0.001 HIS A 8 PHE 0.014 0.001 PHE B 70 TYR 0.011 0.001 TYR C 353 ARG 0.008 0.000 ARG C 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 11) link_NAG-ASN : angle 4.71406 ( 33) link_BETA1-4 : bond 0.00451 ( 5) link_BETA1-4 : angle 1.24567 ( 15) hydrogen bonds : bond 0.05622 ( 458) hydrogen bonds : angle 5.16052 ( 1380) SS BOND : bond 0.00338 ( 18) SS BOND : angle 0.91961 ( 36) glycosidic custom : bond 0.00729 ( 3) glycosidic custom : angle 1.55084 ( 9) covalent geometry : bond 0.00248 (12268) covalent geometry : angle 0.54585 (16616) *********************** 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: 18 poor density : 69 time to evaluate : 1.559 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 1.1299 time to fit residues: 102.2376 Evaluate side-chains 72 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 16 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 218 GLN C 355 HIS C 440 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.040106 restraints weight = 37406.356| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 4.05 r_work: 0.2314 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12305 Z= 0.276 Angle : 0.676 17.890 16709 Z= 0.339 Chirality : 0.045 0.283 1833 Planarity : 0.004 0.038 2144 Dihedral : 7.768 84.415 2077 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.41 % Allowed : 12.15 % 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 (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: 0.17 (0.22), residues: 1447 helix: 2.20 (0.27), residues: 377 sheet: 0.82 (0.33), residues: 238 loop : -1.16 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 350 HIS 0.008 0.001 HIS A 8 PHE 0.024 0.002 PHE A 439 TYR 0.012 0.001 TYR A 353 ARG 0.005 0.001 ARG C 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 11) link_NAG-ASN : angle 4.34281 ( 33) link_BETA1-4 : bond 0.00220 ( 5) link_BETA1-4 : angle 1.43623 ( 15) hydrogen bonds : bond 0.06953 ( 458) hydrogen bonds : angle 5.06459 ( 1380) SS BOND : bond 0.00340 ( 18) SS BOND : angle 0.90585 ( 36) glycosidic custom : bond 0.00366 ( 3) glycosidic custom : angle 1.08119 ( 9) covalent geometry : bond 0.00662 (12268) covalent geometry : angle 0.64636 (16616) *********************** 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 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 449 ASP cc_start: 0.9615 (m-30) cc_final: 0.8961 (p0) REVERT: C 450 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9336 (ttpp) outliers start: 31 outliers final: 14 residues processed: 95 average time/residue: 1.0621 time to fit residues: 111.8627 Evaluate side-chains 78 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 453 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 451 VAL Chi-restraints excluded: chain B residue 462 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 454 GLN A 458 ASN C 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.041001 restraints weight = 36859.168| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 4.04 r_work: 0.2338 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12305 Z= 0.181 Angle : 0.603 17.059 16709 Z= 0.298 Chirality : 0.043 0.253 1833 Planarity : 0.003 0.037 2144 Dihedral : 7.324 81.868 2077 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.02 % Allowed : 13.24 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1447 helix: 2.34 (0.27), residues: 377 sheet: 0.88 (0.33), residues: 237 loop : -1.16 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 421 HIS 0.005 0.001 HIS C 355 PHE 0.016 0.001 PHE A 469 TYR 0.018 0.001 TYR A 488 ARG 0.004 0.000 ARG C 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 11) link_NAG-ASN : angle 4.10867 ( 33) link_BETA1-4 : bond 0.00259 ( 5) link_BETA1-4 : angle 1.22564 ( 15) hydrogen bonds : bond 0.06223 ( 458) hydrogen bonds : angle 4.90340 ( 1380) SS BOND : bond 0.00253 ( 18) SS BOND : angle 0.83067 ( 36) glycosidic custom : bond 0.00291 ( 3) glycosidic custom : angle 0.93202 ( 9) covalent geometry : bond 0.00424 (12268) covalent geometry : angle 0.57339 (16616) *********************** 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 91 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8833 (ptt) cc_final: 0.8625 (pmm) REVERT: C 449 ASP cc_start: 0.9603 (m-30) cc_final: 0.8944 (p0) outliers start: 26 outliers final: 14 residues processed: 87 average time/residue: 1.0988 time to fit residues: 106.6108 Evaluate side-chains 78 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE 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 355 HIS Chi-restraints excluded: chain C residue 367 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.040735 restraints weight = 37209.886| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 4.08 r_work: 0.2332 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12305 Z= 0.192 Angle : 0.607 19.289 16709 Z= 0.297 Chirality : 0.044 0.305 1833 Planarity : 0.003 0.037 2144 Dihedral : 7.151 82.495 2077 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.71 % Allowed : 13.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1447 helix: 2.35 (0.27), residues: 377 sheet: 0.87 (0.32), residues: 248 loop : -1.15 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 122 HIS 0.004 0.001 HIS A 8 PHE 0.016 0.001 PHE C 469 TYR 0.010 0.001 TYR B 271 ARG 0.006 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 11) link_NAG-ASN : angle 4.46785 ( 33) link_BETA1-4 : bond 0.00268 ( 5) link_BETA1-4 : angle 1.27305 ( 15) hydrogen bonds : bond 0.06125 ( 458) hydrogen bonds : angle 4.81732 ( 1380) SS BOND : bond 0.00254 ( 18) SS BOND : angle 0.80583 ( 36) glycosidic custom : bond 0.00203 ( 3) glycosidic custom : angle 0.81758 ( 9) covalent geometry : bond 0.00457 (12268) covalent geometry : angle 0.57252 (16616) *********************** 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 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9136 (m-80) cc_final: 0.8586 (m-80) REVERT: C 449 ASP cc_start: 0.9596 (m-30) cc_final: 0.8951 (p0) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 1.1689 time to fit residues: 111.6687 Evaluate side-chains 79 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 355 HIS Chi-restraints excluded: chain C residue 367 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 72 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 = 0.3032 r_free = 0.3032 target = 0.059911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.040942 restraints weight = 37127.962| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 4.00 r_work: 0.2332 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12305 Z= 0.205 Angle : 0.609 18.418 16709 Z= 0.300 Chirality : 0.044 0.274 1833 Planarity : 0.003 0.037 2144 Dihedral : 7.052 82.801 2077 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.79 % Allowed : 13.86 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1447 helix: 2.33 (0.27), residues: 377 sheet: 0.88 (0.32), residues: 248 loop : -1.18 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 122 HIS 0.005 0.001 HIS A 8 PHE 0.018 0.002 PHE A 70 TYR 0.010 0.001 TYR B 271 ARG 0.004 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 11) link_NAG-ASN : angle 4.21137 ( 33) link_BETA1-4 : bond 0.00272 ( 5) link_BETA1-4 : angle 1.19031 ( 15) hydrogen bonds : bond 0.06159 ( 458) hydrogen bonds : angle 4.82816 ( 1380) SS BOND : bond 0.00273 ( 18) SS BOND : angle 0.92044 ( 36) glycosidic custom : bond 0.00271 ( 3) glycosidic custom : angle 0.79603 ( 9) covalent geometry : bond 0.00487 (12268) covalent geometry : angle 0.57867 (16616) *********************** 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 88 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9195 (m-80) cc_final: 0.8609 (m-80) outliers start: 23 outliers final: 14 residues processed: 84 average time/residue: 1.2459 time to fit residues: 116.3691 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 : 2.311 ------------------------------------------------------------------------------- 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 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 367 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- 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 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.041834 restraints weight = 36980.501| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 4.04 r_work: 0.2356 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12305 Z= 0.127 Angle : 0.576 17.185 16709 Z= 0.280 Chirality : 0.043 0.245 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.683 81.636 2077 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.64 % Allowed : 14.17 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.22), residues: 1447 helix: 2.42 (0.27), residues: 377 sheet: 0.97 (0.32), residues: 248 loop : -1.07 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 149 HIS 0.004 0.001 HIS C 355 PHE 0.020 0.001 PHE C 469 TYR 0.010 0.001 TYR B 271 ARG 0.003 0.000 ARG C 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 11) link_NAG-ASN : angle 4.05985 ( 33) link_BETA1-4 : bond 0.00326 ( 5) link_BETA1-4 : angle 1.16833 ( 15) hydrogen bonds : bond 0.05536 ( 458) hydrogen bonds : angle 4.67576 ( 1380) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.83039 ( 36) glycosidic custom : bond 0.00236 ( 3) glycosidic custom : angle 0.73426 ( 9) covalent geometry : bond 0.00289 (12268) covalent geometry : angle 0.54566 (16616) *********************** 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 89 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9163 (m-80) cc_final: 0.8612 (m-80) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 1.1648 time to fit residues: 112.7663 Evaluate side-chains 78 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.041283 restraints weight = 37442.881| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 4.05 r_work: 0.2343 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12305 Z= 0.168 Angle : 0.609 19.506 16709 Z= 0.293 Chirality : 0.044 0.282 1833 Planarity : 0.003 0.035 2144 Dihedral : 6.701 82.027 2077 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.40 % Allowed : 14.49 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.22), residues: 1447 helix: 2.40 (0.27), residues: 377 sheet: 0.55 (0.31), residues: 278 loop : -1.14 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 421 HIS 0.004 0.001 HIS A 8 PHE 0.020 0.001 PHE B 70 TYR 0.009 0.001 TYR B 271 ARG 0.003 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 11) link_NAG-ASN : angle 4.53673 ( 33) link_BETA1-4 : bond 0.00369 ( 5) link_BETA1-4 : angle 1.31423 ( 15) hydrogen bonds : bond 0.05723 ( 458) hydrogen bonds : angle 4.65995 ( 1380) SS BOND : bond 0.00235 ( 18) SS BOND : angle 0.82645 ( 36) glycosidic custom : bond 0.00144 ( 3) glycosidic custom : angle 0.66930 ( 9) covalent geometry : bond 0.00395 (12268) covalent geometry : angle 0.57303 (16616) *********************** 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 85 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9226 (m-80) cc_final: 0.8636 (m-80) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 1.0289 time to fit residues: 93.9726 Evaluate side-chains 78 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 280 THR 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 111 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.041975 restraints weight = 37066.967| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 4.04 r_work: 0.2359 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12305 Z= 0.129 Angle : 0.592 18.632 16709 Z= 0.284 Chirality : 0.043 0.265 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.584 81.122 2077 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.32 % Allowed : 14.88 % 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 (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: 0.34 (0.22), residues: 1447 helix: 2.41 (0.27), residues: 377 sheet: 0.62 (0.31), residues: 278 loop : -1.07 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 343 HIS 0.003 0.001 HIS A 354 PHE 0.021 0.001 PHE C 469 TYR 0.010 0.001 TYR B 271 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 11) link_NAG-ASN : angle 4.30267 ( 33) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 1.16872 ( 15) hydrogen bonds : bond 0.05393 ( 458) hydrogen bonds : angle 4.59775 ( 1380) SS BOND : bond 0.00188 ( 18) SS BOND : angle 0.82591 ( 36) glycosidic custom : bond 0.00187 ( 3) glycosidic custom : angle 0.68272 ( 9) covalent geometry : bond 0.00295 (12268) covalent geometry : angle 0.55926 (16616) *********************** 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: 17 poor density : 69 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: B 469 PHE cc_start: 0.9239 (m-80) cc_final: 0.8632 (m-80) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 1.0852 time to fit residues: 99.2791 Evaluate side-chains 75 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 280 THR 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 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 98 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.0040 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.0034 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.061884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.042848 restraints weight = 36570.614| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 4.01 r_work: 0.2385 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1785 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= 0.110 Angle : 0.599 17.467 16709 Z= 0.285 Chirality : 0.043 0.239 1833 Planarity : 0.003 0.033 2144 Dihedral : 6.444 80.352 2076 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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 (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: 0.40 (0.22), residues: 1447 helix: 2.43 (0.27), residues: 377 sheet: 0.71 (0.31), residues: 278 loop : -1.03 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 343 HIS 0.002 0.000 HIS C 273 PHE 0.022 0.001 PHE B 70 TYR 0.010 0.001 TYR B 271 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 11) link_NAG-ASN : angle 4.15307 ( 33) link_BETA1-4 : bond 0.00388 ( 5) link_BETA1-4 : angle 1.19264 ( 15) hydrogen bonds : bond 0.05125 ( 458) hydrogen bonds : angle 4.56083 ( 1380) SS BOND : bond 0.00154 ( 18) SS BOND : angle 0.81528 ( 36) glycosidic custom : bond 0.00166 ( 3) glycosidic custom : angle 0.64359 ( 9) covalent geometry : bond 0.00242 (12268) covalent geometry : angle 0.56890 (16616) ********************** 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 82 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.8823 (p) REVERT: B 469 PHE cc_start: 0.9241 (m-80) cc_final: 0.8645 (m-80) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 1.0108 time to fit residues: 90.6270 Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 280 THR 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 56 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 102 optimal weight: 0.0000 chunk 113 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.062397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.043397 restraints weight = 36600.782| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 4.02 r_work: 0.2405 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12305 Z= 0.103 Angle : 0.592 16.905 16709 Z= 0.283 Chirality : 0.043 0.229 1833 Planarity : 0.003 0.032 2144 Dihedral : 6.314 79.436 2076 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.01 % Allowed : 15.34 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.22), residues: 1447 helix: 2.43 (0.27), residues: 377 sheet: 0.76 (0.31), residues: 278 loop : -0.99 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 343 HIS 0.004 0.000 HIS A 355 PHE 0.027 0.001 PHE A 70 TYR 0.010 0.001 TYR B 271 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 11) link_NAG-ASN : angle 4.04102 ( 33) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 1.18747 ( 15) hydrogen bonds : bond 0.04824 ( 458) hydrogen bonds : angle 4.47855 ( 1380) SS BOND : bond 0.00141 ( 18) SS BOND : angle 0.80275 ( 36) glycosidic custom : bond 0.00191 ( 3) glycosidic custom : angle 0.65546 ( 9) covalent geometry : bond 0.00225 (12268) covalent geometry : angle 0.56360 (16616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.99 seconds wall clock time: 118 minutes 27.74 seconds (7107.74 seconds total)