Starting phenix.real_space_refine on Thu May 22 00:56:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h13_34423/05_2025/8h13_34423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h13_34423/05_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_34423/05_2025/8h13_34423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h13_34423/05_2025/8h13_34423.map" model { file = "/net/cci-nas-00/data/ceres_data/8h13_34423/05_2025/8h13_34423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h13_34423/05_2025/8h13_34423.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.70, per 1000 atoms: 0.53 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: 4.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 3.73 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: 10.08 Time building geometry restraints manager: 5.90 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.320 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.400 ------------------------------------------------------------------------------- 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 : 3.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.003 TRP B 868 HIS 0.012 0.002 HIS A1065 PHE 0.028 0.002 PHE C 387 TYR 0.035 0.002 TYR A 689 ARG 0.008 0.001 ARG B 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 21) link_NAG-ASN : angle 2.67585 ( 63) hydrogen bonds : bond 0.20054 ( 827) hydrogen bonds : angle 8.30440 ( 2553) SS BOND : bond 0.03408 ( 36) SS BOND : angle 2.07392 ( 72) covalent geometry : bond 0.00447 (22584) covalent geometry : angle 0.85576 (30666) *********************** 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 : 2.591 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: 0.2778 time to fit residues: 124.3383 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 : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 117 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 112 optimal weight: 0.3980 chunk 218 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 549 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135572 restraints weight = 32547.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134169 restraints weight = 64865.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133524 restraints weight = 54623.515| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22641 Z= 0.122 Angle : 0.585 9.017 30801 Z= 0.305 Chirality : 0.043 0.156 3555 Planarity : 0.004 0.050 3906 Dihedral : 6.491 59.240 3429 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2709 helix: 1.58 (0.20), residues: 660 sheet: -0.12 (0.20), residues: 627 loop : -1.70 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 868 HIS 0.003 0.001 HIS B1046 PHE 0.022 0.001 PHE A 387 TYR 0.021 0.001 TYR B 886 ARG 0.005 0.000 ARG B 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 21) link_NAG-ASN : angle 1.98207 ( 63) hydrogen bonds : bond 0.05401 ( 827) hydrogen bonds : angle 5.76852 ( 2553) SS BOND : bond 0.00317 ( 36) SS BOND : angle 1.59426 ( 72) covalent geometry : bond 0.00270 (22584) covalent geometry : angle 0.57461 (30666) *********************** 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 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.617 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8036 (tptp) cc_final: 0.7824 (mmmm) REVERT: A 1011 MET cc_start: 0.8504 (tmm) cc_final: 0.7804 (ttm) REVERT: B 56 GLN cc_start: 0.8018 (tp40) cc_final: 0.7142 (mt0) REVERT: B 257 LEU cc_start: 0.7586 (mm) cc_final: 0.7377 (mt) REVERT: B 649 ASP cc_start: 0.8483 (t0) cc_final: 0.8129 (m-30) REVERT: C 118 ASN cc_start: 0.7069 (m-40) cc_final: 0.6769 (t0) REVERT: C 257 LEU cc_start: 0.7336 (mm) cc_final: 0.6975 (mt) REVERT: C 572 ASP cc_start: 0.8576 (m-30) cc_final: 0.8198 (m-30) REVERT: C 689 TYR cc_start: 0.7281 (t80) cc_final: 0.6762 (t80) REVERT: C 915 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7442 (tp-100) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2934 time to fit residues: 129.9034 Evaluate side-chains 197 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 169 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 243 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3818 r_free = 0.3818 target = 0.160404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143212 restraints weight = 32715.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141624 restraints weight = 64907.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140119 restraints weight = 67072.138| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22641 Z= 0.125 Angle : 0.580 23.419 30801 Z= 0.294 Chirality : 0.043 0.166 3555 Planarity : 0.004 0.040 3906 Dihedral : 6.225 57.676 3429 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2709 helix: 1.92 (0.21), residues: 645 sheet: 0.21 (0.21), residues: 588 loop : -1.65 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 340 HIS 0.004 0.001 HIS B1046 PHE 0.019 0.001 PHE B 387 TYR 0.012 0.001 TYR A 886 ARG 0.003 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 21) link_NAG-ASN : angle 1.89856 ( 63) hydrogen bonds : bond 0.05142 ( 827) hydrogen bonds : angle 5.25328 ( 2553) SS BOND : bond 0.00369 ( 36) SS BOND : angle 1.80262 ( 72) covalent geometry : bond 0.00293 (22584) covalent geometry : angle 0.56822 (30666) *********************** 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 270 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.569 Fit side-chains revert: symmetry clash REVERT: A 1011 MET cc_start: 0.8752 (tmm) cc_final: 0.8132 (ttm) REVERT: B 56 GLN cc_start: 0.7988 (tp40) cc_final: 0.7095 (mt0) REVERT: B 548 PHE cc_start: 0.7750 (t80) cc_final: 0.7537 (t80) REVERT: C 118 ASN cc_start: 0.7586 (m-40) cc_final: 0.7096 (t0) REVERT: C 257 LEU cc_start: 0.7393 (mm) cc_final: 0.7035 (mt) REVERT: C 518 ASP cc_start: 0.7510 (t0) cc_final: 0.7222 (t0) REVERT: C 572 ASP cc_start: 0.8535 (m-30) cc_final: 0.8134 (m-30) REVERT: C 649 ASP cc_start: 0.8031 (t0) cc_final: 0.7679 (m-30) REVERT: C 915 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7303 (tp-100) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2892 time to fit residues: 129.3719 Evaluate side-chains 196 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 162 optimal weight: 1.9990 chunk 166 optimal weight: 0.0570 chunk 20 optimal weight: 8.9990 chunk 245 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 199 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3835 r_free = 0.3835 target = 0.161827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142654 restraints weight = 33154.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142275 restraints weight = 63273.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141216 restraints weight = 51744.640| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22641 Z= 0.111 Angle : 0.566 23.819 30801 Z= 0.286 Chirality : 0.043 0.157 3555 Planarity : 0.003 0.040 3906 Dihedral : 5.985 56.104 3429 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2709 helix: 2.35 (0.21), residues: 624 sheet: 0.13 (0.20), residues: 627 loop : -1.61 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 340 HIS 0.003 0.001 HIS C1065 PHE 0.019 0.001 PHE C 220 TYR 0.012 0.001 TYR B 886 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 21) link_NAG-ASN : angle 1.76296 ( 63) hydrogen bonds : bond 0.04698 ( 827) hydrogen bonds : angle 4.99388 ( 2553) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.89612 ( 72) covalent geometry : bond 0.00252 (22584) covalent geometry : angle 0.55408 (30666) *********************** 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 269 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.458 Fit side-chains revert: symmetry clash REVERT: A 1011 MET cc_start: 0.8735 (tmm) cc_final: 0.8107 (ttm) REVERT: B 56 GLN cc_start: 0.8192 (tp40) cc_final: 0.7046 (mt0) REVERT: B 496 VAL cc_start: 0.8353 (t) cc_final: 0.8141 (m) REVERT: B 868 TRP cc_start: 0.6050 (p-90) cc_final: 0.5777 (p-90) REVERT: C 118 ASN cc_start: 0.7542 (m-40) cc_final: 0.7111 (t0) REVERT: C 257 LEU cc_start: 0.7383 (mm) cc_final: 0.7072 (mt) REVERT: C 572 ASP cc_start: 0.8440 (m-30) cc_final: 0.8055 (m-30) REVERT: C 649 ASP cc_start: 0.7763 (t0) cc_final: 0.7362 (m-30) REVERT: C 915 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7243 (tp-100) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2959 time to fit residues: 129.5894 Evaluate side-chains 197 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 24 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 170 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3828 r_free = 0.3828 target = 0.161178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144378 restraints weight = 32933.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143363 restraints weight = 66064.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143083 restraints weight = 61983.981| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22641 Z= 0.118 Angle : 0.553 11.336 30801 Z= 0.285 Chirality : 0.043 0.175 3555 Planarity : 0.003 0.041 3906 Dihedral : 5.879 54.274 3429 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2709 helix: 2.50 (0.21), residues: 612 sheet: 0.28 (0.21), residues: 621 loop : -1.54 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 340 HIS 0.004 0.001 HIS B1046 PHE 0.030 0.001 PHE B 548 TYR 0.012 0.001 TYR B 491 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 21) link_NAG-ASN : angle 1.73325 ( 63) hydrogen bonds : bond 0.04762 ( 827) hydrogen bonds : angle 4.85422 ( 2553) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.78586 ( 72) covalent geometry : bond 0.00273 (22584) covalent geometry : angle 0.54163 (30666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.457 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8823 (t0) cc_final: 0.8503 (t70) REVERT: A 340 TRP cc_start: 0.6426 (t60) cc_final: 0.6117 (t-100) REVERT: A 1011 MET cc_start: 0.8723 (tmm) cc_final: 0.8178 (ttm) REVERT: B 56 GLN cc_start: 0.8164 (tp40) cc_final: 0.6862 (mt0) REVERT: B 277 ASP cc_start: 0.8945 (t0) cc_final: 0.8730 (t70) REVERT: B 868 TRP cc_start: 0.6128 (p-90) cc_final: 0.5799 (p-90) REVERT: C 277 ASP cc_start: 0.8831 (t0) cc_final: 0.8443 (t70) REVERT: C 572 ASP cc_start: 0.8359 (m-30) cc_final: 0.7991 (m-30) REVERT: C 649 ASP cc_start: 0.7973 (t0) cc_final: 0.7678 (m-30) REVERT: C 851 MET cc_start: 0.7721 (mmm) cc_final: 0.7497 (mmt) REVERT: C 915 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7226 (tp-100) REVERT: C 1011 MET cc_start: 0.8727 (tmm) cc_final: 0.8191 (ttm) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2706 time to fit residues: 120.3529 Evaluate side-chains 189 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 228 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 249 optimal weight: 0.0470 chunk 251 optimal weight: 0.0070 chunk 7 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3846 r_free = 0.3846 target = 0.162776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145587 restraints weight = 32662.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144903 restraints weight = 62982.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144415 restraints weight = 60201.551| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22641 Z= 0.100 Angle : 0.529 7.373 30801 Z= 0.274 Chirality : 0.043 0.154 3555 Planarity : 0.003 0.039 3906 Dihedral : 5.617 53.235 3429 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2709 helix: 2.60 (0.21), residues: 624 sheet: 0.33 (0.22), residues: 549 loop : -1.46 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.003 0.001 HIS C1065 PHE 0.025 0.001 PHE C 805 TYR 0.015 0.001 TYR A 338 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 21) link_NAG-ASN : angle 1.66577 ( 63) hydrogen bonds : bond 0.04287 ( 827) hydrogen bonds : angle 4.70959 ( 2553) SS BOND : bond 0.00216 ( 36) SS BOND : angle 1.67109 ( 72) covalent geometry : bond 0.00221 (22584) covalent geometry : angle 0.51866 (30666) *********************** 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 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.314 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8797 (t0) cc_final: 0.8491 (t70) REVERT: A 340 TRP cc_start: 0.6530 (t60) cc_final: 0.6029 (t-100) REVERT: A 379 PHE cc_start: 0.8367 (m-10) cc_final: 0.8096 (m-80) REVERT: A 1011 MET cc_start: 0.8713 (tmm) cc_final: 0.8131 (ttm) REVERT: B 56 GLN cc_start: 0.8072 (tp40) cc_final: 0.6796 (mt0) REVERT: B 257 LEU cc_start: 0.7706 (mm) cc_final: 0.7449 (mt) REVERT: B 379 PHE cc_start: 0.8039 (m-10) cc_final: 0.7649 (m-80) REVERT: C 257 LEU cc_start: 0.7252 (mm) cc_final: 0.7008 (mt) REVERT: C 277 ASP cc_start: 0.8819 (t0) cc_final: 0.8510 (t70) REVERT: C 572 ASP cc_start: 0.8378 (m-30) cc_final: 0.8003 (m-30) REVERT: C 649 ASP cc_start: 0.7945 (t0) cc_final: 0.7472 (m-30) REVERT: C 851 MET cc_start: 0.7704 (mmm) cc_final: 0.7501 (mmt) REVERT: C 915 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7185 (tp-100) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2855 time to fit residues: 126.6585 Evaluate side-chains 184 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 68 optimal weight: 0.7980 chunk 259 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 166 optimal weight: 0.4980 chunk 200 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 737 GLN B 759 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3839 r_free = 0.3839 target = 0.162194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143086 restraints weight = 32840.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140932 restraints weight = 62109.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138409 restraints weight = 49178.583| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22641 Z= 0.109 Angle : 0.533 8.628 30801 Z= 0.276 Chirality : 0.043 0.154 3555 Planarity : 0.003 0.038 3906 Dihedral : 5.522 53.685 3429 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2709 helix: 2.58 (0.21), residues: 624 sheet: 0.38 (0.21), residues: 618 loop : -1.49 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.006 0.001 HIS C1065 PHE 0.031 0.001 PHE A 387 TYR 0.012 0.001 TYR A 491 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 21) link_NAG-ASN : angle 1.66148 ( 63) hydrogen bonds : bond 0.04449 ( 827) hydrogen bonds : angle 4.67729 ( 2553) SS BOND : bond 0.00233 ( 36) SS BOND : angle 1.79755 ( 72) covalent geometry : bond 0.00251 (22584) covalent geometry : angle 0.52129 (30666) *********************** 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 252 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.427 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8831 (t0) cc_final: 0.8446 (t70) REVERT: A 340 TRP cc_start: 0.6401 (t60) cc_final: 0.6166 (t60) REVERT: A 379 PHE cc_start: 0.8408 (m-10) cc_final: 0.8160 (m-10) REVERT: A 1011 MET cc_start: 0.8749 (tmm) cc_final: 0.8155 (ttm) REVERT: B 56 GLN cc_start: 0.8251 (tp40) cc_final: 0.6843 (mt0) REVERT: B 257 LEU cc_start: 0.7853 (mm) cc_final: 0.7569 (mt) REVERT: B 379 PHE cc_start: 0.8001 (m-10) cc_final: 0.7763 (m-80) REVERT: C 257 LEU cc_start: 0.7455 (mm) cc_final: 0.7122 (mt) REVERT: C 277 ASP cc_start: 0.8841 (t0) cc_final: 0.8488 (t70) REVERT: C 572 ASP cc_start: 0.8404 (m-30) cc_final: 0.8001 (m-30) REVERT: C 649 ASP cc_start: 0.8083 (t0) cc_final: 0.7530 (m-30) REVERT: C 657 CYS cc_start: 0.5319 (m) cc_final: 0.4995 (m) REVERT: C 679 MET cc_start: 0.8798 (mmm) cc_final: 0.8035 (tpt) REVERT: C 851 MET cc_start: 0.7745 (mmm) cc_final: 0.7489 (mmt) REVERT: C 915 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7257 (tp-100) REVERT: C 1011 MET cc_start: 0.8885 (tmm) cc_final: 0.8205 (ttm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2723 time to fit residues: 115.3427 Evaluate side-chains 183 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 41 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 114 optimal weight: 0.0270 chunk 137 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3833 r_free = 0.3833 target = 0.161497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145172 restraints weight = 32944.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144755 restraints weight = 63658.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140452 restraints weight = 62994.324| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 22641 Z= 0.121 Angle : 0.549 7.234 30801 Z= 0.284 Chirality : 0.043 0.151 3555 Planarity : 0.003 0.038 3906 Dihedral : 5.496 54.264 3429 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2709 helix: 2.33 (0.21), residues: 633 sheet: 0.33 (0.21), residues: 621 loop : -1.45 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 423 HIS 0.005 0.001 HIS C1065 PHE 0.031 0.001 PHE A 387 TYR 0.016 0.001 TYR A 338 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 21) link_NAG-ASN : angle 1.68651 ( 63) hydrogen bonds : bond 0.04686 ( 827) hydrogen bonds : angle 4.70176 ( 2553) SS BOND : bond 0.00258 ( 36) SS BOND : angle 1.98307 ( 72) covalent geometry : bond 0.00289 (22584) covalent geometry : angle 0.53611 (30666) *********************** 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 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.319 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8752 (t0) cc_final: 0.8435 (t70) REVERT: A 379 PHE cc_start: 0.8406 (m-10) cc_final: 0.8125 (m-10) REVERT: A 1011 MET cc_start: 0.8639 (tmm) cc_final: 0.8052 (ttm) REVERT: B 56 GLN cc_start: 0.8153 (tp40) cc_final: 0.6773 (mt0) REVERT: B 58 LEU cc_start: 0.7831 (mt) cc_final: 0.7598 (mt) REVERT: B 379 PHE cc_start: 0.8115 (m-10) cc_final: 0.7745 (m-80) REVERT: B 657 CYS cc_start: 0.5475 (m) cc_final: 0.5214 (m) REVERT: B 679 MET cc_start: 0.8477 (tpp) cc_final: 0.7982 (tpt) REVERT: C 257 LEU cc_start: 0.7445 (mm) cc_final: 0.7116 (mt) REVERT: C 277 ASP cc_start: 0.8716 (t0) cc_final: 0.8441 (t70) REVERT: C 518 ASP cc_start: 0.7412 (t0) cc_final: 0.7097 (t0) REVERT: C 572 ASP cc_start: 0.8363 (m-30) cc_final: 0.8017 (m-30) REVERT: C 649 ASP cc_start: 0.8146 (t0) cc_final: 0.7661 (m-30) REVERT: C 657 CYS cc_start: 0.5360 (m) cc_final: 0.4664 (m) REVERT: C 679 MET cc_start: 0.8780 (mmm) cc_final: 0.8017 (tpt) REVERT: C 915 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7102 (tp-100) REVERT: C 1011 MET cc_start: 0.8747 (tmm) cc_final: 0.8083 (ttp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2735 time to fit residues: 118.4739 Evaluate side-chains 183 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 142 optimal weight: 2.9990 chunk 251 optimal weight: 0.0270 chunk 241 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 103 optimal weight: 0.0370 chunk 222 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 737 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN C 56 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142903 restraints weight = 32769.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141548 restraints weight = 57697.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140729 restraints weight = 61974.104| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22641 Z= 0.110 Angle : 0.541 8.846 30801 Z= 0.280 Chirality : 0.043 0.207 3555 Planarity : 0.003 0.038 3906 Dihedral : 5.390 54.055 3429 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2709 helix: 2.59 (0.21), residues: 615 sheet: 0.32 (0.22), residues: 603 loop : -1.44 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 423 HIS 0.013 0.001 HIS A1065 PHE 0.031 0.001 PHE B 387 TYR 0.013 0.001 TYR A 491 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 21) link_NAG-ASN : angle 1.67692 ( 63) hydrogen bonds : bond 0.04511 ( 827) hydrogen bonds : angle 4.63631 ( 2553) SS BOND : bond 0.00252 ( 36) SS BOND : angle 1.76913 ( 72) covalent geometry : bond 0.00252 (22584) covalent geometry : angle 0.52985 (30666) *********************** 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 258 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 2.329 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8714 (t0) cc_final: 0.8413 (t70) REVERT: A 1011 MET cc_start: 0.8723 (tmm) cc_final: 0.8131 (ttm) REVERT: B 56 GLN cc_start: 0.8132 (tp40) cc_final: 0.7542 (tp40) REVERT: B 379 PHE cc_start: 0.8029 (m-10) cc_final: 0.7792 (m-80) REVERT: C 257 LEU cc_start: 0.7568 (mm) cc_final: 0.7131 (mt) REVERT: C 277 ASP cc_start: 0.8705 (t0) cc_final: 0.8385 (t70) REVERT: C 572 ASP cc_start: 0.8381 (m-30) cc_final: 0.8018 (m-30) REVERT: C 649 ASP cc_start: 0.8128 (t0) cc_final: 0.7648 (m-30) REVERT: C 657 CYS cc_start: 0.5422 (m) cc_final: 0.5008 (m) REVERT: C 679 MET cc_start: 0.8810 (mmm) cc_final: 0.8020 (tpt) REVERT: C 915 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7139 (tp-100) REVERT: C 1011 MET cc_start: 0.8833 (tmm) cc_final: 0.8079 (ttp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2642 time to fit residues: 114.3241 Evaluate side-chains 186 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 109 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 276 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3789 r_free = 0.3789 target = 0.158010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145086 restraints weight = 33379.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142707 restraints weight = 66425.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138058 restraints weight = 73552.890| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 22641 Z= 0.239 Angle : 0.677 8.549 30801 Z= 0.352 Chirality : 0.046 0.198 3555 Planarity : 0.004 0.044 3906 Dihedral : 5.971 56.976 3429 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2709 helix: 1.77 (0.20), residues: 630 sheet: 0.13 (0.22), residues: 603 loop : -1.52 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 868 HIS 0.010 0.001 HIS B1046 PHE 0.030 0.002 PHE B 387 TYR 0.020 0.002 TYR C 899 ARG 0.006 0.001 ARG B1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 21) link_NAG-ASN : angle 1.95736 ( 63) hydrogen bonds : bond 0.06367 ( 827) hydrogen bonds : angle 5.05133 ( 2553) SS BOND : bond 0.00437 ( 36) SS BOND : angle 2.11092 ( 72) covalent geometry : bond 0.00585 (22584) covalent geometry : angle 0.66477 (30666) ********************** 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 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 2.560 Fit side-chains revert: symmetry clash REVERT: A 277 ASP cc_start: 0.8717 (t0) cc_final: 0.8475 (t70) REVERT: A 281 ASN cc_start: 0.8593 (m-40) cc_final: 0.8392 (m-40) REVERT: A 1011 MET cc_start: 0.8727 (tmm) cc_final: 0.8428 (ttm) REVERT: B 56 GLN cc_start: 0.8273 (tp40) cc_final: 0.7661 (tp40) REVERT: B 379 PHE cc_start: 0.8063 (m-10) cc_final: 0.7819 (m-80) REVERT: B 657 CYS cc_start: 0.5900 (m) cc_final: 0.5654 (m) REVERT: B 679 MET cc_start: 0.8639 (tpp) cc_final: 0.8061 (tpt) REVERT: C 118 ASN cc_start: 0.7425 (m-40) cc_final: 0.6949 (t0) REVERT: C 572 ASP cc_start: 0.8411 (m-30) cc_final: 0.8147 (m-30) REVERT: C 649 ASP cc_start: 0.8119 (t0) cc_final: 0.7759 (m-30) REVERT: C 679 MET cc_start: 0.8746 (mmm) cc_final: 0.8459 (mmm) REVERT: C 840 LEU cc_start: 0.8738 (mt) cc_final: 0.8498 (mt) REVERT: C 1011 MET cc_start: 0.8769 (tmm) cc_final: 0.8143 (ttm) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2893 time to fit residues: 116.1521 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 : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 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 = 0.3742 r_free = 0.3742 target = 0.153943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128397 restraints weight = 33696.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126591 restraints weight = 73467.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127393 restraints weight = 66123.743| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22641 Z= 0.174 Angle : 0.619 8.024 30801 Z= 0.322 Chirality : 0.045 0.194 3555 Planarity : 0.004 0.039 3906 Dihedral : 5.955 59.295 3429 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2709 helix: 1.86 (0.20), residues: 630 sheet: 0.10 (0.22), residues: 588 loop : -1.50 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 423 HIS 0.007 0.001 HIS B1046 PHE 0.030 0.002 PHE B 387 TYR 0.014 0.001 TYR B 338 ARG 0.005 0.000 ARG B 395 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 21) link_NAG-ASN : angle 1.97783 ( 63) hydrogen bonds : bond 0.05780 ( 827) hydrogen bonds : angle 4.96668 ( 2553) SS BOND : bond 0.00348 ( 36) SS BOND : angle 1.96152 ( 72) covalent geometry : bond 0.00422 (22584) covalent geometry : angle 0.60608 (30666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5323.82 seconds wall clock time: 95 minutes 19.02 seconds (5719.02 seconds total)