Starting phenix.real_space_refine on Wed May 14 15:34:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhg_38350/05_2025/8xhg_38350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhg_38350/05_2025/8xhg_38350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhg_38350/05_2025/8xhg_38350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhg_38350/05_2025/8xhg_38350.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhg_38350/05_2025/8xhg_38350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhg_38350/05_2025/8xhg_38350.cif" } resolution = 2.54 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= 0.001 sd= 0.026 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 72 5.16 5 C 7463 2.51 5 N 2022 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11939 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3881 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3885 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3890 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: "A" 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 Chain: "B" 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: 7.59, per 1000 atoms: 0.64 Number of scatterers: 11939 At special positions: 0 Unit cell: (86.7, 87.55, 152.15, 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 72 16.00 O 2382 8.00 N 2022 7.00 C 7463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.02 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.04 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " 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 BETA1-3 " GAL D 1 " - " NAG D 2 " " GAL E 1 " - " NAG E 2 " " GAL F 1 " - " NAG F 2 " BETA1-4 " NAG D 2 " - " GAL D 3 " " NAG E 2 " - " GAL E 3 " " NAG F 2 " - " GAL F 3 " BETA2-6 " GAL D 3 " - " SIA D 4 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 3 " - " SIA E 4 " " GAL F 3 " - " SIA F 4 " NAG-ASN " NAG A 601 " - " ASN A 169 " " NAG A 602 " - " ASN A 484 " " NAG A 603 " - " ASN A 28 " " NAG B 601 " - " ASN B 169 " " NAG B 602 " - " ASN B 484 " " NAG B 603 " - " ASN B 28 " " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 28 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 34 sheets defined 28.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.982A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.845A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 367 through 388 removed outlier: 3.738A pdb=" N LYS C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.768A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.974A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.902A pdb=" N ASP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.888A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 388 Processing helix chain 'A' and resid 404 through 457 removed outlier: 3.798A pdb=" N ASP A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 488 through 502 removed outlier: 4.385A pdb=" N TYR A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.829A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 388 removed outlier: 3.859A pdb=" N THR B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 457 removed outlier: 3.530A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 502 removed outlier: 4.321A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 361 through 364 removed outlier: 3.966A pdb=" N ASN C 358 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 468 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.262A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.531A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.591A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.591A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.433A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.267A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 394 " --> pdb=" O GLY C 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.517A pdb=" N ILE A 8 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 468 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.275A pdb=" N GLU A 19 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AB5, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 49 removed outlier: 7.480A pdb=" N LEU A 46 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR A 280 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.689A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.842A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100 removed outlier: 8.101A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AC2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.577A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.232A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 304 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 394 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 362 through 364 removed outlier: 3.644A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 8 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 468 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AD1, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.742A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.737A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.552A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.965A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.724A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.972A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1377 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: 4.24 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3907 1.35 - 1.47: 3000 1.47 - 1.60: 5182 1.60 - 1.72: 0 1.72 - 1.84: 108 Bond restraints: 12197 Sorted by residual: bond pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" CG LEU B 456 " pdb=" CD2 LEU B 456 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" C6 GAL E 3 " pdb=" O6 GAL E 3 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.69e+00 ... (remaining 12192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.65: 16491 7.65 - 15.30: 5 15.30 - 22.95: 3 22.95 - 30.60: 6 30.60 - 38.26: 2 Bond angle restraints: 16507 Sorted by residual: angle pdb=" C2 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 107.49 145.75 -38.26 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C4 GAL E 1 " pdb=" C3 GAL E 1 " pdb=" O3 GAL E 1 " ideal model delta sigma weight residual 113.26 82.11 31.15 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C3 NAG E 2 " pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 107.29 137.88 -30.59 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C5 GAL F 3 " pdb=" C6 GAL F 3 " pdb=" O6 GAL F 3 " ideal model delta sigma weight residual 109.08 138.05 -28.97 3.00e+00 1.11e-01 9.32e+01 angle pdb=" C5 GAL D 3 " pdb=" C6 GAL D 3 " pdb=" O6 GAL D 3 " ideal model delta sigma weight residual 109.08 137.34 -28.26 3.00e+00 1.11e-01 8.87e+01 ... (remaining 16502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 6653 23.20 - 46.40: 764 46.40 - 69.59: 153 69.59 - 92.79: 32 92.79 - 115.99: 6 Dihedral angle restraints: 7608 sinusoidal: 3399 harmonic: 4209 Sorted by residual: dihedral pdb=" CB CYS B 95 " pdb=" SG CYS B 95 " pdb=" SG CYS B 139 " pdb=" CB CYS B 139 " ideal model delta sinusoidal sigma weight residual 93.00 28.18 64.82 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 72 " pdb=" CB CYS B 72 " ideal model delta sinusoidal sigma weight residual -86.00 -22.64 -63.36 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS C 47 " pdb=" SG CYS C 47 " pdb=" SG CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sinusoidal sigma weight residual -86.00 -27.01 -58.99 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 7605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 1828 0.341 - 0.682: 0 0.682 - 1.024: 1 1.024 - 1.365: 2 1.365 - 1.706: 1 Chirality restraints: 1832 Sorted by residual: chirality pdb=" C2 SIA E 4 " pdb=" O6 GAL E 3 " pdb=" C1 SIA E 4 " pdb=" O6 SIA E 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.68 0.18 2.00e-02 2.50e+03 8.04e+01 chirality pdb=" C4 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" C5 NAG E 2 " pdb=" O4 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.53 -0.82 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" C2 SIA F 4 " pdb=" O6 GAL F 3 " pdb=" C1 SIA F 4 " pdb=" O6 SIA F 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.64 0.14 2.00e-02 2.50e+03 5.19e+01 ... (remaining 1829 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 458 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C ASP C 458 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP C 458 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 459 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 458 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" CG ASP A 458 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 458 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 458 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 442 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" CG ASP A 442 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP A 442 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 442 " -0.009 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 297 2.68 - 3.24: 10301 3.24 - 3.79: 17625 3.79 - 4.35: 23863 4.35 - 4.90: 40870 Nonbonded interactions: 92956 Sorted by model distance: nonbonded pdb=" OH TYR A 449 " pdb=" OE2 GLU A 462 " model vdw 2.129 3.040 nonbonded pdb=" O6 SIA F 4 " pdb=" O8 SIA F 4 " model vdw 2.168 3.040 nonbonded pdb=" NH2 ARG B 126 " pdb=" O LYS B 165 " model vdw 2.177 3.120 nonbonded pdb=" ND2 ASN A 459 " pdb=" OG SER A 496 " model vdw 2.188 3.120 nonbonded pdb=" OE2 GLU A 190 " pdb=" O9 SIA F 4 " model vdw 2.197 3.040 ... (remaining 92951 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 6 through 501 or resid 602 through 603)) selection = (chain 'B' and (resid 6 through 327 or resid 336 through 501 or resid 602 throug \ h 603)) selection = (chain 'C' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ h 602)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.390 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.100 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12232 Z= 0.192 Angle : 1.062 38.256 16594 Z= 0.422 Chirality : 0.074 1.706 1832 Planarity : 0.004 0.034 2117 Dihedral : 19.671 115.989 4864 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 4.56 % Allowed : 29.58 % Favored : 65.87 % 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: -0.01 (0.22), residues: 1456 helix: 2.49 (0.27), residues: 360 sheet: 0.01 (0.33), residues: 287 loop : -1.25 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 81 HIS 0.009 0.001 HIS A 356 PHE 0.015 0.001 PHE A 258 TYR 0.015 0.001 TYR A 103 ARG 0.008 0.001 ARG B 436 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 8) link_NAG-ASN : angle 1.17168 ( 24) link_BETA1-4 : bond 0.03776 ( 3) link_BETA1-4 : angle 16.10317 ( 9) hydrogen bonds : bond 0.19466 ( 470) hydrogen bonds : angle 6.86036 ( 1377) SS BOND : bond 0.00612 ( 18) SS BOND : angle 1.96014 ( 36) glycosidic custom : bond 0.05964 ( 3) glycosidic custom : angle 10.34058 ( 9) link_BETA1-3 : bond 0.04904 ( 3) link_BETA1-3 : angle 6.58214 ( 9) covalent geometry : bond 0.00402 (12197) covalent geometry : angle 0.94909 (16507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.6594 (t80) cc_final: 0.6309 (t80) outliers start: 59 outliers final: 53 residues processed: 412 average time/residue: 1.3297 time to fit residues: 587.3853 Evaluate side-chains 409 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 356 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN C 356 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 244 ASN A 459 ASN B 160 ASN B 186 ASN B 196 GLN B 210 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107055 restraints weight = 15932.664| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.79 r_work: 0.3358 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12232 Z= 0.210 Angle : 0.633 9.375 16594 Z= 0.320 Chirality : 0.044 0.195 1832 Planarity : 0.004 0.034 2117 Dihedral : 11.363 86.452 2115 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 6.18 % Allowed : 25.56 % Favored : 68.26 % 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: 0.04 (0.22), residues: 1456 helix: 2.33 (0.27), residues: 380 sheet: 0.29 (0.32), residues: 296 loop : -1.33 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 81 HIS 0.007 0.001 HIS A 356 PHE 0.015 0.002 PHE B 148 TYR 0.014 0.002 TYR B 449 ARG 0.006 0.001 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 8) link_NAG-ASN : angle 1.43516 ( 24) link_BETA1-4 : bond 0.01092 ( 3) link_BETA1-4 : angle 2.67628 ( 9) hydrogen bonds : bond 0.06313 ( 470) hydrogen bonds : angle 5.17849 ( 1377) SS BOND : bond 0.00436 ( 18) SS BOND : angle 1.38898 ( 36) glycosidic custom : bond 0.01049 ( 3) glycosidic custom : angle 2.19134 ( 9) link_BETA1-3 : bond 0.00213 ( 3) link_BETA1-3 : angle 2.44455 ( 9) covalent geometry : bond 0.00502 (12197) covalent geometry : angle 0.62116 (16507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 350 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 497 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6983 (ttpt) REVERT: A 477 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: B 436 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7829 (mpp-170) outliers start: 80 outliers final: 46 residues processed: 392 average time/residue: 1.4157 time to fit residues: 593.8326 Evaluate side-chains 395 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 346 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 120 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 224 ASN A 356 HIS A 459 ASN B 160 ASN B 186 ASN B 210 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107234 restraints weight = 16077.792| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.80 r_work: 0.3357 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12232 Z= 0.186 Angle : 0.585 9.338 16594 Z= 0.301 Chirality : 0.043 0.192 1832 Planarity : 0.004 0.033 2117 Dihedral : 9.673 87.022 2064 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 6.33 % Allowed : 24.94 % Favored : 68.73 % 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: 0.05 (0.22), residues: 1456 helix: 2.44 (0.27), residues: 381 sheet: 0.22 (0.31), residues: 302 loop : -1.35 (0.19), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 81 HIS 0.006 0.001 HIS A 356 PHE 0.015 0.002 PHE B 148 TYR 0.013 0.001 TYR A 103 ARG 0.006 0.001 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 8) link_NAG-ASN : angle 1.48418 ( 24) link_BETA1-4 : bond 0.00380 ( 3) link_BETA1-4 : angle 2.21829 ( 9) hydrogen bonds : bond 0.05934 ( 470) hydrogen bonds : angle 4.86020 ( 1377) SS BOND : bond 0.00448 ( 18) SS BOND : angle 1.51022 ( 36) glycosidic custom : bond 0.00621 ( 3) glycosidic custom : angle 1.28558 ( 9) link_BETA1-3 : bond 0.00324 ( 3) link_BETA1-3 : angle 1.75879 ( 9) covalent geometry : bond 0.00443 (12197) covalent geometry : angle 0.57514 (16507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 350 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7791 (mtm-85) REVERT: C 497 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7033 (ttpt) REVERT: A 116 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6271 (t80) REVERT: A 477 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: B 436 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7790 (mtp180) REVERT: B 497 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7550 (tmtm) outliers start: 82 outliers final: 46 residues processed: 394 average time/residue: 1.3052 time to fit residues: 552.5568 Evaluate side-chains 409 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN C 356 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 224 ASN B 186 ASN B 210 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106684 restraints weight = 15909.505| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.78 r_work: 0.3352 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12232 Z= 0.229 Angle : 0.607 9.656 16594 Z= 0.314 Chirality : 0.044 0.189 1832 Planarity : 0.004 0.050 2117 Dihedral : 9.274 87.453 2055 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 6.87 % Allowed : 25.02 % Favored : 68.11 % 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: -0.02 (0.22), residues: 1456 helix: 2.40 (0.27), residues: 380 sheet: 0.14 (0.31), residues: 304 loop : -1.39 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 81 HIS 0.006 0.001 HIS A 13 PHE 0.016 0.002 PHE B 148 TYR 0.015 0.002 TYR A 103 ARG 0.010 0.001 ARG A 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 1.53266 ( 24) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 1.64655 ( 9) hydrogen bonds : bond 0.06036 ( 470) hydrogen bonds : angle 4.82499 ( 1377) SS BOND : bond 0.00475 ( 18) SS BOND : angle 1.69478 ( 36) glycosidic custom : bond 0.00368 ( 3) glycosidic custom : angle 0.77848 ( 9) link_BETA1-3 : bond 0.00257 ( 3) link_BETA1-3 : angle 1.24626 ( 9) covalent geometry : bond 0.00555 (12197) covalent geometry : angle 0.59854 (16507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 352 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7698 (tpt170) REVERT: C 279 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: C 384 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8411 (m) REVERT: C 497 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7067 (ttpt) REVERT: A 27 ARG cc_start: 0.7905 (mpt180) cc_final: 0.7588 (mmt-90) REVERT: A 116 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6191 (t80) REVERT: A 476 ASP cc_start: 0.7813 (m-30) cc_final: 0.7609 (m-30) REVERT: A 477 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6560 (tm-30) REVERT: B 22 ASP cc_start: 0.7933 (p0) cc_final: 0.7625 (p0) REVERT: B 436 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7791 (mtp180) outliers start: 89 outliers final: 57 residues processed: 401 average time/residue: 1.2950 time to fit residues: 557.8384 Evaluate side-chains 415 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 126 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 224 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 186 ASN B 210 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108081 restraints weight = 15978.721| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.80 r_work: 0.3372 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12232 Z= 0.134 Angle : 0.547 8.286 16594 Z= 0.284 Chirality : 0.041 0.169 1832 Planarity : 0.004 0.040 2117 Dihedral : 8.970 89.075 2051 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 5.87 % Allowed : 26.33 % Favored : 67.80 % 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: 0.17 (0.22), residues: 1456 helix: 2.58 (0.27), residues: 380 sheet: 0.28 (0.31), residues: 309 loop : -1.32 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 81 HIS 0.004 0.001 HIS A 13 PHE 0.011 0.001 PHE B 148 TYR 0.013 0.001 TYR A 103 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 1.45320 ( 24) link_BETA1-4 : bond 0.00317 ( 3) link_BETA1-4 : angle 1.44496 ( 9) hydrogen bonds : bond 0.05286 ( 470) hydrogen bonds : angle 4.67017 ( 1377) SS BOND : bond 0.00518 ( 18) SS BOND : angle 1.49127 ( 36) glycosidic custom : bond 0.00252 ( 3) glycosidic custom : angle 0.68247 ( 9) link_BETA1-3 : bond 0.00281 ( 3) link_BETA1-3 : angle 1.03153 ( 9) covalent geometry : bond 0.00308 (12197) covalent geometry : angle 0.53930 (16507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 351 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 384 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8357 (m) REVERT: C 494 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: C 497 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7039 (ttpt) REVERT: A 27 ARG cc_start: 0.7857 (mpt180) cc_final: 0.7583 (mmt-90) REVERT: A 116 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6214 (t80) REVERT: A 394 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: A 477 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: B 22 ASP cc_start: 0.7914 (p0) cc_final: 0.7572 (p0) outliers start: 76 outliers final: 51 residues processed: 393 average time/residue: 1.2557 time to fit residues: 530.4846 Evaluate side-chains 413 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 356 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN C 356 HIS A 210 ASN A 224 ASN A 356 HIS B 160 ASN B 186 ASN B 210 ASN B 360 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106832 restraints weight = 16200.572| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.80 r_work: 0.3355 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12232 Z= 0.210 Angle : 0.595 10.679 16594 Z= 0.307 Chirality : 0.044 0.193 1832 Planarity : 0.004 0.032 2117 Dihedral : 8.750 89.449 2046 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 6.95 % Allowed : 25.79 % Favored : 67.26 % 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: 0.04 (0.22), residues: 1456 helix: 2.39 (0.27), residues: 381 sheet: 0.24 (0.31), residues: 304 loop : -1.36 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 81 HIS 0.006 0.001 HIS A 13 PHE 0.015 0.002 PHE B 148 TYR 0.016 0.002 TYR A 103 ARG 0.009 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 8) link_NAG-ASN : angle 1.49177 ( 24) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 1.31382 ( 9) hydrogen bonds : bond 0.05727 ( 470) hydrogen bonds : angle 4.72077 ( 1377) SS BOND : bond 0.00573 ( 18) SS BOND : angle 1.62493 ( 36) glycosidic custom : bond 0.00278 ( 3) glycosidic custom : angle 0.58313 ( 9) link_BETA1-3 : bond 0.00283 ( 3) link_BETA1-3 : angle 0.93133 ( 9) covalent geometry : bond 0.00508 (12197) covalent geometry : angle 0.58748 (16507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 361 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 279 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: C 384 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8411 (m) REVERT: C 494 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: C 497 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7102 (ttpt) REVERT: A 27 ARG cc_start: 0.7909 (mpt180) cc_final: 0.7603 (mmt-90) REVERT: A 116 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6120 (t80) REVERT: A 354 TYR cc_start: 0.8774 (m-80) cc_final: 0.8565 (m-80) REVERT: A 394 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: A 457 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7814 (ttp80) REVERT: A 476 ASP cc_start: 0.7783 (m-30) cc_final: 0.7580 (m-30) REVERT: A 477 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: A 494 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: B 22 ASP cc_start: 0.7903 (p0) cc_final: 0.7555 (p0) REVERT: B 157 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8720 (tttt) REVERT: B 281 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7938 (mmmt) outliers start: 90 outliers final: 56 residues processed: 409 average time/residue: 1.3411 time to fit residues: 589.8414 Evaluate side-chains 425 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 359 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN C 356 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS A 210 ASN A 224 ASN B 160 ASN B 186 ASN B 210 ASN B 360 GLN B 455 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107656 restraints weight = 16035.563| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.80 r_work: 0.3361 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12232 Z= 0.157 Angle : 0.569 10.844 16594 Z= 0.294 Chirality : 0.042 0.186 1832 Planarity : 0.004 0.032 2117 Dihedral : 8.623 87.780 2046 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 6.18 % Allowed : 26.33 % Favored : 67.49 % 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: 0.10 (0.22), residues: 1456 helix: 2.46 (0.27), residues: 381 sheet: 0.29 (0.31), residues: 304 loop : -1.34 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 81 HIS 0.005 0.001 HIS A 13 PHE 0.014 0.001 PHE B 148 TYR 0.015 0.001 TYR A 103 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 1.45835 ( 24) link_BETA1-4 : bond 0.00316 ( 3) link_BETA1-4 : angle 1.26684 ( 9) hydrogen bonds : bond 0.05413 ( 470) hydrogen bonds : angle 4.68743 ( 1377) SS BOND : bond 0.00558 ( 18) SS BOND : angle 1.50809 ( 36) glycosidic custom : bond 0.00246 ( 3) glycosidic custom : angle 0.57867 ( 9) link_BETA1-3 : bond 0.00293 ( 3) link_BETA1-3 : angle 0.88587 ( 9) covalent geometry : bond 0.00372 (12197) covalent geometry : angle 0.56243 (16507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 279 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: C 384 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8367 (m) REVERT: C 494 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: C 497 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7085 (ttpt) REVERT: A 27 ARG cc_start: 0.7879 (mpt180) cc_final: 0.7619 (mmt-90) REVERT: A 116 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6105 (t80) REVERT: A 394 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: A 457 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7800 (ttp80) REVERT: A 477 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 494 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6787 (mm-30) REVERT: B 22 ASP cc_start: 0.7888 (p0) cc_final: 0.7565 (p0) REVERT: B 157 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8719 (tttt) REVERT: B 281 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7918 (mmmt) outliers start: 80 outliers final: 57 residues processed: 402 average time/residue: 1.3166 time to fit residues: 568.9416 Evaluate side-chains 429 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 362 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN C 356 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 224 ASN A 459 ASN B 7 GLN B 160 ASN B 186 ASN B 210 ASN B 455 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107725 restraints weight = 16163.966| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.81 r_work: 0.3367 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12232 Z= 0.155 Angle : 0.567 10.558 16594 Z= 0.294 Chirality : 0.042 0.199 1832 Planarity : 0.004 0.031 2117 Dihedral : 8.504 86.094 2044 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Rotamer: Outliers : 5.95 % Allowed : 26.64 % Favored : 67.41 % 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: 0.12 (0.22), residues: 1456 helix: 2.48 (0.27), residues: 380 sheet: 0.31 (0.32), residues: 294 loop : -1.31 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 81 HIS 0.006 0.001 HIS A 356 PHE 0.013 0.001 PHE B 148 TYR 0.015 0.001 TYR A 103 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 8) link_NAG-ASN : angle 1.44675 ( 24) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 1.22425 ( 9) hydrogen bonds : bond 0.05332 ( 470) hydrogen bonds : angle 4.65387 ( 1377) SS BOND : bond 0.00587 ( 18) SS BOND : angle 1.50688 ( 36) glycosidic custom : bond 0.00213 ( 3) glycosidic custom : angle 0.56688 ( 9) link_BETA1-3 : bond 0.00295 ( 3) link_BETA1-3 : angle 0.85739 ( 9) covalent geometry : bond 0.00366 (12197) covalent geometry : angle 0.56006 (16507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 362 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 279 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: C 384 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8400 (m) REVERT: C 494 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7307 (pp20) REVERT: C 497 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7080 (ttpt) REVERT: A 27 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7592 (mmt-90) REVERT: A 116 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6080 (t80) REVERT: A 394 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: A 476 ASP cc_start: 0.7788 (m-30) cc_final: 0.7582 (m-30) REVERT: A 494 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: B 22 ASP cc_start: 0.7908 (p0) cc_final: 0.7582 (p0) REVERT: B 157 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8729 (tttt) REVERT: B 281 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7899 (mmmt) outliers start: 77 outliers final: 58 residues processed: 404 average time/residue: 1.3115 time to fit residues: 568.7106 Evaluate side-chains 423 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 357 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 356 HIS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 143 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN C 283 GLN A 210 ASN A 224 ASN B 160 ASN B 186 ASN B 210 ASN B 360 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107778 restraints weight = 16067.157| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.80 r_work: 0.3370 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12232 Z= 0.149 Angle : 0.578 10.550 16594 Z= 0.300 Chirality : 0.042 0.183 1832 Planarity : 0.004 0.031 2117 Dihedral : 8.331 84.302 2041 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 5.25 % Allowed : 27.18 % Favored : 67.57 % 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: 0.16 (0.22), residues: 1456 helix: 2.50 (0.27), residues: 381 sheet: 0.34 (0.32), residues: 294 loop : -1.29 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 81 HIS 0.005 0.001 HIS A 13 PHE 0.012 0.001 PHE B 148 TYR 0.015 0.001 TYR A 103 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 1.43306 ( 24) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 1.18583 ( 9) hydrogen bonds : bond 0.05233 ( 470) hydrogen bonds : angle 4.63242 ( 1377) SS BOND : bond 0.00564 ( 18) SS BOND : angle 1.95298 ( 36) glycosidic custom : bond 0.00314 ( 3) glycosidic custom : angle 0.58247 ( 9) link_BETA1-3 : bond 0.00278 ( 3) link_BETA1-3 : angle 0.82062 ( 9) covalent geometry : bond 0.00353 (12197) covalent geometry : angle 0.56846 (16507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 384 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8397 (m) REVERT: C 494 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: C 497 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7083 (ttpt) REVERT: A 27 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7574 (mmt-90) REVERT: A 116 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6133 (t80) REVERT: A 394 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: A 494 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6727 (mm-30) REVERT: A 497 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7683 (ttpp) REVERT: B 22 ASP cc_start: 0.7894 (p0) cc_final: 0.7570 (p0) REVERT: B 157 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8718 (tttt) REVERT: B 281 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7888 (mmmt) outliers start: 68 outliers final: 51 residues processed: 396 average time/residue: 1.3544 time to fit residues: 575.2356 Evaluate side-chains 420 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN A 210 ASN A 224 ASN B 160 ASN B 186 ASN B 210 ASN B 455 GLN B 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108249 restraints weight = 15998.213| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.80 r_work: 0.3373 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12232 Z= 0.144 Angle : 0.577 10.366 16594 Z= 0.299 Chirality : 0.042 0.199 1832 Planarity : 0.004 0.030 2117 Dihedral : 8.164 82.197 2040 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 4.71 % Allowed : 27.88 % Favored : 67.41 % 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: 0.16 (0.22), residues: 1456 helix: 2.49 (0.27), residues: 379 sheet: 0.36 (0.32), residues: 294 loop : -1.27 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 81 HIS 0.005 0.001 HIS A 356 PHE 0.012 0.001 PHE B 148 TYR 0.015 0.001 TYR A 103 ARG 0.007 0.001 ARG C 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 8) link_NAG-ASN : angle 1.43331 ( 24) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 1.15559 ( 9) hydrogen bonds : bond 0.05143 ( 470) hydrogen bonds : angle 4.61996 ( 1377) SS BOND : bond 0.00595 ( 18) SS BOND : angle 2.07747 ( 36) glycosidic custom : bond 0.00262 ( 3) glycosidic custom : angle 0.54973 ( 9) link_BETA1-3 : bond 0.00325 ( 3) link_BETA1-3 : angle 0.82294 ( 9) covalent geometry : bond 0.00338 (12197) covalent geometry : angle 0.56704 (16507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 188 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 384 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8366 (m) REVERT: C 494 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7273 (pp20) REVERT: C 497 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7100 (ttpt) REVERT: A 27 ARG cc_start: 0.7868 (mpt180) cc_final: 0.7605 (mmt-90) REVERT: A 116 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6060 (t80) REVERT: A 394 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: A 494 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6680 (mm-30) REVERT: A 497 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7667 (ttpp) REVERT: B 22 ASP cc_start: 0.7893 (p0) cc_final: 0.7569 (p0) REVERT: B 157 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8718 (tttt) REVERT: B 281 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7882 (mmmt) outliers start: 61 outliers final: 47 residues processed: 388 average time/residue: 1.2973 time to fit residues: 540.3857 Evaluate side-chains 408 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 353 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN A 210 ASN A 224 ASN A 356 HIS B 160 ASN B 186 ASN B 210 ASN B 455 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107410 restraints weight = 15949.365| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.78 r_work: 0.3363 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12232 Z= 0.194 Angle : 0.609 10.658 16594 Z= 0.316 Chirality : 0.044 0.192 1832 Planarity : 0.004 0.031 2117 Dihedral : 8.112 80.984 2037 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 4.86 % Allowed : 28.19 % Favored : 66.95 % 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: 0.08 (0.22), residues: 1456 helix: 2.38 (0.27), residues: 379 sheet: 0.40 (0.32), residues: 292 loop : -1.33 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 81 HIS 0.005 0.001 HIS A 13 PHE 0.015 0.002 PHE B 148 TYR 0.019 0.002 TYR A 354 ARG 0.007 0.001 ARG B 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 1.45118 ( 24) link_BETA1-4 : bond 0.00325 ( 3) link_BETA1-4 : angle 1.13292 ( 9) hydrogen bonds : bond 0.05514 ( 470) hydrogen bonds : angle 4.68974 ( 1377) SS BOND : bond 0.00580 ( 18) SS BOND : angle 2.04931 ( 36) glycosidic custom : bond 0.00238 ( 3) glycosidic custom : angle 0.53555 ( 9) link_BETA1-3 : bond 0.00316 ( 3) link_BETA1-3 : angle 0.80865 ( 9) covalent geometry : bond 0.00466 (12197) covalent geometry : angle 0.59992 (16507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11453.69 seconds wall clock time: 197 minutes 12.58 seconds (11832.58 seconds total)