Starting phenix.real_space_refine on Sun Aug 24 18:53:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h13_34423/08_2025/8h13_34423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h13_34423/08_2025/8h13_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_34423/08_2025/8h13_34423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h13_34423/08_2025/8h13_34423.map" model { file = "/net/cci-nas-00/data/ceres_data/8h13_34423/08_2025/8h13_34423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h13_34423/08_2025/8h13_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-2.0-5787/lib/python3.9/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 dihedrals: 21 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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.43, per 1000 atoms: 0.25 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: 1.52 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.14 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: 5.63 Time building geometry restraints manager: 2.16 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: 12354 18.00 - 35.99: 1086 35.99 - 53.99: 201 53.99 - 71.99: 54 71.99 - 89.98: 21 Dihedral angle restraints: 13716 sinusoidal: 5598 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 13713 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: 0.06 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: 1.190 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.340 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 14.193 89.982 8376 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 aren 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 covalent geometry : bond 0.00447 (22584) covalent geometry : angle 0.85576 (30666) SS BOND : bond 0.03408 ( 36) SS BOND : angle 2.07392 ( 72) hydrogen bonds : bond 0.20054 ( 827) hydrogen bonds : angle 8.30440 ( 2553) link_NAG-ASN : bond 0.00301 ( 21) link_NAG-ASN : angle 2.67585 ( 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 : 0.669 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: 0.8697 (tmm) cc_final: 0.8066 (ttm) REVERT: B 101 TRP cc_start: 0.8355 (m-90) cc_final: 0.8105 (m-90) REVERT: B 343 LYS cc_start: 0.9096 (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: 0.8407 (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: 0.9042 (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: 0.8454 (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: 0.8081 (ptp) cc_final: 0.7679 (ptp) outliers start: 20 outliers final: 7 residues processed: 272 average time/residue: 0.1223 time to fit residues: 54.9409 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 : 0.707 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 549 GLN A 883 GLN B 32 GLN B 549 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN C 549 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.162408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140898 restraints weight = 32736.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140202 restraints weight = 59051.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139546 restraints weight = 58776.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138724 restraints weight = 49766.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138967 restraints weight = 44958.737| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22641 Z= 0.116 Angle : 0.588 8.783 30801 Z= 0.308 Chirality : 0.043 0.158 3555 Planarity : 0.004 0.051 3906 Dihedral : 6.498 59.877 3429 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.16), residues: 2709 helix: 1.91 (0.21), residues: 627 sheet: 0.04 (0.20), residues: 621 loop : -1.85 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.025 0.001 TYR B 886 PHE 0.026 0.001 PHE A 387 TRP 0.020 0.002 TRP C 868 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00239 (22584) covalent geometry : angle 0.57650 (30666) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.63737 ( 72) hydrogen bonds : bond 0.05581 ( 827) hydrogen bonds : angle 5.98093 ( 2553) link_NAG-ASN : bond 0.00323 ( 21) link_NAG-ASN : angle 2.03861 ( 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 270 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.7897 (tptp) cc_final: 0.7649 (mmmm) REVERT: A 1011 MET cc_start: 0.8656 (tmm) cc_final: 0.7852 (ttm) REVERT: B 56 GLN cc_start: 0.7935 (tp40) cc_final: 0.7076 (mt0) REVERT: B 649 ASP cc_start: 0.8398 (t0) cc_final: 0.8146 (m-30) REVERT: C 118 ASN cc_start: 0.7022 (m-40) cc_final: 0.6796 (t0) REVERT: C 257 LEU cc_start: 0.7233 (mm) cc_final: 0.6914 (mt) REVERT: C 572 ASP cc_start: 0.8446 (m-30) cc_final: 0.8106 (m-30) REVERT: C 689 TYR cc_start: 0.7064 (t80) cc_final: 0.6559 (t80) REVERT: C 915 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7428 (tp-100) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1216 time to fit residues: 54.7053 Evaluate side-chains 202 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 5.9990 chunk 88 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 196 optimal weight: 0.1980 chunk 240 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN B 838 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139610 restraints weight = 33273.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138572 restraints weight = 65510.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135907 restraints weight = 54303.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135234 restraints weight = 67571.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135215 restraints weight = 51696.039| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22641 Z= 0.203 Angle : 0.670 22.054 30801 Z= 0.337 Chirality : 0.045 0.160 3555 Planarity : 0.004 0.043 3906 Dihedral : 6.565 57.334 3429 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.16), residues: 2709 helix: 1.43 (0.20), residues: 663 sheet: 0.17 (0.21), residues: 585 loop : -1.77 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 977 TYR 0.015 0.001 TYR C 53 PHE 0.021 0.002 PHE C 220 TRP 0.020 0.002 TRP A 340 HIS 0.009 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00492 (22584) covalent geometry : angle 0.65774 (30666) SS BOND : bond 0.00476 ( 36) SS BOND : angle 1.97164 ( 72) hydrogen bonds : bond 0.06366 ( 827) hydrogen bonds : angle 5.41226 ( 2553) link_NAG-ASN : bond 0.00265 ( 21) link_NAG-ASN : angle 2.10304 ( 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 269 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.8186 (m-10) cc_final: 0.7885 (m-10) REVERT: A 709 MET cc_start: 0.8780 (mtp) cc_final: 0.8336 (mtp) REVERT: A 1011 MET cc_start: 0.8636 (tmm) cc_final: 0.8422 (ttm) REVERT: B 56 GLN cc_start: 0.8135 (tp40) cc_final: 0.7117 (mt0) REVERT: B 548 PHE cc_start: 0.7854 (t80) cc_final: 0.7582 (t80) REVERT: C 118 ASN cc_start: 0.7607 (m-40) cc_final: 0.7146 (t0) REVERT: C 518 ASP cc_start: 0.7519 (t0) cc_final: 0.7233 (t0) REVERT: C 572 ASP cc_start: 0.8567 (m-30) cc_final: 0.8241 (m-30) REVERT: C 649 ASP cc_start: 0.8049 (t0) cc_final: 0.7646 (m-30) REVERT: C 681 LEU cc_start: 0.7612 (mt) cc_final: 0.7299 (mp) REVERT: C 1011 MET cc_start: 0.8680 (tmm) cc_final: 0.8038 (ttm) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.1297 time to fit residues: 58.0939 Evaluate side-chains 187 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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: 0.8980 chunk 78 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 258 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 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 = 0.3811 r_free = 0.3811 target = 0.159681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137759 restraints weight = 32965.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135345 restraints weight = 67340.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136028 restraints weight = 65392.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135449 restraints weight = 43414.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135944 restraints weight = 41124.686| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22641 Z= 0.126 Angle : 0.588 19.121 30801 Z= 0.298 Chirality : 0.043 0.158 3555 Planarity : 0.004 0.040 3906 Dihedral : 6.222 56.750 3429 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.16), residues: 2709 helix: 1.78 (0.20), residues: 660 sheet: 0.06 (0.21), residues: 627 loop : -1.61 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.016 0.001 TYR A 622 PHE 0.019 0.001 PHE A 387 TRP 0.017 0.001 TRP A 340 HIS 0.004 0.001 HIS C1065 Details of bonding type rmsd covalent geometry : bond 0.00289 (22584) covalent geometry : angle 0.57570 (30666) SS BOND : bond 0.00328 ( 36) SS BOND : angle 1.89155 ( 72) hydrogen bonds : bond 0.05234 ( 827) hydrogen bonds : angle 5.13818 ( 2553) link_NAG-ASN : bond 0.00213 ( 21) link_NAG-ASN : angle 1.92603 ( 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 265 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 679 MET cc_start: 0.8495 (mmm) cc_final: 0.8171 (tpt) REVERT: A 709 MET cc_start: 0.8794 (mtp) cc_final: 0.7829 (mtp) REVERT: C 572 ASP cc_start: 0.8533 (m-30) cc_final: 0.8194 (m-30) REVERT: C 649 ASP cc_start: 0.7927 (t0) cc_final: 0.7409 (m-30) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1275 time to fit residues: 55.4092 Evaluate side-chains 187 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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: 9.9990 chunk 210 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 234 optimal weight: 0.3980 chunk 183 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 32 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.158983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137563 restraints weight = 33039.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136513 restraints weight = 62361.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134116 restraints weight = 48504.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133387 restraints weight = 47790.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133786 restraints weight = 37828.908| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22641 Z= 0.124 Angle : 0.575 15.914 30801 Z= 0.293 Chirality : 0.043 0.169 3555 Planarity : 0.004 0.041 3906 Dihedral : 6.070 55.117 3429 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.16), residues: 2709 helix: 2.16 (0.21), residues: 630 sheet: 0.08 (0.21), residues: 630 loop : -1.57 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.012 0.001 TYR A1049 PHE 0.029 0.001 PHE B 548 TRP 0.011 0.001 TRP A 340 HIS 0.004 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00289 (22584) covalent geometry : angle 0.56384 (30666) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.71356 ( 72) hydrogen bonds : bond 0.05046 ( 827) hydrogen bonds : angle 4.95447 ( 2553) link_NAG-ASN : bond 0.00216 ( 21) link_NAG-ASN : angle 1.84422 ( 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 258 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.568 Fit side-chains REVERT: A 340 TRP cc_start: 0.6291 (t60) cc_final: 0.5912 (t-100) REVERT: A 679 MET cc_start: 0.8506 (mmm) cc_final: 0.8278 (mmm) REVERT: A 709 MET cc_start: 0.8673 (mtp) cc_final: 0.7744 (mtp) REVERT: B 496 VAL cc_start: 0.8581 (t) cc_final: 0.8378 (m) REVERT: C 572 ASP cc_start: 0.8485 (m-30) cc_final: 0.8122 (m-30) REVERT: C 649 ASP cc_start: 0.7985 (t0) cc_final: 0.7653 (m-30) REVERT: C 1011 MET cc_start: 0.8653 (tmm) cc_final: 0.8166 (ttm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1272 time to fit residues: 54.7923 Evaluate side-chains 175 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 245 optimal weight: 0.5980 chunk 265 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 262 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139692 restraints weight = 33209.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139588 restraints weight = 62700.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138281 restraints weight = 48667.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137224 restraints weight = 46909.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137492 restraints weight = 38621.034| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2111 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= 0.113 Angle : 0.552 13.515 30801 Z= 0.283 Chirality : 0.043 0.153 3555 Planarity : 0.003 0.039 3906 Dihedral : 5.863 53.909 3429 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2709 helix: 2.27 (0.21), residues: 630 sheet: 0.15 (0.21), residues: 630 loop : -1.52 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.012 0.001 TYR B 491 PHE 0.023 0.001 PHE A 805 TRP 0.013 0.001 TRP A 340 HIS 0.006 0.001 HIS C1065 Details of bonding type rmsd covalent geometry : bond 0.00259 (22584) covalent geometry : angle 0.54030 (30666) SS BOND : bond 0.00232 ( 36) SS BOND : angle 1.73757 ( 72) hydrogen bonds : bond 0.04764 ( 827) hydrogen bonds : angle 4.81339 ( 2553) link_NAG-ASN : bond 0.00217 ( 21) link_NAG-ASN : angle 1.79565 ( 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 264 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8765 (t0) cc_final: 0.8463 (t70) REVERT: A 340 TRP cc_start: 0.6576 (t60) cc_final: 0.6128 (t-100) REVERT: A 709 MET cc_start: 0.8601 (mtp) cc_final: 0.7720 (mtp) REVERT: B 379 PHE cc_start: 0.8037 (m-10) cc_final: 0.7665 (m-80) REVERT: B 722 MET cc_start: 0.7611 (tpp) cc_final: 0.7222 (tpp) REVERT: C 257 LEU cc_start: 0.7439 (mm) cc_final: 0.7192 (mt) REVERT: C 572 ASP cc_start: 0.8423 (m-30) cc_final: 0.8078 (m-30) REVERT: C 649 ASP cc_start: 0.8093 (t0) cc_final: 0.7776 (m-30) REVERT: C 1011 MET cc_start: 0.8752 (tmm) cc_final: 0.8255 (ttm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1334 time to fit residues: 59.1281 Evaluate side-chains 178 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 0.9980 chunk 278 optimal weight: 0.0770 chunk 262 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 0.0870 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: 2.9990 overall best weight: 0.8318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145010 restraints weight = 32984.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143582 restraints weight = 65276.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141283 restraints weight = 53684.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139271 restraints weight = 64129.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139763 restraints weight = 48230.305| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22641 Z= 0.116 Angle : 0.551 10.133 30801 Z= 0.284 Chirality : 0.043 0.152 3555 Planarity : 0.003 0.039 3906 Dihedral : 5.734 54.053 3429 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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 aren not related in a simple way. whole: -0.23 (0.16), residues: 2709 helix: 2.34 (0.21), residues: 633 sheet: 0.18 (0.21), residues: 627 loop : -1.53 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.015 0.001 TYR A 338 PHE 0.028 0.001 PHE A 387 TRP 0.008 0.001 TRP C 423 HIS 0.005 0.001 HIS C1065 Details of bonding type rmsd covalent geometry : bond 0.00268 (22584) covalent geometry : angle 0.53920 (30666) SS BOND : bond 0.00235 ( 36) SS BOND : angle 1.88742 ( 72) hydrogen bonds : bond 0.04721 ( 827) hydrogen bonds : angle 4.76103 ( 2553) link_NAG-ASN : bond 0.00215 ( 21) link_NAG-ASN : angle 1.76030 ( 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 255 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8724 (t0) cc_final: 0.8384 (t0) REVERT: A 340 TRP cc_start: 0.6580 (t60) cc_final: 0.6023 (t-100) REVERT: A 709 MET cc_start: 0.8571 (mtp) cc_final: 0.7737 (mtp) REVERT: C 257 LEU cc_start: 0.7460 (mm) cc_final: 0.7146 (mt) REVERT: C 572 ASP cc_start: 0.8389 (m-30) cc_final: 0.8075 (m-30) REVERT: C 649 ASP cc_start: 0.7979 (t0) cc_final: 0.7655 (m-30) REVERT: C 1011 MET cc_start: 0.8777 (tmm) cc_final: 0.8195 (ttm) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1264 time to fit residues: 54.3076 Evaluate side-chains 174 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 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: 1.9990 chunk 185 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138046 restraints weight = 32823.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137287 restraints weight = 62154.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135118 restraints weight = 49951.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134144 restraints weight = 48354.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134661 restraints weight = 37826.255| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2307 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= 0.129 Angle : 0.562 8.806 30801 Z= 0.290 Chirality : 0.043 0.150 3555 Planarity : 0.003 0.039 3906 Dihedral : 5.696 54.597 3429 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2709 helix: 2.19 (0.21), residues: 633 sheet: 0.16 (0.21), residues: 627 loop : -1.52 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.016 0.001 TYR B 338 PHE 0.037 0.001 PHE A 387 TRP 0.010 0.001 TRP B 423 HIS 0.005 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00304 (22584) covalent geometry : angle 0.55083 (30666) SS BOND : bond 0.00271 ( 36) SS BOND : angle 1.77322 ( 72) hydrogen bonds : bond 0.04953 ( 827) hydrogen bonds : angle 4.76500 ( 2553) link_NAG-ASN : bond 0.00216 ( 21) link_NAG-ASN : angle 1.79506 ( 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 : 0.824 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8785 (t0) cc_final: 0.8273 (t70) REVERT: A 340 TRP cc_start: 0.6486 (t60) cc_final: 0.6207 (t60) REVERT: A 709 MET cc_start: 0.8615 (mtp) cc_final: 0.7731 (mtp) REVERT: C 257 LEU cc_start: 0.7589 (mm) cc_final: 0.7266 (mt) REVERT: C 572 ASP cc_start: 0.8468 (m-30) cc_final: 0.8171 (m-30) REVERT: C 649 ASP cc_start: 0.8044 (t0) cc_final: 0.7645 (m-30) REVERT: C 1011 MET cc_start: 0.8793 (tmm) cc_final: 0.8178 (ttm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1163 time to fit residues: 50.1067 Evaluate side-chains 182 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 0.0000 chunk 249 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 278 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3816 r_free = 0.3816 target = 0.160176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136756 restraints weight = 32821.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134174 restraints weight = 62664.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134870 restraints weight = 58326.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135052 restraints weight = 40168.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135317 restraints weight = 43748.971| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2362 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= 0.120 Angle : 0.562 8.698 30801 Z= 0.290 Chirality : 0.043 0.209 3555 Planarity : 0.003 0.038 3906 Dihedral : 5.623 54.370 3429 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.16), residues: 2709 helix: 2.30 (0.21), residues: 630 sheet: 0.17 (0.21), residues: 627 loop : -1.50 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.016 0.001 TYR A 338 PHE 0.030 0.001 PHE B 387 TRP 0.010 0.001 TRP C 423 HIS 0.004 0.001 HIS C1065 Details of bonding type rmsd covalent geometry : bond 0.00280 (22584) covalent geometry : angle 0.55077 (30666) SS BOND : bond 0.00245 ( 36) SS BOND : angle 1.71180 ( 72) hydrogen bonds : bond 0.04798 ( 827) hydrogen bonds : angle 4.74341 ( 2553) link_NAG-ASN : bond 0.00399 ( 21) link_NAG-ASN : angle 1.81101 ( 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 : 0.819 Fit side-chains revert: symmetry clash REVERT: A 257 LEU cc_start: 0.7457 (mm) cc_final: 0.7100 (mt) REVERT: A 277 ASP cc_start: 0.8609 (t0) cc_final: 0.8212 (t70) REVERT: A 709 MET cc_start: 0.8628 (mtp) cc_final: 0.7721 (mtp) REVERT: C 572 ASP cc_start: 0.8476 (m-30) cc_final: 0.8179 (m-30) REVERT: C 649 ASP cc_start: 0.8125 (t0) cc_final: 0.7720 (m-30) REVERT: C 1011 MET cc_start: 0.8804 (tmm) cc_final: 0.8163 (ttm) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1163 time to fit residues: 50.1117 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 : 0.646 ------------------------------------------------------------------------------- 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: 0.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 170 optimal weight: 0.4980 chunk 198 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139878 restraints weight = 32817.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137907 restraints weight = 69050.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138556 restraints weight = 63457.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138867 restraints weight = 41807.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138901 restraints weight = 47161.164| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22641 Z= 0.121 Angle : 0.603 37.182 30801 Z= 0.294 Chirality : 0.043 0.197 3555 Planarity : 0.003 0.038 3906 Dihedral : 5.592 58.106 3429 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.16), residues: 2709 helix: 2.28 (0.21), residues: 630 sheet: 0.16 (0.21), residues: 627 loop : -1.47 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.016 0.001 TYR B 338 PHE 0.036 0.001 PHE C 387 TRP 0.010 0.001 TRP C 423 HIS 0.004 0.001 HIS C1065 Details of bonding type rmsd covalent geometry : bond 0.00288 (22584) covalent geometry : angle 0.59318 (30666) SS BOND : bond 0.00311 ( 36) SS BOND : angle 1.75799 ( 72) hydrogen bonds : bond 0.04783 ( 827) hydrogen bonds : angle 4.71545 ( 2553) link_NAG-ASN : bond 0.00241 ( 21) link_NAG-ASN : angle 1.75769 ( 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 242 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.8644 (mtp) cc_final: 0.7756 (mtp) REVERT: C 257 LEU cc_start: 0.7494 (mm) cc_final: 0.7135 (mt) REVERT: C 572 ASP cc_start: 0.8403 (m-30) cc_final: 0.8156 (m-30) REVERT: C 649 ASP cc_start: 0.8130 (t0) cc_final: 0.7710 (m-30) REVERT: C 722 MET cc_start: 0.7555 (tpp) cc_final: 0.7228 (tpt) REVERT: C 1011 MET cc_start: 0.8810 (tmm) cc_final: 0.8191 (ttm) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1102 time to fit residues: 45.3469 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 : 0.669 ------------------------------------------------------------------------------- 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: 0.2980 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 270 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 251 optimal weight: 0.0370 chunk 246 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 221 optimal weight: 10.0000 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142373 restraints weight = 32936.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141768 restraints weight = 61338.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139466 restraints weight = 49577.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138796 restraints weight = 46757.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138994 restraints weight = 44636.891| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 22641 Z= 0.098 Angle : 0.546 16.924 30801 Z= 0.277 Chirality : 0.042 0.195 3555 Planarity : 0.003 0.036 3906 Dihedral : 5.321 55.062 3429 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2709 helix: 2.75 (0.21), residues: 612 sheet: 0.26 (0.21), residues: 639 loop : -1.44 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 395 TYR 0.017 0.001 TYR A 622 PHE 0.030 0.001 PHE C 387 TRP 0.009 0.001 TRP C 423 HIS 0.004 0.001 HIS C1065 Details of bonding type rmsd covalent geometry : bond 0.00219 (22584) covalent geometry : angle 0.53520 (30666) SS BOND : bond 0.00207 ( 36) SS BOND : angle 1.69015 ( 72) hydrogen bonds : bond 0.04116 ( 827) hydrogen bonds : angle 4.57012 ( 2553) link_NAG-ASN : bond 0.00269 ( 21) link_NAG-ASN : angle 1.68125 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.09 seconds wall clock time: 46 minutes 5.76 seconds (2765.76 seconds total)