Starting phenix.real_space_refine on Wed Feb 4 22:18:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oal_70288/02_2026/9oal_70288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oal_70288/02_2026/9oal_70288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oal_70288/02_2026/9oal_70288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oal_70288/02_2026/9oal_70288.map" model { file = "/net/cci-nas-00/data/ceres_data/9oal_70288/02_2026/9oal_70288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oal_70288/02_2026/9oal_70288.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 78 5.16 5 C 8214 2.51 5 N 2208 2.21 5 O 2559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13059 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4314 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 16, 'TRANS': 523} Chain breaks: 4 Chain: "B" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4314 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 16, 'TRANS': 523} Chain breaks: 4 Chain: "C" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4314 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 16, 'TRANS': 523} Chain breaks: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: 3.49, per 1000 atoms: 0.27 Number of scatterers: 13059 At special positions: 0 Unit cell: (122.223, 119.424, 125.022, 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 78 16.00 O 2559 8.00 N 2208 7.00 C 8214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS B 628B" distance=2.02 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS B 634 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 551 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 628B" - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS A 634 " - pdb=" SG CYS C 175 " distance=2.04 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS C 628B" distance=2.05 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS C 634 " distance=2.04 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 551 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 342 " distance=2.03 Simple disulfide: pdb=" SG CYS C 551 " - pdb=" SG CYS C 588 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG D 1 " - " ASN A 163 " " NAG E 1 " - " ASN B 163 " " NAG F 1 " - " ASN C 163 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 685.9 milliseconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 29.3% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 342 through 357 removed outlier: 4.367A pdb=" N GLN A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 501 removed outlier: 3.542A pdb=" N GLN A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 621 through 628A Processing helix chain 'A' and resid 628B through 630 Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 656 through 684 removed outlier: 4.525A pdb=" N ASN A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 342 through 357 removed outlier: 4.366A pdb=" N GLN B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 501 removed outlier: 3.541A pdb=" N GLN B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 511 Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 621 through 628A Processing helix chain 'B' and resid 628B through 630 Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 656 through 684 removed outlier: 4.527A pdb=" N ASN B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 342 through 357 removed outlier: 4.367A pdb=" N GLN C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 501 removed outlier: 3.542A pdb=" N GLN C 471 " --> pdb=" O SER C 467 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 499 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 511 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 621 through 628A Processing helix chain 'C' and resid 628B through 630 Processing helix chain 'C' and resid 637 through 647 Processing helix chain 'C' and resid 656 through 684 removed outlier: 4.526A pdb=" N ASN C 665 " --> pdb=" O PHE C 661 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE C 666 " --> pdb=" O ARG C 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.069A pdb=" N HIS A 299 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS A 86 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER A 305 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY A 80 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 307 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 78 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 79 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.069A pdb=" N HIS A 299 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS A 86 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER A 305 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY A 80 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 307 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 78 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 79 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA6, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.565A pdb=" N SER A 183 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS A 206 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 95 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS A 287 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG A 274 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N THR A 255 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 276 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL A 253 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP A 278 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 251 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 552 Processing sheet with id=AB1, first strand: chain 'A' and resid 593 through 597 removed outlier: 5.938A pdb=" N ASN A 606 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.069A pdb=" N HIS B 299 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS B 86 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B 305 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 80 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 307 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 78 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 79 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.069A pdb=" N HIS B 299 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS B 86 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B 305 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 80 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 307 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 78 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 79 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB7, first strand: chain 'B' and resid 170 through 172 removed outlier: 3.565A pdb=" N SER B 183 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 206 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS B 95 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS B 287 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG B 274 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR B 255 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE B 276 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 253 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP B 278 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE B 251 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AB9, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 552 Processing sheet with id=AC2, first strand: chain 'B' and resid 593 through 597 removed outlier: 5.939A pdb=" N ASN B 606 " --> pdb=" O HIS B 610 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC4, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.068A pdb=" N HIS C 299 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS C 86 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER C 305 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C 80 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE C 307 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR C 78 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 79 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.068A pdb=" N HIS C 299 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS C 86 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER C 305 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C 80 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE C 307 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR C 78 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 79 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=AC8, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.566A pdb=" N SER C 183 " --> pdb=" O CYS C 206 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS C 206 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS C 95 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS C 287 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG C 274 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR C 255 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE C 276 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL C 253 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP C 278 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE C 251 " --> pdb=" O ASP C 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AD1, first strand: chain 'C' and resid 537 through 538 Processing sheet with id=AD2, first strand: chain 'C' and resid 550 through 552 Processing sheet with id=AD3, first strand: chain 'C' and resid 593 through 597 removed outlier: 5.938A pdb=" N ASN C 606 " --> pdb=" O HIS C 610 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS C 610 " --> pdb=" O ASN C 606 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3771 1.33 - 1.46: 3011 1.46 - 1.58: 6415 1.58 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 13311 Sorted by residual: bond pdb=" N VAL C 157 " pdb=" CA VAL C 157 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" N VAL B 157 " pdb=" CA VAL B 157 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 9.91e+00 bond pdb=" N VAL A 157 " pdb=" CA VAL A 157 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.39e+00 bond pdb=" CA SER C 217 " pdb=" CB SER C 217 " ideal model delta sigma weight residual 1.536 1.510 0.026 9.10e-03 1.21e+04 7.95e+00 bond pdb=" N LYS C 124 " pdb=" CA LYS C 124 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.36e+00 ... (remaining 13306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 17125 1.36 - 2.71: 637 2.71 - 4.07: 189 4.07 - 5.42: 42 5.42 - 6.78: 19 Bond angle restraints: 18012 Sorted by residual: angle pdb=" N PHE B 219 " pdb=" CA PHE B 219 " pdb=" CB PHE B 219 " ideal model delta sigma weight residual 111.84 105.27 6.57 1.49e+00 4.50e-01 1.94e+01 angle pdb=" C CYS A 141 " pdb=" N TYR A 142 " pdb=" CA TYR A 142 " ideal model delta sigma weight residual 123.00 117.10 5.90 1.41e+00 5.03e-01 1.75e+01 angle pdb=" C CYS B 141 " pdb=" N TYR B 142 " pdb=" CA TYR B 142 " ideal model delta sigma weight residual 123.00 117.11 5.89 1.41e+00 5.03e-01 1.75e+01 angle pdb=" C CYS C 141 " pdb=" N TYR C 142 " pdb=" CA TYR C 142 " ideal model delta sigma weight residual 123.00 117.13 5.87 1.41e+00 5.03e-01 1.74e+01 angle pdb=" C TYR B 142 " pdb=" CA TYR B 142 " pdb=" CB TYR B 142 " ideal model delta sigma weight residual 110.16 116.61 -6.45 1.66e+00 3.63e-01 1.51e+01 ... (remaining 18007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 7742 21.17 - 42.34: 295 42.34 - 63.50: 48 63.50 - 84.67: 30 84.67 - 105.84: 21 Dihedral angle restraints: 8136 sinusoidal: 3396 harmonic: 4740 Sorted by residual: dihedral pdb=" CA THR B 73 " pdb=" C THR B 73 " pdb=" N ARG B 74 " pdb=" CA ARG B 74 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR A 73 " pdb=" C THR A 73 " pdb=" N ARG A 74 " pdb=" CA ARG A 74 " ideal model delta harmonic sigma weight residual 180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR C 73 " pdb=" C THR C 73 " pdb=" N ARG C 74 " pdb=" CA ARG C 74 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 8133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1780 0.073 - 0.146: 251 0.146 - 0.219: 10 0.219 - 0.292: 5 0.292 - 0.365: 3 Chirality restraints: 2049 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.32e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.31e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.29e+02 ... (remaining 2046 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.253 2.00e-02 2.50e+03 2.16e-01 5.81e+02 pdb=" C7 NAG E 1 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.253 2.00e-02 2.50e+03 2.15e-01 5.80e+02 pdb=" C7 NAG D 1 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.253 2.00e-02 2.50e+03 2.15e-01 5.80e+02 pdb=" C7 NAG F 1 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1585 2.76 - 3.30: 12951 3.30 - 3.83: 20778 3.83 - 4.37: 24913 4.37 - 4.90: 43499 Nonbonded interactions: 103726 Sorted by model distance: nonbonded pdb=" CG1 VAL A 103 " pdb=" OH TYR A 156 " model vdw 2.229 3.460 nonbonded pdb=" CG1 VAL C 103 " pdb=" OH TYR C 156 " model vdw 2.229 3.460 nonbonded pdb=" CG1 VAL B 103 " pdb=" OH TYR B 156 " model vdw 2.229 3.460 nonbonded pdb=" O3 NAG D 1 " pdb=" O5 NAG D 2 " model vdw 2.473 3.040 nonbonded pdb=" O3 NAG F 1 " pdb=" O5 NAG F 2 " model vdw 2.473 3.040 ... (remaining 103721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 0.042 13341 Z= 0.248 Angle : 0.714 6.863 18081 Z= 0.426 Chirality : 0.051 0.365 2049 Planarity : 0.011 0.216 2310 Dihedral : 14.090 105.839 5013 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.21 % Allowed : 0.97 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1590 helix: 0.53 (0.25), residues: 384 sheet: 0.07 (0.23), residues: 450 loop : -0.09 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 469 TYR 0.014 0.002 TYR A 130 PHE 0.014 0.001 PHE B 244 TRP 0.008 0.001 TRP B 382 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00408 (13311) covalent geometry : angle 0.69954 (18012) SS BOND : bond 0.00726 ( 21) SS BOND : angle 1.47925 ( 42) hydrogen bonds : bond 0.13747 ( 579) hydrogen bonds : angle 6.88333 ( 1809) link_BETA1-4 : bond 0.01986 ( 6) link_BETA1-4 : angle 3.16835 ( 18) link_NAG-ASN : bond 0.00921 ( 3) link_NAG-ASN : angle 3.95329 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 68 CYS cc_start: 0.6590 (m) cc_final: 0.6310 (m) REVERT: A 69 PRO cc_start: 0.8723 (Cg_endo) cc_final: 0.8448 (Cg_exo) REVERT: A 79 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 125 PHE cc_start: 0.7930 (m-80) cc_final: 0.7205 (m-80) REVERT: A 209 THR cc_start: 0.8275 (m) cc_final: 0.7690 (p) REVERT: A 260 VAL cc_start: 0.7921 (t) cc_final: 0.7636 (p) REVERT: A 316 ILE cc_start: 0.8685 (mm) cc_final: 0.8482 (mm) REVERT: A 321 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 486 GLU cc_start: 0.8187 (tp30) cc_final: 0.7852 (tp30) REVERT: A 492 MET cc_start: 0.8885 (ttp) cc_final: 0.8684 (ttp) REVERT: B 79 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6924 (mt-10) REVERT: B 125 PHE cc_start: 0.7885 (m-80) cc_final: 0.7210 (m-80) REVERT: B 142 TYR cc_start: 0.8190 (m-80) cc_final: 0.7792 (m-80) REVERT: B 143 ASN cc_start: 0.7511 (t0) cc_final: 0.6813 (p0) REVERT: B 166 VAL cc_start: 0.8110 (t) cc_final: 0.7737 (p) REVERT: B 244 PHE cc_start: 0.8460 (t80) cc_final: 0.8058 (t80) REVERT: B 273 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7799 (ttp80) REVERT: B 316 ILE cc_start: 0.8692 (mm) cc_final: 0.8434 (mt) REVERT: B 321 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 474 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7707 (mtp-110) REVERT: B 549 THR cc_start: 0.8239 (p) cc_final: 0.8023 (t) REVERT: B 574 THR cc_start: 0.8857 (m) cc_final: 0.8652 (p) REVERT: B 577 GLU cc_start: 0.8223 (tt0) cc_final: 0.8020 (tt0) REVERT: B 609 HIS cc_start: 0.8026 (t70) cc_final: 0.7816 (t70) REVERT: C 58 ASP cc_start: 0.7779 (m-30) cc_final: 0.7511 (m-30) REVERT: C 87 ASP cc_start: 0.7355 (p0) cc_final: 0.7127 (p0) REVERT: C 127 VAL cc_start: 0.8481 (t) cc_final: 0.8034 (p) REVERT: C 142 TYR cc_start: 0.7941 (m-80) cc_final: 0.7705 (m-80) REVERT: C 143 ASN cc_start: 0.7432 (t0) cc_final: 0.6414 (p0) REVERT: C 165 THR cc_start: 0.8003 (p) cc_final: 0.7801 (p) REVERT: C 166 VAL cc_start: 0.7951 (t) cc_final: 0.7704 (p) REVERT: C 214 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7745 (tttt) REVERT: C 273 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7604 (ttp-170) REVERT: C 316 ILE cc_start: 0.8836 (mm) cc_final: 0.8518 (mm) REVERT: C 320 GLN cc_start: 0.7705 (tt0) cc_final: 0.7484 (tt0) REVERT: C 321 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7279 (mm-30) REVERT: C 486 GLU cc_start: 0.8131 (tp30) cc_final: 0.7757 (tp30) REVERT: C 490 GLN cc_start: 0.8081 (mt0) cc_final: 0.7840 (mt0) REVERT: C 549 THR cc_start: 0.8280 (p) cc_final: 0.8010 (t) REVERT: C 569 GLU cc_start: 0.7460 (tt0) cc_final: 0.7218 (tt0) REVERT: C 677 ASP cc_start: 0.7814 (m-30) cc_final: 0.7508 (m-30) outliers start: 3 outliers final: 2 residues processed: 435 average time/residue: 0.1573 time to fit residues: 92.1733 Evaluate side-chains 300 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain C residue 99 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 299 HIS A 320 GLN A 490 GLN A 606 ASN B 299 HIS ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN B 606 ASN C 228 GLN C 299 HIS C 487 GLN C 589 GLN C 606 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108788 restraints weight = 21364.326| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.84 r_work: 0.3271 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13341 Z= 0.221 Angle : 0.642 7.735 18081 Z= 0.342 Chirality : 0.048 0.158 2049 Planarity : 0.004 0.048 2310 Dihedral : 9.277 60.543 1954 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.00 % Allowed : 8.56 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1590 helix: 1.53 (0.25), residues: 387 sheet: -0.13 (0.23), residues: 432 loop : 0.08 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 474 TYR 0.021 0.002 TYR A 99 PHE 0.024 0.002 PHE B 276 TRP 0.009 0.002 TRP B 382 HIS 0.006 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00513 (13311) covalent geometry : angle 0.63144 (18012) SS BOND : bond 0.00532 ( 21) SS BOND : angle 1.25049 ( 42) hydrogen bonds : bond 0.04493 ( 579) hydrogen bonds : angle 5.25942 ( 1809) link_BETA1-4 : bond 0.00766 ( 6) link_BETA1-4 : angle 2.10431 ( 18) link_NAG-ASN : bond 0.00983 ( 3) link_NAG-ASN : angle 3.56661 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 313 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7905 (m-80) cc_final: 0.7120 (m-80) REVERT: A 209 THR cc_start: 0.8190 (m) cc_final: 0.7516 (p) REVERT: A 237 ASP cc_start: 0.8013 (t0) cc_final: 0.7599 (t0) REVERT: A 260 VAL cc_start: 0.7909 (t) cc_final: 0.7559 (p) REVERT: A 321 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 340 PHE cc_start: 0.8371 (m-10) cc_final: 0.7905 (m-80) REVERT: A 486 GLU cc_start: 0.8275 (tp30) cc_final: 0.7939 (tp30) REVERT: B 125 PHE cc_start: 0.8023 (m-80) cc_final: 0.7235 (m-80) REVERT: B 143 ASN cc_start: 0.7558 (t0) cc_final: 0.6942 (p0) REVERT: B 179 ARG cc_start: 0.7495 (mpp80) cc_final: 0.7173 (mpp80) REVERT: B 180 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7378 (mtp85) REVERT: B 237 ASP cc_start: 0.8206 (t0) cc_final: 0.7905 (t0) REVERT: B 244 PHE cc_start: 0.8672 (t80) cc_final: 0.8149 (t80) REVERT: B 256 ASN cc_start: 0.8467 (t0) cc_final: 0.8266 (t0) REVERT: B 273 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7535 (ttp80) REVERT: B 314 SER cc_start: 0.7610 (m) cc_final: 0.7321 (p) REVERT: B 341 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8132 (mptt) REVERT: B 469 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7741 (mmm-85) REVERT: B 474 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7561 (mtp-110) REVERT: B 488 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8795 (ttmm) REVERT: B 549 THR cc_start: 0.8511 (p) cc_final: 0.8175 (t) REVERT: B 574 THR cc_start: 0.8844 (m) cc_final: 0.8615 (p) REVERT: B 577 GLU cc_start: 0.8398 (tt0) cc_final: 0.8112 (tt0) REVERT: B 586 GLU cc_start: 0.8444 (pt0) cc_final: 0.8229 (pt0) REVERT: B 589 GLN cc_start: 0.8088 (mm110) cc_final: 0.7739 (mm110) REVERT: C 69 PRO cc_start: 0.8881 (Cg_endo) cc_final: 0.8511 (Cg_exo) REVERT: C 179 ARG cc_start: 0.7159 (mpp80) cc_final: 0.6736 (mpp80) REVERT: C 237 ASP cc_start: 0.8311 (t0) cc_final: 0.8069 (m-30) REVERT: C 273 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7693 (ttp80) REVERT: C 316 ILE cc_start: 0.8826 (mm) cc_final: 0.8535 (mm) REVERT: C 320 GLN cc_start: 0.7900 (tt0) cc_final: 0.7615 (tt0) REVERT: C 321 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7109 (mm-30) REVERT: C 340 PHE cc_start: 0.8375 (m-80) cc_final: 0.7858 (m-80) REVERT: C 474 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7762 (mtp-110) REVERT: C 486 GLU cc_start: 0.8213 (tp30) cc_final: 0.7712 (tp30) REVERT: C 487 GLN cc_start: 0.8186 (mt0) cc_final: 0.7766 (mp10) REVERT: C 677 ASP cc_start: 0.8009 (m-30) cc_final: 0.7660 (m-30) outliers start: 29 outliers final: 18 residues processed: 332 average time/residue: 0.1499 time to fit residues: 67.9220 Evaluate side-chains 284 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 256 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 56 HIS C 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107768 restraints weight = 21650.131| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.95 r_work: 0.3242 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13341 Z= 0.202 Angle : 0.581 6.364 18081 Z= 0.312 Chirality : 0.046 0.148 2049 Planarity : 0.004 0.047 2310 Dihedral : 7.013 55.730 1952 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.76 % Allowed : 9.45 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1590 helix: 2.01 (0.25), residues: 375 sheet: -0.02 (0.23), residues: 426 loop : -0.01 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 474 TYR 0.019 0.002 TYR C 99 PHE 0.030 0.002 PHE C 251 TRP 0.011 0.001 TRP C 382 HIS 0.006 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00473 (13311) covalent geometry : angle 0.57278 (18012) SS BOND : bond 0.00260 ( 21) SS BOND : angle 0.91307 ( 42) hydrogen bonds : bond 0.04251 ( 579) hydrogen bonds : angle 4.97269 ( 1809) link_BETA1-4 : bond 0.00353 ( 6) link_BETA1-4 : angle 2.12818 ( 18) link_NAG-ASN : bond 0.00555 ( 3) link_NAG-ASN : angle 2.88293 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: A 125 PHE cc_start: 0.7884 (m-80) cc_final: 0.7060 (m-80) REVERT: A 209 THR cc_start: 0.8109 (m) cc_final: 0.7468 (p) REVERT: A 237 ASP cc_start: 0.8025 (t0) cc_final: 0.7605 (t0) REVERT: A 260 VAL cc_start: 0.7776 (t) cc_final: 0.7419 (p) REVERT: A 321 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 340 PHE cc_start: 0.8353 (m-10) cc_final: 0.7724 (m-80) REVERT: A 341 LYS cc_start: 0.8786 (mttm) cc_final: 0.8472 (mmtm) REVERT: A 486 GLU cc_start: 0.8311 (tp30) cc_final: 0.7962 (tp30) REVERT: A 487 GLN cc_start: 0.8341 (mt0) cc_final: 0.7950 (mm110) REVERT: A 512 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8549 (ptpt) REVERT: A 587 VAL cc_start: 0.8453 (t) cc_final: 0.8090 (p) REVERT: A 589 GLN cc_start: 0.8296 (mp10) cc_final: 0.8052 (mp10) REVERT: A 669 GLN cc_start: 0.8306 (mt0) cc_final: 0.7951 (mt0) REVERT: B 125 PHE cc_start: 0.8000 (m-80) cc_final: 0.7203 (m-80) REVERT: B 143 ASN cc_start: 0.7542 (t0) cc_final: 0.6891 (p0) REVERT: B 179 ARG cc_start: 0.7579 (mpp80) cc_final: 0.7139 (mpp80) REVERT: B 180 ARG cc_start: 0.7597 (mtp85) cc_final: 0.7265 (mtp85) REVERT: B 244 PHE cc_start: 0.8591 (t80) cc_final: 0.8053 (t80) REVERT: B 256 ASN cc_start: 0.8515 (t0) cc_final: 0.8134 (t0) REVERT: B 314 SER cc_start: 0.7558 (m) cc_final: 0.7310 (p) REVERT: B 323 THR cc_start: 0.7899 (m) cc_final: 0.7698 (m) REVERT: B 474 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7605 (mtp-110) REVERT: B 488 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8727 (ttmm) REVERT: B 506 MET cc_start: 0.8508 (mmm) cc_final: 0.8271 (mmp) REVERT: B 574 THR cc_start: 0.8842 (m) cc_final: 0.8586 (p) REVERT: B 589 GLN cc_start: 0.8160 (mm110) cc_final: 0.7906 (mp10) REVERT: C 142 TYR cc_start: 0.7816 (m-80) cc_final: 0.7274 (m-10) REVERT: C 143 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.6726 (p0) REVERT: C 179 ARG cc_start: 0.7323 (mpp80) cc_final: 0.6710 (mpp80) REVERT: C 237 ASP cc_start: 0.8323 (t0) cc_final: 0.7987 (m-30) REVERT: C 273 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7704 (ttp80) REVERT: C 316 ILE cc_start: 0.8822 (mm) cc_final: 0.8534 (mm) REVERT: C 320 GLN cc_start: 0.7992 (tt0) cc_final: 0.7738 (tt0) REVERT: C 321 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 340 PHE cc_start: 0.8404 (m-80) cc_final: 0.7807 (m-80) REVERT: C 486 GLU cc_start: 0.8228 (tp30) cc_final: 0.7771 (tp30) REVERT: C 542 MET cc_start: 0.8853 (ptp) cc_final: 0.8569 (ptp) REVERT: C 589 GLN cc_start: 0.7995 (mp10) cc_final: 0.7514 (mp10) REVERT: C 661 PHE cc_start: 0.8617 (t80) cc_final: 0.8400 (t80) REVERT: C 677 ASP cc_start: 0.8071 (m-30) cc_final: 0.7692 (m-30) outliers start: 40 outliers final: 26 residues processed: 303 average time/residue: 0.1506 time to fit residues: 62.0224 Evaluate side-chains 292 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 256 ASN A 320 GLN B 56 HIS ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 56 HIS C 228 GLN C 298 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106536 restraints weight = 21561.946| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.87 r_work: 0.3230 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13341 Z= 0.196 Angle : 0.558 5.960 18081 Z= 0.300 Chirality : 0.045 0.162 2049 Planarity : 0.004 0.052 2310 Dihedral : 6.340 56.733 1952 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.76 % Allowed : 11.46 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1590 helix: 2.18 (0.26), residues: 375 sheet: -0.02 (0.23), residues: 426 loop : -0.04 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 469 TYR 0.017 0.001 TYR C 99 PHE 0.029 0.002 PHE C 251 TRP 0.012 0.001 TRP C 382 HIS 0.006 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00460 (13311) covalent geometry : angle 0.55018 (18012) SS BOND : bond 0.00234 ( 21) SS BOND : angle 0.83502 ( 42) hydrogen bonds : bond 0.04081 ( 579) hydrogen bonds : angle 4.89354 ( 1809) link_BETA1-4 : bond 0.00320 ( 6) link_BETA1-4 : angle 1.94796 ( 18) link_NAG-ASN : bond 0.00433 ( 3) link_NAG-ASN : angle 2.92429 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7963 (m-80) cc_final: 0.7139 (m-80) REVERT: A 209 THR cc_start: 0.8182 (m) cc_final: 0.7511 (p) REVERT: A 212 MET cc_start: 0.8071 (mmp) cc_final: 0.7848 (mmp) REVERT: A 237 ASP cc_start: 0.7954 (t0) cc_final: 0.7567 (t0) REVERT: A 260 VAL cc_start: 0.7779 (t) cc_final: 0.7437 (p) REVERT: A 340 PHE cc_start: 0.8405 (m-10) cc_final: 0.7730 (m-80) REVERT: A 341 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8456 (mmtm) REVERT: A 486 GLU cc_start: 0.8338 (tp30) cc_final: 0.7985 (tp30) REVERT: A 587 VAL cc_start: 0.8516 (t) cc_final: 0.8222 (p) REVERT: A 627 SER cc_start: 0.8264 (m) cc_final: 0.7935 (t) REVERT: B 125 PHE cc_start: 0.8064 (m-80) cc_final: 0.7265 (m-80) REVERT: B 179 ARG cc_start: 0.7602 (mpp80) cc_final: 0.7099 (mpp80) REVERT: B 180 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7249 (mtp85) REVERT: B 244 PHE cc_start: 0.8651 (t80) cc_final: 0.8301 (t80) REVERT: B 256 ASN cc_start: 0.8537 (t0) cc_final: 0.8080 (t0) REVERT: B 314 SER cc_start: 0.7558 (m) cc_final: 0.7325 (p) REVERT: B 323 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7677 (m) REVERT: B 474 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7628 (mtp-110) REVERT: B 488 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8748 (ttmm) REVERT: B 574 THR cc_start: 0.8835 (m) cc_final: 0.8589 (p) REVERT: B 608 TYR cc_start: 0.8863 (m-80) cc_final: 0.7795 (m-80) REVERT: C 142 TYR cc_start: 0.7783 (m-80) cc_final: 0.7387 (m-10) REVERT: C 143 ASN cc_start: 0.7747 (t0) cc_final: 0.6931 (p0) REVERT: C 179 ARG cc_start: 0.7412 (mpp80) cc_final: 0.6758 (mpp80) REVERT: C 237 ASP cc_start: 0.8292 (t0) cc_final: 0.7996 (m-30) REVERT: C 273 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7666 (ttp80) REVERT: C 316 ILE cc_start: 0.8825 (mm) cc_final: 0.8545 (mm) REVERT: C 320 GLN cc_start: 0.7945 (tt0) cc_final: 0.7622 (tt0) REVERT: C 321 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7176 (mm-30) REVERT: C 340 PHE cc_start: 0.8406 (m-80) cc_final: 0.7781 (m-80) REVERT: C 486 GLU cc_start: 0.8211 (tp30) cc_final: 0.7679 (tp30) REVERT: C 542 MET cc_start: 0.8953 (ptp) cc_final: 0.8610 (ptp) REVERT: C 550 MET cc_start: 0.7968 (tpp) cc_final: 0.7528 (mpp) REVERT: C 589 GLN cc_start: 0.8021 (mp10) cc_final: 0.7562 (mp10) REVERT: C 642 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7854 (mp0) REVERT: C 661 PHE cc_start: 0.8627 (t80) cc_final: 0.8373 (t80) REVERT: C 677 ASP cc_start: 0.8024 (m-30) cc_final: 0.7612 (m-30) outliers start: 40 outliers final: 29 residues processed: 297 average time/residue: 0.1490 time to fit residues: 60.3551 Evaluate side-chains 305 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 298 GLN Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 0.0060 chunk 141 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 133 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 256 ASN A 320 GLN A 600 ASN B 56 HIS B 143 ASN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN C 56 HIS C 228 GLN C 320 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107514 restraints weight = 21797.187| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.95 r_work: 0.3241 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13341 Z= 0.144 Angle : 0.533 6.727 18081 Z= 0.288 Chirality : 0.044 0.148 2049 Planarity : 0.003 0.046 2310 Dihedral : 5.833 56.499 1950 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.76 % Allowed : 13.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1590 helix: 2.36 (0.26), residues: 375 sheet: 0.05 (0.23), residues: 426 loop : -0.02 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 474 TYR 0.019 0.001 TYR B 142 PHE 0.031 0.001 PHE C 251 TRP 0.011 0.001 TRP C 382 HIS 0.006 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00329 (13311) covalent geometry : angle 0.52546 (18012) SS BOND : bond 0.00198 ( 21) SS BOND : angle 0.74397 ( 42) hydrogen bonds : bond 0.03788 ( 579) hydrogen bonds : angle 4.77086 ( 1809) link_BETA1-4 : bond 0.00352 ( 6) link_BETA1-4 : angle 1.84324 ( 18) link_NAG-ASN : bond 0.00273 ( 3) link_NAG-ASN : angle 2.80931 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.7920 (m-80) cc_final: 0.7087 (m-80) REVERT: A 209 THR cc_start: 0.8130 (m) cc_final: 0.7461 (p) REVERT: A 212 MET cc_start: 0.8134 (mmp) cc_final: 0.7872 (mmp) REVERT: A 237 ASP cc_start: 0.7919 (t0) cc_final: 0.7611 (t0) REVERT: A 256 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8149 (t0) REVERT: A 260 VAL cc_start: 0.7728 (t) cc_final: 0.7379 (p) REVERT: A 340 PHE cc_start: 0.8352 (m-10) cc_final: 0.7655 (m-80) REVERT: A 341 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8445 (mmtm) REVERT: A 486 GLU cc_start: 0.8325 (tp30) cc_final: 0.7968 (tp30) REVERT: A 587 VAL cc_start: 0.8542 (t) cc_final: 0.8288 (p) REVERT: A 627 SER cc_start: 0.8216 (m) cc_final: 0.7886 (t) REVERT: B 125 PHE cc_start: 0.8012 (m-80) cc_final: 0.7199 (m-80) REVERT: B 179 ARG cc_start: 0.7632 (mpp80) cc_final: 0.7082 (mpp80) REVERT: B 180 ARG cc_start: 0.7569 (mtp85) cc_final: 0.7209 (mtp85) REVERT: B 237 ASP cc_start: 0.8347 (t0) cc_final: 0.8094 (t0) REVERT: B 244 PHE cc_start: 0.8635 (t80) cc_final: 0.8335 (t80) REVERT: B 256 ASN cc_start: 0.8598 (t0) cc_final: 0.8132 (t0) REVERT: B 260 VAL cc_start: 0.7879 (t) cc_final: 0.7508 (p) REVERT: B 314 SER cc_start: 0.7638 (m) cc_final: 0.7386 (p) REVERT: B 323 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7608 (m) REVERT: B 341 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8176 (mmtm) REVERT: B 360 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7681 (t0) REVERT: B 474 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7580 (mtp-110) REVERT: B 488 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8725 (ttmm) REVERT: B 574 THR cc_start: 0.8822 (m) cc_final: 0.8573 (p) REVERT: B 579 PHE cc_start: 0.8890 (m-80) cc_final: 0.8615 (m-80) REVERT: B 583 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8484 (mtmm) REVERT: C 142 TYR cc_start: 0.7764 (m-80) cc_final: 0.7351 (m-10) REVERT: C 143 ASN cc_start: 0.7818 (t0) cc_final: 0.6746 (p0) REVERT: C 179 ARG cc_start: 0.7438 (mpp80) cc_final: 0.6811 (mpp80) REVERT: C 237 ASP cc_start: 0.8255 (t0) cc_final: 0.7971 (m-30) REVERT: C 273 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7652 (ttp80) REVERT: C 316 ILE cc_start: 0.8785 (mm) cc_final: 0.8510 (mm) REVERT: C 320 GLN cc_start: 0.7919 (tt0) cc_final: 0.7565 (tt0) REVERT: C 321 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7167 (mm-30) REVERT: C 340 PHE cc_start: 0.8367 (m-80) cc_final: 0.7704 (m-80) REVERT: C 486 GLU cc_start: 0.8244 (tp30) cc_final: 0.7740 (tp30) REVERT: C 542 MET cc_start: 0.8902 (ptp) cc_final: 0.8544 (ptp) REVERT: C 589 GLN cc_start: 0.8048 (mp10) cc_final: 0.7602 (mp10) REVERT: C 661 PHE cc_start: 0.8627 (t80) cc_final: 0.8338 (t80) REVERT: C 677 ASP cc_start: 0.8032 (m-30) cc_final: 0.7612 (m-30) outliers start: 40 outliers final: 27 residues processed: 308 average time/residue: 0.1472 time to fit residues: 61.9860 Evaluate side-chains 308 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 85 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 256 ASN B 56 HIS B 320 GLN B 487 GLN C 228 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.127497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107125 restraints weight = 21547.899| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.94 r_work: 0.3236 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13341 Z= 0.181 Angle : 0.549 7.402 18081 Z= 0.296 Chirality : 0.045 0.148 2049 Planarity : 0.003 0.051 2310 Dihedral : 5.653 57.580 1950 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.76 % Allowed : 13.80 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1590 helix: 2.27 (0.26), residues: 375 sheet: 0.04 (0.23), residues: 426 loop : -0.04 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 474 TYR 0.015 0.001 TYR B 644 PHE 0.031 0.002 PHE C 251 TRP 0.013 0.001 TRP C 382 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00426 (13311) covalent geometry : angle 0.54265 (18012) SS BOND : bond 0.00231 ( 21) SS BOND : angle 0.77717 ( 42) hydrogen bonds : bond 0.03867 ( 579) hydrogen bonds : angle 4.78564 ( 1809) link_BETA1-4 : bond 0.00243 ( 6) link_BETA1-4 : angle 1.79526 ( 18) link_NAG-ASN : bond 0.00390 ( 3) link_NAG-ASN : angle 2.65481 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8062 (m-80) cc_final: 0.7238 (m-80) REVERT: A 139 TYR cc_start: 0.8042 (m-80) cc_final: 0.7769 (m-80) REVERT: A 209 THR cc_start: 0.8137 (m) cc_final: 0.7449 (p) REVERT: A 237 ASP cc_start: 0.7910 (t0) cc_final: 0.7612 (t0) REVERT: A 260 VAL cc_start: 0.7746 (t) cc_final: 0.7253 (p) REVERT: A 340 PHE cc_start: 0.8366 (m-10) cc_final: 0.7545 (m-80) REVERT: A 341 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8413 (mmtm) REVERT: A 362 TYR cc_start: 0.8598 (m-10) cc_final: 0.7823 (m-10) REVERT: A 486 GLU cc_start: 0.8314 (tp30) cc_final: 0.7959 (tp30) REVERT: A 487 GLN cc_start: 0.8307 (mt0) cc_final: 0.8104 (mm110) REVERT: A 550 MET cc_start: 0.8112 (mmm) cc_final: 0.7733 (tpp) REVERT: A 627 SER cc_start: 0.8252 (m) cc_final: 0.7912 (t) REVERT: A 658 GLU cc_start: 0.7610 (tt0) cc_final: 0.7405 (tt0) REVERT: B 125 PHE cc_start: 0.8031 (m-80) cc_final: 0.7216 (m-80) REVERT: B 142 TYR cc_start: 0.8201 (m-80) cc_final: 0.7966 (m-10) REVERT: B 179 ARG cc_start: 0.7680 (mpp80) cc_final: 0.7160 (mpp80) REVERT: B 237 ASP cc_start: 0.8342 (t0) cc_final: 0.8006 (t0) REVERT: B 244 PHE cc_start: 0.8620 (t80) cc_final: 0.8342 (t80) REVERT: B 256 ASN cc_start: 0.8655 (t0) cc_final: 0.8189 (t0) REVERT: B 260 VAL cc_start: 0.7894 (t) cc_final: 0.7447 (p) REVERT: B 314 SER cc_start: 0.7638 (m) cc_final: 0.7386 (p) REVERT: B 323 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7622 (m) REVERT: B 360 ASP cc_start: 0.7989 (t70) cc_final: 0.7694 (t0) REVERT: B 474 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7576 (mtp-110) REVERT: B 488 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8730 (ttmm) REVERT: B 574 THR cc_start: 0.8817 (m) cc_final: 0.8557 (p) REVERT: B 583 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8486 (mtmm) REVERT: B 627 SER cc_start: 0.8086 (m) cc_final: 0.7717 (t) REVERT: C 142 TYR cc_start: 0.7809 (m-80) cc_final: 0.7420 (m-10) REVERT: C 143 ASN cc_start: 0.7858 (t0) cc_final: 0.6712 (p0) REVERT: C 179 ARG cc_start: 0.7479 (mpp80) cc_final: 0.6825 (mpp80) REVERT: C 237 ASP cc_start: 0.8253 (t0) cc_final: 0.7876 (t0) REVERT: C 273 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7650 (ttp80) REVERT: C 316 ILE cc_start: 0.8811 (mm) cc_final: 0.8510 (mm) REVERT: C 320 GLN cc_start: 0.7918 (tt0) cc_final: 0.7579 (tt0) REVERT: C 321 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7158 (mm-30) REVERT: C 340 PHE cc_start: 0.8424 (m-80) cc_final: 0.7787 (m-80) REVERT: C 486 GLU cc_start: 0.8202 (tp30) cc_final: 0.7698 (tp30) REVERT: C 542 MET cc_start: 0.8952 (ptp) cc_final: 0.8593 (ptp) REVERT: C 589 GLN cc_start: 0.8086 (mp10) cc_final: 0.7614 (mp10) REVERT: C 661 PHE cc_start: 0.8615 (t80) cc_final: 0.8332 (t80) REVERT: C 677 ASP cc_start: 0.7990 (m-30) cc_final: 0.7570 (m-30) outliers start: 40 outliers final: 27 residues processed: 314 average time/residue: 0.1457 time to fit residues: 62.7363 Evaluate side-chains 300 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 58 optimal weight: 0.5980 chunk 128 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 320 GLN B 56 HIS B 320 GLN B 487 GLN B 610 HIS C 228 GLN C 298 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109497 restraints weight = 21592.513| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.94 r_work: 0.3273 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13341 Z= 0.107 Angle : 0.510 8.177 18081 Z= 0.277 Chirality : 0.043 0.141 2049 Planarity : 0.003 0.049 2310 Dihedral : 5.276 57.374 1950 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.42 % Allowed : 14.70 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1590 helix: 2.43 (0.26), residues: 375 sheet: 0.20 (0.23), residues: 444 loop : 0.03 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 474 TYR 0.012 0.001 TYR A 608 PHE 0.034 0.001 PHE C 251 TRP 0.009 0.001 TRP C 382 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00241 (13311) covalent geometry : angle 0.50442 (18012) SS BOND : bond 0.00169 ( 21) SS BOND : angle 0.75068 ( 42) hydrogen bonds : bond 0.03446 ( 579) hydrogen bonds : angle 4.68405 ( 1809) link_BETA1-4 : bond 0.00384 ( 6) link_BETA1-4 : angle 1.72526 ( 18) link_NAG-ASN : bond 0.00102 ( 3) link_NAG-ASN : angle 2.38606 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8033 (m-80) cc_final: 0.7195 (m-80) REVERT: A 209 THR cc_start: 0.8131 (m) cc_final: 0.7457 (p) REVERT: A 237 ASP cc_start: 0.7825 (t0) cc_final: 0.7590 (t0) REVERT: A 257 TYR cc_start: 0.8305 (t80) cc_final: 0.7955 (t80) REVERT: A 260 VAL cc_start: 0.7686 (t) cc_final: 0.7362 (p) REVERT: A 340 PHE cc_start: 0.8330 (m-10) cc_final: 0.7444 (m-80) REVERT: A 341 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8364 (mmtm) REVERT: A 486 GLU cc_start: 0.8246 (tp30) cc_final: 0.7881 (tp30) REVERT: A 487 GLN cc_start: 0.8299 (mt0) cc_final: 0.8041 (mm-40) REVERT: A 549 THR cc_start: 0.8875 (p) cc_final: 0.8651 (p) REVERT: A 627 SER cc_start: 0.8194 (m) cc_final: 0.7800 (t) REVERT: B 125 PHE cc_start: 0.8026 (m-80) cc_final: 0.7230 (m-80) REVERT: B 142 TYR cc_start: 0.8164 (m-80) cc_final: 0.7946 (m-10) REVERT: B 179 ARG cc_start: 0.7665 (mpp80) cc_final: 0.6949 (mpp80) REVERT: B 237 ASP cc_start: 0.8331 (t0) cc_final: 0.7993 (t0) REVERT: B 244 PHE cc_start: 0.8597 (t80) cc_final: 0.8353 (t80) REVERT: B 256 ASN cc_start: 0.8624 (t0) cc_final: 0.8139 (t0) REVERT: B 314 SER cc_start: 0.7559 (m) cc_final: 0.7307 (p) REVERT: B 323 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7509 (m) REVERT: B 341 LYS cc_start: 0.8674 (tppt) cc_final: 0.8176 (mptt) REVERT: B 360 ASP cc_start: 0.7924 (t70) cc_final: 0.7683 (t0) REVERT: B 474 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7568 (mtp-110) REVERT: B 488 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8719 (ttmm) REVERT: B 574 THR cc_start: 0.8804 (m) cc_final: 0.8558 (p) REVERT: B 579 PHE cc_start: 0.8869 (m-80) cc_final: 0.8567 (m-80) REVERT: B 583 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8459 (mtmm) REVERT: B 597 GLN cc_start: 0.8810 (tt0) cc_final: 0.8591 (tt0) REVERT: B 627 SER cc_start: 0.7977 (m) cc_final: 0.7566 (t) REVERT: C 143 ASN cc_start: 0.7813 (t0) cc_final: 0.6734 (p0) REVERT: C 179 ARG cc_start: 0.7476 (mpp80) cc_final: 0.6824 (mpp80) REVERT: C 214 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7857 (ttpt) REVERT: C 237 ASP cc_start: 0.8194 (t0) cc_final: 0.7855 (t0) REVERT: C 260 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8542 (p) REVERT: C 273 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7605 (ttp80) REVERT: C 316 ILE cc_start: 0.8600 (mm) cc_final: 0.8305 (mt) REVERT: C 320 GLN cc_start: 0.7879 (tt0) cc_final: 0.7505 (tt0) REVERT: C 321 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7087 (mm-30) REVERT: C 340 PHE cc_start: 0.8360 (m-80) cc_final: 0.7744 (m-80) REVERT: C 341 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8233 (mmtm) REVERT: C 474 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7683 (mtp-110) REVERT: C 475 MET cc_start: 0.8464 (ttm) cc_final: 0.8189 (mtp) REVERT: C 486 GLU cc_start: 0.8198 (tp30) cc_final: 0.7818 (tp30) REVERT: C 488 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8839 (ttpp) REVERT: C 542 MET cc_start: 0.8791 (ptp) cc_final: 0.8443 (ptp) REVERT: C 589 GLN cc_start: 0.8078 (mp10) cc_final: 0.7595 (mp10) REVERT: C 643 LEU cc_start: 0.8038 (tp) cc_final: 0.7833 (tt) REVERT: C 661 PHE cc_start: 0.8641 (t80) cc_final: 0.8328 (t80) REVERT: C 677 ASP cc_start: 0.7990 (m-30) cc_final: 0.7576 (m-30) outliers start: 35 outliers final: 23 residues processed: 301 average time/residue: 0.1391 time to fit residues: 57.2081 Evaluate side-chains 306 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 298 GLN Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS B 487 GLN C 56 HIS C 228 GLN C 487 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107555 restraints weight = 21522.145| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.93 r_work: 0.3242 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13341 Z= 0.186 Angle : 0.546 8.301 18081 Z= 0.295 Chirality : 0.044 0.147 2049 Planarity : 0.004 0.048 2310 Dihedral : 5.314 57.916 1950 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.28 % Allowed : 15.11 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1590 helix: 2.40 (0.26), residues: 375 sheet: 0.22 (0.23), residues: 444 loop : -0.01 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 474 TYR 0.016 0.001 TYR C 362 PHE 0.032 0.001 PHE C 251 TRP 0.014 0.001 TRP C 382 HIS 0.007 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00442 (13311) covalent geometry : angle 0.54078 (18012) SS BOND : bond 0.00210 ( 21) SS BOND : angle 0.85956 ( 42) hydrogen bonds : bond 0.03741 ( 579) hydrogen bonds : angle 4.71170 ( 1809) link_BETA1-4 : bond 0.00362 ( 6) link_BETA1-4 : angle 1.77329 ( 18) link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 2.22706 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8099 (m-80) cc_final: 0.7241 (m-80) REVERT: A 139 TYR cc_start: 0.8031 (m-80) cc_final: 0.7712 (m-80) REVERT: A 209 THR cc_start: 0.8174 (m) cc_final: 0.7456 (p) REVERT: A 256 ASN cc_start: 0.8719 (t0) cc_final: 0.8228 (t0) REVERT: A 260 VAL cc_start: 0.7681 (t) cc_final: 0.7164 (p) REVERT: A 340 PHE cc_start: 0.8323 (m-10) cc_final: 0.7254 (m-80) REVERT: A 341 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8391 (mmtm) REVERT: A 362 TYR cc_start: 0.8586 (m-10) cc_final: 0.8023 (m-10) REVERT: A 364 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8280 (mtpp) REVERT: A 486 GLU cc_start: 0.8262 (tp30) cc_final: 0.7956 (tp30) REVERT: A 627 SER cc_start: 0.8251 (m) cc_final: 0.7907 (t) REVERT: A 663 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 125 PHE cc_start: 0.8057 (m-80) cc_final: 0.7238 (m-80) REVERT: B 142 TYR cc_start: 0.8201 (m-80) cc_final: 0.7980 (m-10) REVERT: B 179 ARG cc_start: 0.7708 (mpp80) cc_final: 0.6950 (mpp80) REVERT: B 237 ASP cc_start: 0.8272 (t0) cc_final: 0.7951 (t0) REVERT: B 244 PHE cc_start: 0.8623 (t80) cc_final: 0.8368 (t80) REVERT: B 256 ASN cc_start: 0.8669 (t0) cc_final: 0.8214 (t0) REVERT: B 314 SER cc_start: 0.7597 (m) cc_final: 0.7338 (p) REVERT: B 321 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7290 (mm-30) REVERT: B 323 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7591 (m) REVERT: B 341 LYS cc_start: 0.8721 (tppt) cc_final: 0.8178 (mptt) REVERT: B 351 MET cc_start: 0.7894 (mmt) cc_final: 0.7314 (mmt) REVERT: B 360 ASP cc_start: 0.7930 (t70) cc_final: 0.7687 (t0) REVERT: B 474 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7566 (mtp-110) REVERT: B 488 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8725 (ttmm) REVERT: B 574 THR cc_start: 0.8799 (m) cc_final: 0.8537 (p) REVERT: B 579 PHE cc_start: 0.8890 (m-80) cc_final: 0.8583 (m-80) REVERT: B 583 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8472 (mtmm) REVERT: B 608 TYR cc_start: 0.8701 (m-80) cc_final: 0.8480 (m-80) REVERT: B 627 SER cc_start: 0.8101 (m) cc_final: 0.7724 (t) REVERT: C 142 TYR cc_start: 0.7625 (m-80) cc_final: 0.7208 (m-10) REVERT: C 143 ASN cc_start: 0.7818 (t0) cc_final: 0.6742 (p0) REVERT: C 179 ARG cc_start: 0.7519 (mpp80) cc_final: 0.6852 (mpp80) REVERT: C 214 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7904 (ttpt) REVERT: C 237 ASP cc_start: 0.8230 (t0) cc_final: 0.7917 (t0) REVERT: C 260 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8548 (p) REVERT: C 273 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7642 (ttp80) REVERT: C 320 GLN cc_start: 0.7926 (tt0) cc_final: 0.7573 (tt0) REVERT: C 321 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7140 (mm-30) REVERT: C 340 PHE cc_start: 0.8408 (m-80) cc_final: 0.7768 (m-80) REVERT: C 475 MET cc_start: 0.8487 (ttm) cc_final: 0.8277 (mtp) REVERT: C 486 GLU cc_start: 0.8196 (tp30) cc_final: 0.7807 (tp30) REVERT: C 488 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8837 (ttpp) REVERT: C 506 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8492 (mmm) REVERT: C 542 MET cc_start: 0.8969 (ptp) cc_final: 0.8616 (ptp) REVERT: C 589 GLN cc_start: 0.8091 (mp10) cc_final: 0.7645 (mp10) REVERT: C 661 PHE cc_start: 0.8618 (t80) cc_final: 0.8279 (t80) REVERT: C 677 ASP cc_start: 0.7997 (m-30) cc_final: 0.7592 (m-30) outliers start: 33 outliers final: 20 residues processed: 309 average time/residue: 0.1491 time to fit residues: 62.8975 Evaluate side-chains 306 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 66 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN B 56 HIS C 228 GLN C 320 GLN C 487 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106841 restraints weight = 21737.511| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.96 r_work: 0.3223 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13341 Z= 0.198 Angle : 0.561 8.846 18081 Z= 0.302 Chirality : 0.045 0.147 2049 Planarity : 0.004 0.059 2310 Dihedral : 5.308 57.945 1950 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.48 % Allowed : 15.25 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1590 helix: 2.33 (0.26), residues: 375 sheet: 0.20 (0.23), residues: 444 loop : -0.06 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 474 TYR 0.017 0.001 TYR C 362 PHE 0.035 0.002 PHE C 251 TRP 0.013 0.001 TRP C 382 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00470 (13311) covalent geometry : angle 0.55553 (18012) SS BOND : bond 0.00268 ( 21) SS BOND : angle 0.88301 ( 42) hydrogen bonds : bond 0.03827 ( 579) hydrogen bonds : angle 4.75603 ( 1809) link_BETA1-4 : bond 0.00281 ( 6) link_BETA1-4 : angle 1.77221 ( 18) link_NAG-ASN : bond 0.00483 ( 3) link_NAG-ASN : angle 2.25419 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7778 (pttm) REVERT: A 125 PHE cc_start: 0.8119 (m-80) cc_final: 0.7272 (m-80) REVERT: A 209 THR cc_start: 0.8168 (m) cc_final: 0.7461 (p) REVERT: A 237 ASP cc_start: 0.8108 (t0) cc_final: 0.7891 (t0) REVERT: A 256 ASN cc_start: 0.8762 (t0) cc_final: 0.8309 (t0) REVERT: A 260 VAL cc_start: 0.7667 (t) cc_final: 0.7143 (p) REVERT: A 340 PHE cc_start: 0.8332 (m-10) cc_final: 0.7250 (m-80) REVERT: A 341 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8415 (mmtm) REVERT: A 362 TYR cc_start: 0.8596 (m-10) cc_final: 0.8061 (m-10) REVERT: A 364 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8327 (mtpp) REVERT: A 486 GLU cc_start: 0.8329 (tp30) cc_final: 0.8000 (tp30) REVERT: A 487 GLN cc_start: 0.8337 (mt0) cc_final: 0.8109 (mm110) REVERT: A 550 MET cc_start: 0.8170 (tpp) cc_final: 0.7846 (tpt) REVERT: A 627 SER cc_start: 0.8281 (m) cc_final: 0.7941 (t) REVERT: B 125 PHE cc_start: 0.8056 (m-80) cc_final: 0.7232 (m-80) REVERT: B 179 ARG cc_start: 0.7740 (mpp80) cc_final: 0.6980 (mpp80) REVERT: B 237 ASP cc_start: 0.8265 (t0) cc_final: 0.7913 (t0) REVERT: B 244 PHE cc_start: 0.8599 (t80) cc_final: 0.8351 (t80) REVERT: B 256 ASN cc_start: 0.8690 (t0) cc_final: 0.8192 (t0) REVERT: B 314 SER cc_start: 0.7594 (m) cc_final: 0.7347 (p) REVERT: B 321 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7330 (mm-30) REVERT: B 323 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7657 (m) REVERT: B 341 LYS cc_start: 0.8760 (tppt) cc_final: 0.8235 (mptt) REVERT: B 351 MET cc_start: 0.7791 (mmt) cc_final: 0.7362 (mmt) REVERT: B 360 ASP cc_start: 0.7888 (t70) cc_final: 0.7685 (t0) REVERT: B 488 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8733 (ttmm) REVERT: B 574 THR cc_start: 0.8801 (m) cc_final: 0.8536 (p) REVERT: B 579 PHE cc_start: 0.8917 (m-80) cc_final: 0.8626 (m-80) REVERT: B 583 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8510 (mtmm) REVERT: B 597 GLN cc_start: 0.8796 (tt0) cc_final: 0.8592 (tt0) REVERT: B 608 TYR cc_start: 0.8670 (m-80) cc_final: 0.8447 (m-80) REVERT: B 627 SER cc_start: 0.8152 (m) cc_final: 0.7831 (t) REVERT: C 143 ASN cc_start: 0.7754 (t0) cc_final: 0.6667 (p0) REVERT: C 179 ARG cc_start: 0.7575 (mpp80) cc_final: 0.6886 (mpp80) REVERT: C 237 ASP cc_start: 0.8241 (t0) cc_final: 0.7947 (t0) REVERT: C 273 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7646 (ttp80) REVERT: C 321 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 340 PHE cc_start: 0.8463 (m-80) cc_final: 0.7776 (m-80) REVERT: C 474 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7697 (mtp-110) REVERT: C 475 MET cc_start: 0.8490 (ttm) cc_final: 0.8267 (mtp) REVERT: C 486 GLU cc_start: 0.8214 (tp30) cc_final: 0.7821 (tp30) REVERT: C 488 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8829 (ttpp) REVERT: C 506 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8520 (mmm) REVERT: C 542 MET cc_start: 0.8932 (ptp) cc_final: 0.8565 (ptp) REVERT: C 586 GLU cc_start: 0.8448 (pt0) cc_final: 0.8114 (pt0) REVERT: C 589 GLN cc_start: 0.8084 (mp10) cc_final: 0.7397 (mp10) REVERT: C 642 GLU cc_start: 0.7968 (mp0) cc_final: 0.7179 (mp0) REVERT: C 661 PHE cc_start: 0.8596 (t80) cc_final: 0.8272 (t80) REVERT: C 677 ASP cc_start: 0.8008 (m-30) cc_final: 0.7616 (m-30) outliers start: 36 outliers final: 26 residues processed: 308 average time/residue: 0.1497 time to fit residues: 62.7375 Evaluate side-chains 306 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 153 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 108 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS C 228 GLN C 320 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.128627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108464 restraints weight = 21687.288| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.96 r_work: 0.3236 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13341 Z= 0.147 Angle : 0.548 8.507 18081 Z= 0.295 Chirality : 0.044 0.146 2049 Planarity : 0.004 0.058 2310 Dihedral : 5.230 58.985 1950 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.79 % Allowed : 15.80 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1590 helix: 2.40 (0.26), residues: 375 sheet: 0.22 (0.23), residues: 444 loop : -0.05 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 474 TYR 0.016 0.001 TYR C 362 PHE 0.037 0.001 PHE C 251 TRP 0.011 0.001 TRP C 382 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00346 (13311) covalent geometry : angle 0.54095 (18012) SS BOND : bond 0.00203 ( 21) SS BOND : angle 0.93043 ( 42) hydrogen bonds : bond 0.03624 ( 579) hydrogen bonds : angle 4.72324 ( 1809) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 1.76559 ( 18) link_NAG-ASN : bond 0.00381 ( 3) link_NAG-ASN : angle 2.61661 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 281 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7781 (pttm) REVERT: A 125 PHE cc_start: 0.8124 (m-80) cc_final: 0.7255 (m-80) REVERT: A 209 THR cc_start: 0.8171 (m) cc_final: 0.7475 (p) REVERT: A 237 ASP cc_start: 0.8070 (t0) cc_final: 0.7735 (t0) REVERT: A 256 ASN cc_start: 0.8760 (t0) cc_final: 0.8298 (t0) REVERT: A 260 VAL cc_start: 0.7600 (t) cc_final: 0.7253 (p) REVERT: A 340 PHE cc_start: 0.8311 (m-10) cc_final: 0.7296 (m-80) REVERT: A 341 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8362 (mmtm) REVERT: A 362 TYR cc_start: 0.8589 (m-10) cc_final: 0.8046 (m-10) REVERT: A 364 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8317 (mtpp) REVERT: A 486 GLU cc_start: 0.8291 (tp30) cc_final: 0.7979 (tp30) REVERT: A 487 GLN cc_start: 0.8340 (mt0) cc_final: 0.8118 (mm110) REVERT: A 627 SER cc_start: 0.8237 (m) cc_final: 0.7883 (t) REVERT: A 663 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7137 (mm-30) REVERT: B 125 PHE cc_start: 0.8034 (m-80) cc_final: 0.7214 (m-80) REVERT: B 237 ASP cc_start: 0.8344 (t0) cc_final: 0.8021 (t0) REVERT: B 244 PHE cc_start: 0.8585 (t80) cc_final: 0.8321 (t80) REVERT: B 256 ASN cc_start: 0.8695 (t0) cc_final: 0.8205 (t0) REVERT: B 314 SER cc_start: 0.7539 (m) cc_final: 0.7283 (p) REVERT: B 323 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7599 (m) REVERT: B 341 LYS cc_start: 0.8720 (tppt) cc_final: 0.8237 (mptt) REVERT: B 351 MET cc_start: 0.7767 (mmt) cc_final: 0.7362 (mmt) REVERT: B 488 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8713 (ttmm) REVERT: B 574 THR cc_start: 0.8782 (m) cc_final: 0.8518 (p) REVERT: B 579 PHE cc_start: 0.8897 (m-80) cc_final: 0.8596 (m-80) REVERT: B 583 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8463 (mtmm) REVERT: B 627 SER cc_start: 0.8076 (m) cc_final: 0.7755 (t) REVERT: B 669 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8161 (mp10) REVERT: C 143 ASN cc_start: 0.7693 (t0) cc_final: 0.6713 (p0) REVERT: C 179 ARG cc_start: 0.7573 (mpp80) cc_final: 0.6881 (mpp80) REVERT: C 214 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7926 (ttpt) REVERT: C 237 ASP cc_start: 0.8225 (t0) cc_final: 0.7890 (t0) REVERT: C 273 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7597 (ttp80) REVERT: C 321 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7228 (mm-30) REVERT: C 469 ARG cc_start: 0.8459 (tpp80) cc_final: 0.7726 (ttm-80) REVERT: C 474 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7709 (mtp-110) REVERT: C 475 MET cc_start: 0.8474 (ttm) cc_final: 0.8184 (mtp) REVERT: C 486 GLU cc_start: 0.8227 (tp30) cc_final: 0.7790 (tp30) REVERT: C 487 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8103 (mm110) REVERT: C 488 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8853 (ttpp) REVERT: C 542 MET cc_start: 0.8889 (ptp) cc_final: 0.8506 (ptp) REVERT: C 589 GLN cc_start: 0.8092 (mp10) cc_final: 0.7665 (mp10) REVERT: C 642 GLU cc_start: 0.7929 (mp0) cc_final: 0.7584 (mm-30) REVERT: C 661 PHE cc_start: 0.8594 (t80) cc_final: 0.8291 (t80) REVERT: C 677 ASP cc_start: 0.8014 (m-30) cc_final: 0.7617 (m-30) outliers start: 26 outliers final: 21 residues processed: 297 average time/residue: 0.1498 time to fit residues: 60.8727 Evaluate side-chains 304 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 281 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 654 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 4.9990 chunk 15 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 320 GLN B 56 HIS B 597 GLN C 228 GLN C 320 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109138 restraints weight = 21630.709| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.78 r_work: 0.3283 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13341 Z= 0.171 Angle : 0.564 8.893 18081 Z= 0.302 Chirality : 0.044 0.148 2049 Planarity : 0.004 0.056 2310 Dihedral : 5.244 59.629 1950 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.86 % Allowed : 15.80 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1590 helix: 2.35 (0.26), residues: 375 sheet: 0.19 (0.23), residues: 444 loop : -0.10 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 474 TYR 0.022 0.001 TYR B 608 PHE 0.036 0.001 PHE C 251 TRP 0.012 0.001 TRP C 382 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00406 (13311) covalent geometry : angle 0.55690 (18012) SS BOND : bond 0.00234 ( 21) SS BOND : angle 0.98774 ( 42) hydrogen bonds : bond 0.03699 ( 579) hydrogen bonds : angle 4.76356 ( 1809) link_BETA1-4 : bond 0.00305 ( 6) link_BETA1-4 : angle 1.72611 ( 18) link_NAG-ASN : bond 0.00487 ( 3) link_NAG-ASN : angle 2.79552 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3384.94 seconds wall clock time: 59 minutes 1.11 seconds (3541.11 seconds total)