Starting phenix.real_space_refine on Sat Jul 4 16:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h13_34423/07_2026/8h13_34423.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 111 5.16 5 C 14124 2.51 5 N 3645 2.21 5 O 4233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22113 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7273 Classifications: {'peptide': 931} Link IDs: {'PTRANS': 42, 'TRANS': 888} Chain breaks: 13 Chain: "B" Number of atoms: 7273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7273 Classifications: {'peptide': 931} Link IDs: {'PTRANS': 42, 'TRANS': 888} Chain breaks: 13 Chain: "C" Number of atoms: 7273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7273 Classifications: {'peptide': 931} Link IDs: {'PTRANS': 42, 'TRANS': 888} Chain breaks: 13 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.92, per 1000 atoms: 0.18 Number of scatterers: 22113 At special positions: 0 Unit cell: (130.95, 130.95, 167.4, 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 111 16.00 O 4233 8.00 N 3645 7.00 C 14124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS C 969 " distance=2.14 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 969 " - pdb=" SG CYS B 400 " distance=1.87 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 969 " - pdb=" SG CYS C 400 " distance=2.07 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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 NAG-ASN " NAG A1201 " - " ASN A1080 " " NAG A1202 " - " ASN A 318 " " NAG A1203 " - " ASN A 602 " " NAG A1204 " - " ASN A 691 " " NAG A1205 " - " ASN A 699 " " NAG A1206 " - " ASN A 783 " " NAG A1207 " - " ASN A1056 " " NAG B1201 " - " ASN B1080 " " NAG B1202 " - " ASN B 318 " " NAG B1203 " - " ASN B 602 " " NAG B1204 " - " ASN B 691 " " NAG B1205 " - " ASN B 699 " " NAG B1206 " - " ASN B 783 " " NAG B1207 " - " ASN B1056 " " NAG C1201 " - " ASN C1080 " " NAG C1202 " - " ASN C 318 " " NAG C1203 " - " ASN C 602 " " NAG C1204 " - " ASN C 691 " " NAG C1205 " - " ASN C 699 " " NAG C1206 " - " ASN C 783 " " NAG C1207 " - " ASN C1056 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 851.6 milliseconds 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 54 sheets defined 25.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.154A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.745A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 738 removed outlier: 3.824A pdb=" N TYR A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 765 removed outlier: 4.098A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 removed outlier: 3.935A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.641A pdb=" N GLY A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.066A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.989A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 948 removed outlier: 3.725A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 970 through 1015 removed outlier: 4.396A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.153A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 removed outlier: 3.744A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 738 removed outlier: 3.824A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 765 removed outlier: 4.098A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 removed outlier: 3.935A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.639A pdb=" N GLY B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.066A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.989A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 948 removed outlier: 3.726A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 964 Processing helix chain 'B' and resid 970 through 1015 removed outlier: 4.396A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.154A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 376 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.745A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 603 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 738 removed outlier: 3.824A pdb=" N TYR C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 765 removed outlier: 4.098A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN C 746 " --> pdb=" O CYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 806 removed outlier: 3.935A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 867 removed outlier: 3.641A pdb=" N GLY C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.066A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 removed outlier: 3.989A pdb=" N THR C 923 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 948 removed outlier: 3.725A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 Processing helix chain 'C' and resid 970 through 1015 removed outlier: 4.396A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.858A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 67 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 69 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 252 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 187 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 91 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 183 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.858A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 67 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 69 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 252 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 187 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 91 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 183 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 5.477A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 313 " --> pdb=" O ASN C 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.504A pdb=" N TYR A 53 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 59 removed outlier: 3.518A pdb=" N LYS A 258 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 165 removed outlier: 4.078A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 114 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.601A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 315 removed outlier: 3.646A pdb=" N VAL A 313 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.643A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 498 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 365 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.643A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 498 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 494 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 389 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.825A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.543A pdb=" N TYR A 440 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 479 " --> pdb=" O TYR A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.055A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 683 through 684 removed outlier: 7.321A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.594A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A1050 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.594A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A1050 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 718 removed outlier: 3.503A pdb=" N THR A 841 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AC1, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AC2, first strand: chain 'A' and resid 1102 through 1104 removed outlier: 3.647A pdb=" N ILE A1063 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 32 through 35 removed outlier: 7.858A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 69 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 187 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 91 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 183 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 32 through 35 removed outlier: 7.858A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 69 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 187 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 91 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 183 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.506A pdb=" N TYR B 53 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.518A pdb=" N LYS B 258 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 164 through 165 removed outlier: 4.078A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 114 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 298 through 306 removed outlier: 5.602A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 313 through 315 removed outlier: 3.646A pdb=" N VAL B 313 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.644A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 498 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 365 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.644A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 498 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 494 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 389 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.825A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 439 through 441 removed outlier: 3.543A pdb=" N TYR B 440 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 479 " --> pdb=" O TYR B 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.055A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 683 through 684 removed outlier: 7.345A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.595A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.595A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 718 removed outlier: 3.503A pdb=" N THR B 841 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AE2, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.647A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 32 through 35 removed outlier: 7.858A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 67 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 69 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR C 252 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 187 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 91 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 183 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 32 through 35 removed outlier: 7.858A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 67 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 69 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR C 252 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 187 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 91 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 183 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 52 through 54 removed outlier: 3.505A pdb=" N TYR C 53 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 58 through 59 removed outlier: 3.519A pdb=" N LYS C 258 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 164 through 165 removed outlier: 4.077A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 114 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 298 through 306 removed outlier: 5.602A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 342 through 345 removed outlier: 3.644A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 498 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 365 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 342 through 345 removed outlier: 3.644A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 498 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 494 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 389 " --> pdb=" O TYR C 494 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.825A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 439 through 441 removed outlier: 3.543A pdb=" N TYR C 440 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 479 " --> pdb=" O TYR C 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.055A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.594A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C1050 " --> pdb=" O SER C 701 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.594A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C1050 " --> pdb=" O SER C 701 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 717 through 718 removed outlier: 3.502A pdb=" N THR C 841 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF9, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 3.647A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) 908 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7029 1.34 - 1.46: 5575 1.46 - 1.59: 9830 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 22584 Sorted by residual: bond pdb=" C1 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C1 NAG C1202 " pdb=" O5 NAG C1202 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" C1 NAG C1206 " pdb=" O5 NAG C1206 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C THR B 616 " pdb=" N PRO B 617 " ideal model delta sigma weight residual 1.334 1.376 -0.043 2.34e-02 1.83e+03 3.31e+00 ... (remaining 22579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 30366 3.26 - 6.51: 252 6.51 - 9.77: 36 9.77 - 13.02: 6 13.02 - 16.28: 6 Bond angle restraints: 30666 Sorted by residual: angle pdb=" CA GLN A 549 " pdb=" CB GLN A 549 " pdb=" CG GLN A 549 " ideal model delta sigma weight residual 114.10 125.09 -10.99 2.00e+00 2.50e-01 3.02e+01 angle pdb=" CA GLN C 549 " pdb=" CB GLN C 549 " pdb=" CG GLN C 549 " ideal model delta sigma weight residual 114.10 125.06 -10.96 2.00e+00 2.50e-01 3.00e+01 angle pdb=" CA GLN B 549 " pdb=" CB GLN B 549 " pdb=" CG GLN B 549 " ideal model delta sigma weight residual 114.10 125.03 -10.93 2.00e+00 2.50e-01 2.99e+01 angle pdb=" CB MET A 851 " pdb=" CG MET A 851 " pdb=" SD MET A 851 " ideal model delta sigma weight residual 112.70 128.98 -16.28 3.00e+00 1.11e-01 2.94e+01 angle pdb=" CB MET C 851 " pdb=" CG MET C 851 " pdb=" SD MET C 851 " ideal model delta sigma weight residual 112.70 128.97 -16.27 3.00e+00 1.11e-01 2.94e+01 ... (remaining 30661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11985 18.00 - 35.99: 1047 35.99 - 53.99: 177 53.99 - 71.99: 45 71.99 - 89.98: 21 Dihedral angle restraints: 13275 sinusoidal: 5157 harmonic: 8118 Sorted by residual: dihedral pdb=" CB CYS B 720 " pdb=" SG CYS B 720 " pdb=" SG CYS B 742 " pdb=" CB CYS B 742 " ideal model delta sinusoidal sigma weight residual 93.00 23.23 69.77 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS C 720 " pdb=" SG CYS C 720 " pdb=" SG CYS C 742 " pdb=" CB CYS C 742 " ideal model delta sinusoidal sigma weight residual 93.00 23.27 69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 720 " pdb=" SG CYS A 720 " pdb=" SG CYS A 742 " pdb=" CB CYS A 742 " ideal model delta sinusoidal sigma weight residual 93.00 23.31 69.69 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 13272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2845 0.062 - 0.123: 620 0.123 - 0.185: 75 0.185 - 0.246: 12 0.246 - 0.308: 3 Chirality restraints: 3555 Sorted by residual: chirality pdb=" CB THR C 425 " pdb=" CA THR C 425 " pdb=" OG1 THR C 425 " pdb=" CG2 THR C 425 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB THR B 425 " pdb=" CA THR B 425 " pdb=" OG1 THR B 425 " pdb=" CG2 THR B 425 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB THR A 425 " pdb=" CA THR A 425 " pdb=" OG1 THR A 425 " pdb=" CG2 THR A 425 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 3552 not shown) Planarity restraints: 3927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 222 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO A 223 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 222 " 0.051 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO B 223 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 222 " -0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO C 223 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " -0.043 5.00e-02 4.00e+02 ... (remaining 3924 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4814 2.78 - 3.31: 18761 3.31 - 3.84: 33856 3.84 - 4.37: 36155 4.37 - 4.90: 64355 Nonbonded interactions: 157941 Sorted by model distance: nonbonded pdb=" O SER B 556 " pdb=" OG SER B 556 " model vdw 2.254 3.040 nonbonded pdb=" O SER A 556 " pdb=" OG SER A 556 " model vdw 2.254 3.040 nonbonded pdb=" O SER C 556 " pdb=" OG SER C 556 " model vdw 2.255 3.040 nonbonded pdb=" O GLU A1013 " pdb=" OG SER A1019 " model vdw 2.308 3.040 nonbonded pdb=" O GLU C1013 " pdb=" OG SER C1019 " model vdw 2.308 3.040 ... (remaining 157936 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' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.840 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.470 Find NCS groups from input model: 0.140 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 22641 Z= 0.216 Angle : 0.868 16.277 30801 Z= 0.454 Chirality : 0.052 0.308 3555 Planarity : 0.005 0.079 3906 Dihedral : 14.147 89.982 7935 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.83 % Allowed : 1.41 % Favored : 97.76 % 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: -1.27 (0.15), residues: 2709 helix: 0.87 (0.20), residues: 636 sheet: -0.23 (0.20), residues: 615 loop : -1.99 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 48 TYR 0.035 0.002 TYR A 689 PHE 0.028 0.002 PHE C 387 TRP 0.040 0.003 TRP B 868 HIS 0.012 0.002 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (22584) covalent geometry : angle 0.85576 / 0.45 (30666) SS BOND : bond 0.03408 / 2.81 ( 36) SS BOND : angle 2.07392 / 1.45 ( 72) hydrogen bonds : bond 0.20054 / 13.18 ( 827) hydrogen bonds : angle 8.30440 / 5.72 ( 2553) link_NAG-ASN : bond 0.00301 / 0.19 ( 21) link_NAG-ASN : angle 2.67585 / 1.88 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8187 (mt) cc_final: 0.7950 (mt) REVERT: A 657 CYS cc_start: 0.6224 (m) cc_final: 0.5560 (m) REVERT: A 1011 MET cc_start: 0.8698 (tmm) cc_final: 0.8066 (ttm) REVERT: B 101 TRP cc_start: 0.8354 (m-90) cc_final: 0.8105 (m-90) REVERT: B 343 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8598 (mmmt) REVERT: B 722 MET cc_start: 0.8117 (tpp) cc_final: 0.7853 (tpp) REVERT: B 1032 MET cc_start: 0.8408 (ptp) cc_final: 0.8090 (ptp) REVERT: C 118 ASN cc_start: 0.7384 (m-40) cc_final: 0.6892 (t0) REVERT: C 257 LEU cc_start: 0.7584 (mm) cc_final: 0.7383 (mt) REVERT: C 343 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8641 (mmmt) REVERT: C 572 ASP cc_start: 0.8596 (m-30) cc_final: 0.8242 (m-30) REVERT: C 899 TYR cc_start: 0.8453 (m-10) cc_final: 0.8083 (m-10) REVERT: C 915 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7742 (tp-100) REVERT: C 1032 MET cc_start: 0.8080 (ptp) cc_final: 0.7678 (ptp) outliers start: 20 outliers final: 7 residues processed: 272 average time/residue: 0.1132 time to fit residues: 51.1211 Evaluate side-chains 198 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0030 chunk 111 optimal weight: 1.9990 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 GLN A 883 GLN B 32 GLN B 549 GLN B 766 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN C 883 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146423 restraints weight = 32857.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145782 restraints weight = 57003.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144541 restraints weight = 54011.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143239 restraints weight = 55716.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142909 restraints weight = 56475.240| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22641 Z= 0.111 Angle : 0.571 8.607 30801 Z= 0.299 Chirality : 0.043 0.162 3555 Planarity : 0.004 0.048 3906 Dihedral : 4.666 23.328 2988 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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 (0.16), residues: 2709 helix: 1.88 (0.21), residues: 642 sheet: -0.06 (0.20), residues: 609 loop : -1.73 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 449 TYR 0.019 0.001 TYR B 886 PHE 0.022 0.001 PHE A 387 TRP 0.020 0.002 TRP C 868 HIS 0.003 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (22584) covalent geometry : angle 0.55977 / 0.30 (30666) SS BOND : bond 0.00334 / 0.24 ( 36) SS BOND : angle 1.62083 / 1.06 ( 72) hydrogen bonds : bond 0.04871 / 3.09 ( 827) hydrogen bonds : angle 5.71129 / 3.94 ( 2553) link_NAG-ASN : bond 0.00317 / 0.20 ( 21) link_NAG-ASN : angle 1.91976 / 1.33 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 1011 MET cc_start: 0.8656 (tmm) cc_final: 0.7821 (ttm) REVERT: B 56 GLN cc_start: 0.7893 (tp40) cc_final: 0.7112 (mt0) REVERT: B 592 SER cc_start: 0.8856 (m) cc_final: 0.8437 (t) REVERT: B 649 ASP cc_start: 0.8418 (t0) cc_final: 0.8148 (m-30) REVERT: C 257 LEU cc_start: 0.7182 (mm) cc_final: 0.6857 (mt) REVERT: C 572 ASP cc_start: 0.8500 (m-30) cc_final: 0.8123 (m-30) REVERT: C 649 ASP cc_start: 0.8135 (t0) cc_final: 0.7635 (m-30) REVERT: C 689 TYR cc_start: 0.7069 (t80) cc_final: 0.6506 (t80) REVERT: C 915 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7417 (tp-100) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1165 time to fit residues: 55.7131 Evaluate side-chains 196 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 127 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 877 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN C 877 GLN ** C1036 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 = 0.3751 r_free = 0.3751 target = 0.154488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.130044 restraints weight = 33333.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124904 restraints weight = 38256.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124965 restraints weight = 49410.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125572 restraints weight = 40717.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125835 restraints weight = 35052.411| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22641 Z= 0.247 Angle : 0.713 24.015 30801 Z= 0.361 Chirality : 0.047 0.157 3555 Planarity : 0.004 0.042 3906 Dihedral : 4.973 27.242 2988 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.12 % Allowed : 6.42 % Favored : 93.46 % 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: -0.85 (0.16), residues: 2709 helix: 1.22 (0.20), residues: 663 sheet: 0.14 (0.21), residues: 585 loop : -1.80 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1001 TYR 0.016 0.002 TYR C 53 PHE 0.022 0.002 PHE C1024 TRP 0.020 0.002 TRP A 340 HIS 0.011 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (22584) covalent geometry : angle 0.70030 / 0.36 (30666) SS BOND : bond 0.00636 / 0.40 ( 36) SS BOND : angle 2.10619 / 1.49 ( 72) hydrogen bonds : bond 0.07050 / 4.47 ( 827) hydrogen bonds : angle 5.56619 / 3.82 ( 2553) link_NAG-ASN : bond 0.00363 / 0.22 ( 21) link_NAG-ASN : angle 2.16015 / 1.46 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.8074 (mmm) cc_final: 0.7874 (mtm) REVERT: B 56 GLN cc_start: 0.8256 (tp40) cc_final: 0.6859 (mt0) REVERT: B 379 PHE cc_start: 0.8294 (m-80) cc_final: 0.8079 (m-80) REVERT: B 548 PHE cc_start: 0.8244 (t80) cc_final: 0.8037 (t80) REVERT: B 649 ASP cc_start: 0.8323 (t0) cc_final: 0.8048 (m-30) REVERT: B 746 ASN cc_start: 0.8691 (t0) cc_final: 0.8473 (m-40) REVERT: B 785 SER cc_start: 0.8705 (p) cc_final: 0.8460 (p) REVERT: C 118 ASN cc_start: 0.7450 (m-40) cc_final: 0.6889 (t0) REVERT: C 518 ASP cc_start: 0.7838 (t0) cc_final: 0.7502 (t0) REVERT: C 572 ASP cc_start: 0.8692 (m-30) cc_final: 0.8255 (m-30) REVERT: C 649 ASP cc_start: 0.8092 (t0) cc_final: 0.7634 (m-30) REVERT: C 681 LEU cc_start: 0.7707 (mt) cc_final: 0.7468 (mp) REVERT: C 1011 MET cc_start: 0.8763 (tmm) cc_final: 0.8297 (ttm) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.1103 time to fit residues: 46.4788 Evaluate side-chains 185 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 258 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139187 restraints weight = 32905.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137774 restraints weight = 60658.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135833 restraints weight = 55828.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134811 restraints weight = 51984.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135275 restraints weight = 43038.479| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 22641 Z= 0.128 Angle : 0.601 23.950 30801 Z= 0.305 Chirality : 0.043 0.167 3555 Planarity : 0.004 0.039 3906 Dihedral : 4.659 26.055 2988 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -0.52 (0.16), residues: 2709 helix: 1.88 (0.20), residues: 642 sheet: 0.21 (0.21), residues: 606 loop : -1.70 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 758 TYR 0.013 0.001 TYR C 886 PHE 0.023 0.001 PHE B 805 TRP 0.022 0.001 TRP A 340 HIS 0.005 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (22584) covalent geometry : angle 0.58714 / 0.30 (30666) SS BOND : bond 0.00729 / 0.44 ( 36) SS BOND : angle 2.11229 / 1.45 ( 72) hydrogen bonds : bond 0.05419 / 3.42 ( 827) hydrogen bonds : angle 5.20135 / 3.57 ( 2553) link_NAG-ASN : bond 0.00206 / 0.13 ( 21) link_NAG-ASN : angle 1.90217 / 1.30 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: C 257 LEU cc_start: 0.7641 (mm) cc_final: 0.7426 (mt) REVERT: C 572 ASP cc_start: 0.8543 (m-30) cc_final: 0.8195 (m-30) REVERT: C 649 ASP cc_start: 0.8010 (t0) cc_final: 0.7707 (m-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1105 time to fit residues: 49.1278 Evaluate side-chains 188 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.0060 chunk 210 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 138 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS A 766 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140420 restraints weight = 33061.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140316 restraints weight = 61357.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139199 restraints weight = 53472.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138683 restraints weight = 42790.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138832 restraints weight = 38804.714| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22641 Z= 0.106 Angle : 0.550 9.686 30801 Z= 0.285 Chirality : 0.043 0.175 3555 Planarity : 0.003 0.039 3906 Dihedral : 4.381 24.551 2988 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % 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: -0.31 (0.16), residues: 2709 helix: 2.57 (0.21), residues: 606 sheet: 0.18 (0.22), residues: 549 loop : -1.60 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.014 0.001 TYR A1049 PHE 0.029 0.001 PHE B 548 TRP 0.008 0.001 TRP A 423 HIS 0.004 0.001 HIS B1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (22584) covalent geometry : angle 0.53955 / 0.28 (30666) SS BOND : bond 0.00306 / 0.19 ( 36) SS BOND : angle 1.70478 / 1.21 ( 72) hydrogen bonds : bond 0.04654 / 2.92 ( 827) hydrogen bonds : angle 4.87597 / 3.35 ( 2553) link_NAG-ASN : bond 0.00219 / 0.13 ( 21) link_NAG-ASN : angle 1.70410 / 1.17 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 TRP cc_start: 0.6736 (t60) cc_final: 0.6208 (t-100) REVERT: A 679 MET cc_start: 0.8423 (mmm) cc_final: 0.8152 (tpt) REVERT: A 709 MET cc_start: 0.8684 (mtp) cc_final: 0.8058 (mtp) REVERT: B 496 VAL cc_start: 0.8404 (t) cc_final: 0.8194 (m) REVERT: B 679 MET cc_start: 0.8808 (tpp) cc_final: 0.8382 (mmt) REVERT: B 722 MET cc_start: 0.7632 (tpp) cc_final: 0.7246 (tpp) REVERT: C 572 ASP cc_start: 0.8418 (m-30) cc_final: 0.8083 (m-30) REVERT: C 649 ASP cc_start: 0.7897 (t0) cc_final: 0.7463 (m-30) REVERT: C 851 MET cc_start: 0.7708 (mmm) cc_final: 0.7457 (mmt) REVERT: C 1011 MET cc_start: 0.8585 (tmm) cc_final: 0.8175 (ttm) outliers start: 1 outliers final: 1 residues processed: 267 average time/residue: 0.1207 time to fit residues: 54.1193 Evaluate side-chains 185 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 212 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 243 optimal weight: 0.1980 chunk 273 optimal weight: 0.0370 chunk 245 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 262 optimal weight: 4.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139347 restraints weight = 33232.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138528 restraints weight = 62939.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138007 restraints weight = 54639.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137196 restraints weight = 44047.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137559 restraints weight = 40491.711| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22641 Z= 0.105 Angle : 0.534 8.364 30801 Z= 0.277 Chirality : 0.043 0.157 3555 Planarity : 0.003 0.038 3906 Dihedral : 4.229 23.191 2988 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -0.21 (0.16), residues: 2709 helix: 2.65 (0.21), residues: 609 sheet: 0.21 (0.22), residues: 549 loop : -1.53 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.014 0.001 TYR A 410 PHE 0.023 0.001 PHE A 805 TRP 0.012 0.001 TRP A 340 HIS 0.006 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (22584) covalent geometry : angle 0.52244 / 0.27 (30666) SS BOND : bond 0.00274 / 0.18 ( 36) SS BOND : angle 1.90010 / 1.36 ( 72) hydrogen bonds : bond 0.04514 / 2.83 ( 827) hydrogen bonds : angle 4.74338 / 3.26 ( 2553) link_NAG-ASN : bond 0.00217 / 0.13 ( 21) link_NAG-ASN : angle 1.63128 / 1.11 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.928 Fit side-chains REVERT: A 277 ASP cc_start: 0.8811 (t0) cc_final: 0.8509 (t70) REVERT: A 340 TRP cc_start: 0.6578 (t60) cc_final: 0.6310 (t60) REVERT: A 709 MET cc_start: 0.8592 (mtp) cc_final: 0.7958 (mtp) REVERT: B 277 ASP cc_start: 0.8916 (t0) cc_final: 0.8712 (t70) REVERT: B 679 MET cc_start: 0.8761 (tpp) cc_final: 0.8560 (tpp) REVERT: C 257 LEU cc_start: 0.7468 (mm) cc_final: 0.7235 (mt) REVERT: C 572 ASP cc_start: 0.8442 (m-30) cc_final: 0.8079 (m-30) REVERT: C 649 ASP cc_start: 0.7899 (t0) cc_final: 0.7513 (m-30) REVERT: C 1011 MET cc_start: 0.8768 (tmm) cc_final: 0.8167 (ttm) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1163 time to fit residues: 49.8713 Evaluate side-chains 180 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 7 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139053 restraints weight = 32996.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136163 restraints weight = 66374.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136028 restraints weight = 71546.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134775 restraints weight = 53007.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135255 restraints weight = 50083.292| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22641 Z= 0.197 Angle : 0.631 8.711 30801 Z= 0.326 Chirality : 0.045 0.162 3555 Planarity : 0.004 0.041 3906 Dihedral : 4.530 24.515 2988 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2709 helix: 1.95 (0.20), residues: 630 sheet: 0.21 (0.21), residues: 606 loop : -1.64 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.014 0.001 TYR A 338 PHE 0.023 0.002 PHE C 220 TRP 0.010 0.001 TRP A 340 HIS 0.008 0.001 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (22584) covalent geometry : angle 0.61769 / 0.32 (30666) SS BOND : bond 0.00382 / 0.28 ( 36) SS BOND : angle 2.16512 / 1.53 ( 72) hydrogen bonds : bond 0.06024 / 3.79 ( 827) hydrogen bonds : angle 4.99338 / 3.42 ( 2553) link_NAG-ASN : bond 0.00286 / 0.17 ( 21) link_NAG-ASN : angle 1.84070 / 1.24 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8723 (t0) cc_final: 0.8414 (t0) REVERT: A 709 MET cc_start: 0.8656 (mtp) cc_final: 0.8035 (mtp) REVERT: C 572 ASP cc_start: 0.8455 (m-30) cc_final: 0.8158 (m-30) REVERT: C 649 ASP cc_start: 0.8193 (t0) cc_final: 0.7752 (m-30) REVERT: C 1011 MET cc_start: 0.8806 (tmm) cc_final: 0.8301 (ttm) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1158 time to fit residues: 47.5148 Evaluate side-chains 173 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 130 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 191 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN C 56 GLN ** C 877 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 = 0.3815 r_free = 0.3815 target = 0.159977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137778 restraints weight = 32812.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138169 restraints weight = 58005.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136766 restraints weight = 49754.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136009 restraints weight = 44403.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136247 restraints weight = 38456.755| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22641 Z= 0.113 Angle : 0.565 7.805 30801 Z= 0.292 Chirality : 0.043 0.150 3555 Planarity : 0.003 0.038 3906 Dihedral : 4.379 23.969 2988 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.31 (0.16), residues: 2709 helix: 2.07 (0.21), residues: 651 sheet: 0.09 (0.21), residues: 627 loop : -1.50 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.015 0.001 TYR B 338 PHE 0.031 0.001 PHE B 387 TRP 0.011 0.001 TRP A 340 HIS 0.012 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (22584) covalent geometry : angle 0.55231 / 0.29 (30666) SS BOND : bond 0.00238 / 0.17 ( 36) SS BOND : angle 1.98569 / 1.39 ( 72) hydrogen bonds : bond 0.04900 / 3.07 ( 827) hydrogen bonds : angle 4.83700 / 3.31 ( 2553) link_NAG-ASN : bond 0.00407 / 0.23 ( 21) link_NAG-ASN : angle 1.77252 / 1.20 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 257 LEU cc_start: 0.7446 (mm) cc_final: 0.7091 (mt) REVERT: A 277 ASP cc_start: 0.8691 (t0) cc_final: 0.8320 (t70) REVERT: A 340 TRP cc_start: 0.6193 (t60) cc_final: 0.5815 (t-100) REVERT: A 573 ILE cc_start: 0.9420 (mt) cc_final: 0.9167 (mt) REVERT: A 709 MET cc_start: 0.8558 (mtp) cc_final: 0.7881 (mtp) REVERT: A 851 MET cc_start: 0.7771 (tpp) cc_final: 0.7555 (mmm) REVERT: B 257 LEU cc_start: 0.8193 (mt) cc_final: 0.7979 (mt) REVERT: B 679 MET cc_start: 0.8622 (tpp) cc_final: 0.8324 (mmt) REVERT: C 572 ASP cc_start: 0.8454 (m-30) cc_final: 0.8176 (m-30) REVERT: C 649 ASP cc_start: 0.8145 (t0) cc_final: 0.7573 (m-30) REVERT: C 851 MET cc_start: 0.8077 (mtt) cc_final: 0.7626 (ttm) REVERT: C 1011 MET cc_start: 0.8698 (tmm) cc_final: 0.8148 (ttm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1089 time to fit residues: 47.3919 Evaluate side-chains 173 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 62 optimal weight: 0.0470 chunk 249 optimal weight: 0.5980 chunk 266 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 278 optimal weight: 0.3980 chunk 112 optimal weight: 0.0970 chunk 241 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143267 restraints weight = 32881.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142005 restraints weight = 58208.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140129 restraints weight = 62521.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139204 restraints weight = 57992.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139587 restraints weight = 48730.566| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 22641 Z= 0.101 Angle : 0.583 38.926 30801 Z= 0.282 Chirality : 0.043 0.212 3555 Planarity : 0.003 0.037 3906 Dihedral : 4.212 22.698 2988 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2709 helix: 2.48 (0.21), residues: 633 sheet: 0.22 (0.21), residues: 621 loop : -1.47 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.017 0.001 TYR A 338 PHE 0.030 0.001 PHE B 387 TRP 0.010 0.001 TRP C 423 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (22584) covalent geometry : angle 0.57305 / 0.28 (30666) SS BOND : bond 0.00265 / 0.22 ( 36) SS BOND : angle 1.82090 / 1.30 ( 72) hydrogen bonds : bond 0.04293 / 2.68 ( 827) hydrogen bonds : angle 4.68197 / 3.21 ( 2553) link_NAG-ASN : bond 0.00247 / 0.15 ( 21) link_NAG-ASN : angle 1.60724 / 1.10 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 573 ILE cc_start: 0.9401 (mt) cc_final: 0.9149 (mt) REVERT: A 709 MET cc_start: 0.8522 (mtp) cc_final: 0.7980 (mtp) REVERT: B 257 LEU cc_start: 0.8100 (mt) cc_final: 0.7899 (mt) REVERT: B 679 MET cc_start: 0.8745 (tpp) cc_final: 0.8432 (mmt) REVERT: C 257 LEU cc_start: 0.7746 (mt) cc_final: 0.7529 (mt) REVERT: C 518 ASP cc_start: 0.7217 (t0) cc_final: 0.6997 (t0) REVERT: C 572 ASP cc_start: 0.8341 (m-30) cc_final: 0.8057 (m-30) REVERT: C 649 ASP cc_start: 0.8001 (t0) cc_final: 0.7598 (m-30) REVERT: C 679 MET cc_start: 0.8761 (mmm) cc_final: 0.8521 (mmt) REVERT: C 722 MET cc_start: 0.7531 (tpp) cc_final: 0.7211 (tpt) REVERT: C 851 MET cc_start: 0.8049 (mtt) cc_final: 0.7601 (ttm) REVERT: C 915 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7259 (tp40) REVERT: C 1011 MET cc_start: 0.8777 (tmm) cc_final: 0.8125 (ttm) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1187 time to fit residues: 51.2914 Evaluate side-chains 172 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 12 optimal weight: 0.0270 chunk 128 optimal weight: 0.0070 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.9858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139714 restraints weight = 32884.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137605 restraints weight = 61355.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135060 restraints weight = 47521.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134278 restraints weight = 50281.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134781 restraints weight = 41943.805| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22641 Z= 0.124 Angle : 0.573 19.407 30801 Z= 0.291 Chirality : 0.043 0.197 3555 Planarity : 0.003 0.037 3906 Dihedral : 4.216 22.717 2988 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.19 (0.16), residues: 2709 helix: 2.40 (0.21), residues: 630 sheet: 0.21 (0.21), residues: 618 loop : -1.50 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.015 0.001 TYR B 338 PHE 0.033 0.001 PHE C 387 TRP 0.009 0.001 TRP A 340 HIS 0.004 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (22584) covalent geometry : angle 0.56132 / 0.29 (30666) SS BOND : bond 0.00244 / 0.18 ( 36) SS BOND : angle 2.01901 / 1.46 ( 72) hydrogen bonds : bond 0.04752 / 2.97 ( 827) hydrogen bonds : angle 4.67930 / 3.20 ( 2553) link_NAG-ASN : bond 0.00250 / 0.15 ( 21) link_NAG-ASN : angle 1.62815 / 1.10 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.9413 (mt) cc_final: 0.9135 (mt) REVERT: A 709 MET cc_start: 0.8566 (mtp) cc_final: 0.8034 (mtp) REVERT: B 518 ASP cc_start: 0.7474 (t0) cc_final: 0.7238 (t0) REVERT: C 518 ASP cc_start: 0.7388 (t0) cc_final: 0.7077 (t0) REVERT: C 519 LEU cc_start: 0.6796 (tt) cc_final: 0.6596 (tt) REVERT: C 572 ASP cc_start: 0.8477 (m-30) cc_final: 0.8190 (m-30) REVERT: C 649 ASP cc_start: 0.8009 (t0) cc_final: 0.7650 (m-30) REVERT: C 851 MET cc_start: 0.8174 (mtt) cc_final: 0.7734 (ttm) REVERT: C 915 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7324 (tp40) REVERT: C 1011 MET cc_start: 0.8771 (tmm) cc_final: 0.8099 (ttm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1173 time to fit residues: 48.5192 Evaluate side-chains 168 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 100 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 251 optimal weight: 0.1980 chunk 246 optimal weight: 3.9990 chunk 65 optimal weight: 0.0060 chunk 48 optimal weight: 0.0170 chunk 221 optimal weight: 6.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 737 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 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 = 0.3845 r_free = 0.3845 target = 0.162863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145949 restraints weight = 32865.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145743 restraints weight = 59771.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140509 restraints weight = 61208.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138952 restraints weight = 56914.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138609 restraints weight = 60754.313| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22641 Z= 0.099 Angle : 0.545 15.264 30801 Z= 0.279 Chirality : 0.043 0.189 3555 Planarity : 0.003 0.036 3906 Dihedral : 4.101 22.307 2988 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.02 (0.16), residues: 2709 helix: 2.80 (0.21), residues: 609 sheet: 0.31 (0.21), residues: 612 loop : -1.46 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.016 0.001 TYR A 338 PHE 0.029 0.001 PHE C 387 TRP 0.008 0.001 TRP C 423 HIS 0.004 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (22584) covalent geometry : angle 0.53388 / 0.28 (30666) SS BOND : bond 0.00195 / 0.14 ( 36) SS BOND : angle 1.87600 / 1.35 ( 72) hydrogen bonds : bond 0.04210 / 2.63 ( 827) hydrogen bonds : angle 4.58553 / 3.14 ( 2553) link_NAG-ASN : bond 0.00252 / 0.15 ( 21) link_NAG-ASN : angle 1.57740 / 1.08 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.94 seconds wall clock time: 45 minutes 8.15 seconds (2708.15 seconds total)