Starting phenix.real_space_refine on Sat Feb 7 07:59:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4p_48901/02_2026/9n4p_48901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4p_48901/02_2026/9n4p_48901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4p_48901/02_2026/9n4p_48901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4p_48901/02_2026/9n4p_48901.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4p_48901/02_2026/9n4p_48901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4p_48901/02_2026/9n4p_48901.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.032 sd= 1.068 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 179 5.16 5 C 19802 2.51 5 N 4930 2.21 5 O 5871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30797 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "B" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "C" Number of atoms: 6666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6666 Classifications: {'peptide': 841} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 807} Chain: "D" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2705 Classifications: {'peptide': 341} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 321} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 316 Unusual residues: {'NAG': 4, 'POV': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 236 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 160 Unusual residues: {'NAG': 4, 'POV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 250 Unusual residues: {'NAG': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.79, per 1000 atoms: 0.22 Number of scatterers: 30797 At special positions: 0 Unit cell: (124.5, 161.02, 220.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 179 16.00 P 15 15.00 O 5871 8.00 N 4930 7.00 C 19802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.04 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 122 " distance=2.02 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=2.02 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.02 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.02 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA L 3 " - " MAN L 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " BETA1-3 " BMA N 3 " - " BMA N 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1005 " - " ASN A 67 " " NAG A1006 " - " ASN A 73 " " NAG A1007 " - " ASN A 275 " " NAG A1008 " - " ASN A 430 " " NAG B1004 " - " ASN B 73 " " NAG B1005 " - " ASN B 430 " " NAG C1003 " - " ASN C 73 " " NAG C1004 " - " ASN C 275 " " NAG C1005 " - " ASN C 412 " " NAG C1006 " - " ASN C 751 " " NAG D1005 " - " ASN D 67 " " NAG D1006 " - " ASN D 73 " " NAG D1007 " - " ASN D 751 " " NAG E 701 " - " ASN E 311 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 412 " " NAG H 1 " - " ASN A 546 " " NAG I 1 " - " ASN A 751 " " NAG J 1 " - " ASN B 67 " " NAG K 1 " - " ASN B 275 " " NAG L 1 " - " ASN B 378 " " NAG M 1 " - " ASN B 412 " " NAG N 1 " - " ASN B 546 " " NAG O 1 " - " ASN B 751 " " NAG P 1 " - " ASN C 67 " " NAG Q 1 " - " ASN C 378 " " NAG R 1 " - " ASN C 546 " " NAG S 1 " - " ASN D 275 " " NAG T 1 " - " ASN D 378 " " NAG U 1 " - " ASN D 412 " " NAG V 1 " - " ASN D 546 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6866 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 52 sheets defined 42.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.588A pdb=" N ALA A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 4.211A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.912A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.541A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.956A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.788A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 297 removed outlier: 4.027A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.703A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.867A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.620A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 560 through 583 removed outlier: 3.676A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.514A pdb=" N GLY A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 617 " --> pdb=" O TRP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.647A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.775A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.577A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.910A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.600A pdb=" N GLU A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 789 removed outlier: 4.468A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.605A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 853 removed outlier: 3.522A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.588A pdb=" N ALA B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.211A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.912A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.540A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.956A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.787A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 297 removed outlier: 4.027A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.704A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.868A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.620A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.677A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.514A pdb=" N GLY B 615 " --> pdb=" O SER B 611 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 617 " --> pdb=" O TRP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 659 removed outlier: 3.647A pdb=" N ILE B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.776A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.577A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.911A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 728 " --> pdb=" O GLY B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.600A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 789 removed outlier: 4.468A pdb=" N ASP B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 794 through 799 removed outlier: 3.605A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 852 removed outlier: 3.521A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 836 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 846 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 852 " --> pdb=" O LYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 868 removed outlier: 3.899A pdb=" N LEU B 865 " --> pdb=" O MET B 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.588A pdb=" N ALA C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.211A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 removed outlier: 3.912A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.540A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.956A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.788A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 297 removed outlier: 4.027A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.703A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.867A pdb=" N LEU C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.620A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 560 through 583 removed outlier: 3.677A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.514A pdb=" N GLY C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 617 " --> pdb=" O TRP C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.647A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 662 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.775A pdb=" N LYS C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.576A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.911A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.600A pdb=" N GLU C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 789 removed outlier: 4.468A pdb=" N ASP C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 781 " --> pdb=" O LYS C 777 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 787 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 794 through 799 removed outlier: 3.606A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 851 removed outlier: 3.522A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 867 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.588A pdb=" N ALA D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 4.211A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.912A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.540A pdb=" N ILE D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.956A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.788A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 297 removed outlier: 4.027A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.703A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.867A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 475 Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.620A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 560 through 583 removed outlier: 3.677A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.514A pdb=" N GLY D 615 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 617 " --> pdb=" O TRP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 659 removed outlier: 3.646A pdb=" N ILE D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.775A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.576A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.911A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 728 " --> pdb=" O GLY D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.600A pdb=" N GLU D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 789 removed outlier: 4.468A pdb=" N ASP D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 794 through 799 removed outlier: 3.606A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.520A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 836 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 846 " --> pdb=" O PHE D 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 196 removed outlier: 3.868A pdb=" N GLU E 194 " --> pdb=" O SER E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 251 removed outlier: 4.116A pdb=" N LEU E 251 " --> pdb=" O ILE E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 315 Processing helix chain 'E' and resid 346 through 372 removed outlier: 3.616A pdb=" N ILE E 351 " --> pdb=" O HIS E 347 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 360 " --> pdb=" O GLY E 356 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.302A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 removed outlier: 5.859A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 removed outlier: 3.515A pdb=" N VAL A 147 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 226 removed outlier: 6.363A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 433 through 437 removed outlier: 5.919A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 535 through 536 removed outlier: 3.786A pdb=" N LEU A 536 " --> pdb=" O LYS A 762 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.522A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.600A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 685 removed outlier: 5.801A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.302A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 43 removed outlier: 5.859A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.515A pdb=" N VAL B 147 " --> pdb=" O HIS B 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AB8, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.362A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 432 through 437 removed outlier: 5.919A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC2, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC3, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.786A pdb=" N LEU B 536 " --> pdb=" O LYS B 762 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 736 through 738 removed outlier: 3.522A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 681 through 682 removed outlier: 7.601A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 684 through 685 removed outlier: 5.802A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.301A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 41 through 43 removed outlier: 5.859A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.515A pdb=" N VAL C 147 " --> pdb=" O HIS C 129 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 175 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 225 through 226 removed outlier: 6.362A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 432 through 437 removed outlier: 5.920A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AD5, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD6, first strand: chain 'C' and resid 535 through 536 removed outlier: 3.786A pdb=" N LEU C 536 " --> pdb=" O LYS C 762 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 736 through 738 removed outlier: 3.521A pdb=" N MET C 737 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.600A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 684 through 685 removed outlier: 5.802A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 35 through 38 removed outlier: 6.302A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 41 through 43 removed outlier: 5.859A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 129 through 131 removed outlier: 3.516A pdb=" N VAL D 147 " --> pdb=" O HIS D 129 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 175 through 176 Processing sheet with id=AE5, first strand: chain 'D' and resid 225 through 226 removed outlier: 6.362A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 433 through 437 removed outlier: 5.919A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE9, first strand: chain 'D' and resid 535 through 536 removed outlier: 3.786A pdb=" N LEU D 536 " --> pdb=" O LYS D 762 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 736 through 738 removed outlier: 3.522A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 681 through 682 removed outlier: 7.601A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 684 through 685 removed outlier: 5.802A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 73 through 74 Processing sheet with id=AF5, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.715A pdb=" N PHE E 179 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR E 210 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU E 181 " --> pdb=" O THR E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 225 through 227 Processing sheet with id=AF7, first strand: chain 'E' and resid 253 through 255 970 hydrogen bonds defined for protein. 2763 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: 7.11 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4864 1.31 - 1.45: 8864 1.45 - 1.59: 17388 1.59 - 1.72: 34 1.72 - 1.86: 297 Bond restraints: 31447 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.531 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.525 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1 NAG C1006 " pdb=" O5 NAG C1006 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 31442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 41372 3.67 - 7.35: 888 7.35 - 11.02: 114 11.02 - 14.69: 47 14.69 - 18.37: 2 Bond angle restraints: 42423 Sorted by residual: angle pdb=" C GLY D 419 " pdb=" N LYS D 420 " pdb=" CA LYS D 420 " ideal model delta sigma weight residual 120.51 138.88 -18.37 1.45e+00 4.76e-01 1.60e+02 angle pdb=" N GLU C 807 " pdb=" CA GLU C 807 " pdb=" C GLU C 807 " ideal model delta sigma weight residual 113.50 104.84 8.66 1.23e+00 6.61e-01 4.95e+01 angle pdb=" C SER E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 angle pdb=" N LYS C 420 " pdb=" CA LYS C 420 " pdb=" C LYS C 420 " ideal model delta sigma weight residual 108.22 102.40 5.82 9.00e-01 1.23e+00 4.18e+01 angle pdb=" C GLY C 551 " pdb=" N VAL C 552 " pdb=" CA VAL C 552 " ideal model delta sigma weight residual 121.97 132.09 -10.12 1.80e+00 3.09e-01 3.16e+01 ... (remaining 42418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 18949 34.24 - 68.47: 596 68.47 - 102.71: 228 102.71 - 136.95: 77 136.95 - 171.19: 2 Dihedral angle restraints: 19852 sinusoidal: 9180 harmonic: 10672 Sorted by residual: dihedral pdb=" CA SER C 429 " pdb=" C SER C 429 " pdb=" N ASN C 430 " pdb=" CA ASN C 430 " ideal model delta harmonic sigma weight residual -180.00 -110.08 -69.92 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CA CYS C 871 " pdb=" C CYS C 871 " pdb=" N GLN C 872 " pdb=" CA GLN C 872 " ideal model delta harmonic sigma weight residual -180.00 -126.68 -53.32 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA PRO C 805 " pdb=" C PRO C 805 " pdb=" N GLU C 806 " pdb=" CA GLU C 806 " ideal model delta harmonic sigma weight residual -180.00 -132.54 -47.46 0 5.00e+00 4.00e-02 9.01e+01 ... (remaining 19849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 4739 0.186 - 0.372: 71 0.372 - 0.558: 6 0.558 - 0.744: 3 0.744 - 0.930: 3 Chirality restraints: 4822 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 751 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN D 378 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.89e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 4819 not shown) Planarity restraints: 5263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 804 " 0.035 2.00e-02 2.50e+03 6.79e-02 4.60e+01 pdb=" C CYS A 804 " -0.117 2.00e-02 2.50e+03 pdb=" O CYS A 804 " 0.042 2.00e-02 2.50e+03 pdb=" N PRO A 805 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 804 " 0.033 2.00e-02 2.50e+03 6.36e-02 4.05e+01 pdb=" C CYS C 804 " -0.110 2.00e-02 2.50e+03 pdb=" O CYS C 804 " 0.041 2.00e-02 2.50e+03 pdb=" N PRO C 805 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 804 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.51e+01 pdb=" C CYS B 804 " 0.103 2.00e-02 2.50e+03 pdb=" O CYS B 804 " -0.037 2.00e-02 2.50e+03 pdb=" N PRO B 805 " -0.035 2.00e-02 2.50e+03 ... (remaining 5260 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3066 2.73 - 3.27: 28890 3.27 - 3.82: 48347 3.82 - 4.36: 57129 4.36 - 4.90: 96762 Nonbonded interactions: 234194 Sorted by model distance: nonbonded pdb=" O SER E 52 " pdb=" OH TYR E 156 " model vdw 2.191 3.040 nonbonded pdb=" OE2 GLU B 787 " pdb=" OG1 THR C 520 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR E 220 " pdb=" OD2 ASP E 262 " model vdw 2.275 3.040 nonbonded pdb=" O LEU D 453 " pdb=" ND2 ASN E 232 " model vdw 2.277 3.120 nonbonded pdb=" O ASP E 109 " pdb=" OG SER E 115 " model vdw 2.283 3.040 ... (remaining 234189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 850 or resid 1003)) selection = (chain 'B' and (resid 33 through 850 or resid 1003)) selection = (chain 'C' and (resid 33 through 850 or resid 1002)) selection = (chain 'D' and resid 33 through 1001) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' } 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=0.45 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.650 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.010 0.135 31527 Z= 0.452 Angle : 1.464 27.007 42648 Z= 0.755 Chirality : 0.068 0.930 4822 Planarity : 0.008 0.068 5232 Dihedral : 20.056 171.186 12941 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.68 % Allowed : 12.16 % Favored : 87.16 % Rotamer: Outliers : 0.53 % Allowed : 5.37 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 2.65 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.75 (0.10), residues: 3669 helix: -3.90 (0.07), residues: 1473 sheet: -4.01 (0.20), residues: 451 loop : -3.63 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 374 TYR 0.021 0.003 TYR E 156 PHE 0.044 0.003 PHE E 158 TRP 0.027 0.003 TRP B 353 HIS 0.021 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00958 (31447) covalent geometry : angle 1.38332 (42423) SS BOND : bond 0.00892 ( 15) SS BOND : angle 2.13369 ( 30) hydrogen bonds : bond 0.29705 ( 970) hydrogen bonds : angle 9.25118 ( 2763) link_ALPHA1-3 : bond 0.00803 ( 5) link_ALPHA1-3 : angle 4.11555 ( 15) link_ALPHA1-6 : bond 0.00745 ( 5) link_ALPHA1-6 : angle 2.26824 ( 15) link_BETA1-3 : bond 0.00230 ( 1) link_BETA1-3 : angle 5.66947 ( 3) link_BETA1-4 : bond 0.02181 ( 23) link_BETA1-4 : angle 6.17145 ( 69) link_NAG-ASN : bond 0.01292 ( 31) link_NAG-ASN : angle 8.72962 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 931 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.7589 (mt) cc_final: 0.7037 (pt) REVERT: A 89 PHE cc_start: 0.7991 (t80) cc_final: 0.7584 (t80) REVERT: A 286 ASN cc_start: 0.7611 (m110) cc_final: 0.7395 (t0) REVERT: A 337 PHE cc_start: 0.7472 (t80) cc_final: 0.7061 (t80) REVERT: A 487 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7841 (mtpp) REVERT: A 705 MET cc_start: 0.8620 (mtp) cc_final: 0.8390 (mtt) REVERT: A 708 PHE cc_start: 0.7645 (t80) cc_final: 0.7203 (t80) REVERT: A 808 GLU cc_start: 0.6261 (pp20) cc_final: 0.5433 (tm-30) REVERT: A 857 PHE cc_start: 0.6011 (m-10) cc_final: 0.5714 (m-80) REVERT: B 106 ILE cc_start: 0.9118 (mt) cc_final: 0.8874 (mm) REVERT: B 482 LEU cc_start: 0.8013 (mt) cc_final: 0.7687 (tt) REVERT: B 799 TRP cc_start: 0.7419 (m100) cc_final: 0.6662 (m100) REVERT: B 861 MET cc_start: 0.4718 (mmp) cc_final: 0.3780 (tmm) REVERT: C 79 ASP cc_start: 0.8273 (t0) cc_final: 0.7637 (t70) REVERT: C 82 LYS cc_start: 0.8432 (mttp) cc_final: 0.8226 (mmmt) REVERT: C 182 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7500 (tt) REVERT: C 205 PRO cc_start: 0.7742 (Cg_exo) cc_final: 0.7534 (Cg_endo) REVERT: C 413 MET cc_start: 0.7914 (mmm) cc_final: 0.7646 (mmt) REVERT: C 565 MET cc_start: 0.6975 (mmt) cc_final: 0.6758 (mmp) REVERT: C 607 THR cc_start: 0.8054 (p) cc_final: 0.7467 (p) REVERT: C 610 ASN cc_start: 0.8778 (m-40) cc_final: 0.8481 (m110) REVERT: D 79 ASP cc_start: 0.7369 (t0) cc_final: 0.6983 (t0) REVERT: D 141 ASN cc_start: 0.8369 (t160) cc_final: 0.8084 (t0) REVERT: D 226 VAL cc_start: 0.8764 (t) cc_final: 0.8270 (t) REVERT: D 316 MET cc_start: 0.8731 (ttp) cc_final: 0.8474 (ttp) REVERT: D 351 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8256 (mttm) REVERT: E 49 VAL cc_start: 0.7889 (t) cc_final: 0.7689 (t) REVERT: E 176 ASP cc_start: 0.6154 (p0) cc_final: 0.5936 (p0) REVERT: E 195 GLN cc_start: 0.7744 (mt0) cc_final: 0.7492 (mt0) REVERT: E 334 LYS cc_start: 0.5374 (mmmm) cc_final: 0.5025 (mptt) REVERT: E 378 MET cc_start: 0.3163 (mpt) cc_final: 0.2080 (mmp) outliers start: 17 outliers final: 2 residues processed: 941 average time/residue: 0.1935 time to fit residues: 286.0760 Evaluate side-chains 487 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 484 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain E residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 186 GLN A 196 ASN A 591 ASN A 593 HIS A 596 ASN A 610 ASN A 792 HIS A 849 ASN B 123 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 141 ASN B 196 ASN B 423 ASN B 456 ASN B 591 ASN B 593 HIS B 596 ASN B 849 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 196 ASN C 456 ASN C 591 ASN C 593 HIS C 596 ASN C 622 GLN C 849 ASN D 98 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 350 HIS D 591 ASN D 593 HIS D 596 ASN D 605 ASN D 621 GLN D 622 GLN ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN E 312 ASN E 321 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.169376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137052 restraints weight = 59699.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137728 restraints weight = 32177.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.139103 restraints weight = 27145.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139214 restraints weight = 22933.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139672 restraints weight = 21180.922| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31527 Z= 0.163 Angle : 0.906 22.073 42648 Z= 0.427 Chirality : 0.052 0.632 4822 Planarity : 0.006 0.074 5232 Dihedral : 21.253 166.049 5953 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.68 % Favored : 90.05 % Rotamer: Outliers : 2.68 % Allowed : 13.08 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.12), residues: 3669 helix: -1.78 (0.11), residues: 1515 sheet: -3.51 (0.21), residues: 443 loop : -3.40 (0.13), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 583 TYR 0.025 0.002 TYR B 590 PHE 0.028 0.002 PHE D 228 TRP 0.046 0.002 TRP B 613 HIS 0.010 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00341 (31447) covalent geometry : angle 0.84637 (42423) SS BOND : bond 0.01262 ( 15) SS BOND : angle 2.28534 ( 30) hydrogen bonds : bond 0.04944 ( 970) hydrogen bonds : angle 5.29265 ( 2763) link_ALPHA1-3 : bond 0.01337 ( 5) link_ALPHA1-3 : angle 2.54215 ( 15) link_ALPHA1-6 : bond 0.01004 ( 5) link_ALPHA1-6 : angle 2.59257 ( 15) link_BETA1-3 : bond 0.00107 ( 1) link_BETA1-3 : angle 5.61171 ( 3) link_BETA1-4 : bond 0.00953 ( 23) link_BETA1-4 : angle 3.83256 ( 69) link_NAG-ASN : bond 0.01214 ( 31) link_NAG-ASN : angle 5.80764 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 576 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8085 (mp) cc_final: 0.7873 (mp) REVERT: A 169 TRP cc_start: 0.5119 (m-10) cc_final: 0.4865 (m-10) REVERT: A 337 PHE cc_start: 0.7524 (t80) cc_final: 0.7322 (t80) REVERT: A 712 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6777 (mtt180) REVERT: B 106 ILE cc_start: 0.9144 (mt) cc_final: 0.8918 (mm) REVERT: B 107 PHE cc_start: 0.9104 (m-80) cc_final: 0.8817 (m-80) REVERT: B 152 ASP cc_start: 0.8503 (t0) cc_final: 0.8263 (t0) REVERT: B 481 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.6447 (mtp-110) REVERT: B 482 LEU cc_start: 0.7965 (mt) cc_final: 0.7628 (tt) REVERT: B 695 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8774 (pttm) REVERT: B 861 MET cc_start: 0.4978 (mmp) cc_final: 0.3822 (tmm) REVERT: C 79 ASP cc_start: 0.8276 (t0) cc_final: 0.7858 (t70) REVERT: C 82 LYS cc_start: 0.8513 (mttp) cc_final: 0.8235 (mmmt) REVERT: C 86 TYR cc_start: 0.7686 (m-80) cc_final: 0.7408 (m-80) REVERT: C 270 ARG cc_start: 0.7824 (ptp-170) cc_final: 0.7548 (ptm-80) REVERT: C 271 TYR cc_start: 0.6530 (m-80) cc_final: 0.6190 (m-80) REVERT: C 413 MET cc_start: 0.7851 (mmm) cc_final: 0.7219 (mmt) REVERT: C 565 MET cc_start: 0.7596 (mmt) cc_final: 0.7361 (mmp) REVERT: C 645 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (tm) REVERT: C 681 GLU cc_start: 0.7983 (mp0) cc_final: 0.7660 (pt0) REVERT: D 50 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6273 (mtt) REVERT: D 316 MET cc_start: 0.8454 (ttp) cc_final: 0.7560 (ttp) REVERT: D 351 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8237 (mttm) REVERT: D 434 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7874 (tp) REVERT: E 120 ARG cc_start: 0.7983 (ttm170) cc_final: 0.6894 (mtp-110) REVERT: E 137 MET cc_start: 0.4256 (ptp) cc_final: 0.2732 (mtm) REVERT: E 334 LYS cc_start: 0.4912 (mmmm) cc_final: 0.4427 (mptt) REVERT: E 365 SER cc_start: 0.8565 (m) cc_final: 0.7934 (t) REVERT: E 378 MET cc_start: 0.2556 (mpt) cc_final: 0.1368 (mmp) outliers start: 86 outliers final: 33 residues processed: 625 average time/residue: 0.1696 time to fit residues: 175.2251 Evaluate side-chains 481 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 444 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 807 GLU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 191 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 354 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 610 ASN B 123 ASN B 610 ASN B 622 GLN C 98 GLN C 111 HIS C 141 ASN ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 605 ASN D 784 GLN E 305 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.163034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130242 restraints weight = 59429.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131849 restraints weight = 33086.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132914 restraints weight = 29768.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133258 restraints weight = 22477.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134262 restraints weight = 20942.956| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31527 Z= 0.185 Angle : 0.863 19.342 42648 Z= 0.399 Chirality : 0.050 0.479 4822 Planarity : 0.005 0.072 5232 Dihedral : 18.706 163.025 5949 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.63 % Favored : 89.04 % Rotamer: Outliers : 3.56 % Allowed : 14.33 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.13), residues: 3669 helix: -0.78 (0.13), residues: 1545 sheet: -3.46 (0.20), residues: 473 loop : -3.32 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 83 TYR 0.032 0.002 TYR C 195 PHE 0.033 0.002 PHE D 228 TRP 0.040 0.002 TRP B 613 HIS 0.006 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00416 (31447) covalent geometry : angle 0.79852 (42423) SS BOND : bond 0.00900 ( 15) SS BOND : angle 1.75521 ( 30) hydrogen bonds : bond 0.04465 ( 970) hydrogen bonds : angle 4.78507 ( 2763) link_ALPHA1-3 : bond 0.01260 ( 5) link_ALPHA1-3 : angle 2.17587 ( 15) link_ALPHA1-6 : bond 0.01080 ( 5) link_ALPHA1-6 : angle 2.38798 ( 15) link_BETA1-3 : bond 0.00172 ( 1) link_BETA1-3 : angle 6.10852 ( 3) link_BETA1-4 : bond 0.00990 ( 23) link_BETA1-4 : angle 4.05675 ( 69) link_NAG-ASN : bond 0.01267 ( 31) link_NAG-ASN : angle 5.88523 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 475 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 325 ASP cc_start: 0.8587 (m-30) cc_final: 0.8298 (m-30) REVERT: A 669 ASP cc_start: 0.7743 (m-30) cc_final: 0.7221 (m-30) REVERT: B 106 ILE cc_start: 0.9164 (mt) cc_final: 0.8958 (mm) REVERT: B 249 THR cc_start: 0.8566 (m) cc_final: 0.8192 (p) REVERT: B 316 MET cc_start: 0.8435 (ttp) cc_final: 0.8226 (ttp) REVERT: B 340 MET cc_start: 0.6245 (mmm) cc_final: 0.5653 (mmm) REVERT: B 481 ARG cc_start: 0.7086 (ttm-80) cc_final: 0.6649 (mtp-110) REVERT: B 482 LEU cc_start: 0.8007 (mt) cc_final: 0.7702 (tt) REVERT: B 613 TRP cc_start: 0.8199 (t-100) cc_final: 0.7917 (t-100) REVERT: B 627 MET cc_start: 0.6101 (ttp) cc_final: 0.5740 (tmm) REVERT: B 861 MET cc_start: 0.4796 (mmp) cc_final: 0.3682 (tmm) REVERT: C 79 ASP cc_start: 0.8393 (t0) cc_final: 0.8045 (t70) REVERT: C 82 LYS cc_start: 0.8600 (mttp) cc_final: 0.8319 (mmmt) REVERT: C 214 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7210 (mp) REVERT: C 413 MET cc_start: 0.8007 (mmm) cc_final: 0.7316 (mmt) REVERT: C 556 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8168 (tm) REVERT: C 673 ASP cc_start: 0.8111 (t70) cc_final: 0.7768 (t70) REVERT: C 698 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8087 (mttt) REVERT: D 316 MET cc_start: 0.8539 (ttp) cc_final: 0.7804 (ttp) REVERT: D 337 PHE cc_start: 0.8360 (t80) cc_final: 0.7760 (t80) REVERT: D 351 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8310 (mttm) REVERT: D 361 SER cc_start: 0.8490 (t) cc_final: 0.8117 (t) REVERT: D 606 PHE cc_start: 0.8427 (m-80) cc_final: 0.8167 (m-80) REVERT: D 811 GLU cc_start: 0.8206 (pm20) cc_final: 0.7987 (pm20) REVERT: E 76 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.5581 (tt) REVERT: E 102 PHE cc_start: 0.8115 (m-10) cc_final: 0.7787 (m-10) REVERT: E 137 MET cc_start: 0.4692 (ptp) cc_final: 0.3007 (mtm) REVERT: E 334 LYS cc_start: 0.4984 (mmmm) cc_final: 0.4499 (mptt) REVERT: E 363 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.6081 (mp) REVERT: E 365 SER cc_start: 0.8564 (m) cc_final: 0.8030 (t) REVERT: E 378 MET cc_start: 0.2821 (mpt) cc_final: 0.1687 (mmp) outliers start: 114 outliers final: 50 residues processed: 555 average time/residue: 0.1779 time to fit residues: 162.2584 Evaluate side-chains 465 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 410 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 363 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 87 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 192 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 356 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 610 ASN B 677 GLN C 98 GLN ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 605 ASN E 305 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.164042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130654 restraints weight = 58378.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.132155 restraints weight = 31715.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.133504 restraints weight = 27359.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.133749 restraints weight = 21906.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134626 restraints weight = 20318.206| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31527 Z= 0.138 Angle : 0.795 20.239 42648 Z= 0.365 Chirality : 0.047 0.471 4822 Planarity : 0.005 0.070 5232 Dihedral : 17.122 156.827 5949 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.73 % Favored : 90.02 % Rotamer: Outliers : 3.18 % Allowed : 15.42 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.13), residues: 3669 helix: -0.28 (0.13), residues: 1543 sheet: -3.15 (0.21), residues: 457 loop : -3.25 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.022 0.001 TYR D 521 PHE 0.033 0.001 PHE D 228 TRP 0.042 0.001 TRP A 296 HIS 0.007 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00301 (31447) covalent geometry : angle 0.73229 (42423) SS BOND : bond 0.00641 ( 15) SS BOND : angle 1.73443 ( 30) hydrogen bonds : bond 0.03580 ( 970) hydrogen bonds : angle 4.44137 ( 2763) link_ALPHA1-3 : bond 0.01580 ( 5) link_ALPHA1-3 : angle 2.52556 ( 15) link_ALPHA1-6 : bond 0.01164 ( 5) link_ALPHA1-6 : angle 2.15352 ( 15) link_BETA1-3 : bond 0.00443 ( 1) link_BETA1-3 : angle 5.90601 ( 3) link_BETA1-4 : bond 0.00991 ( 23) link_BETA1-4 : angle 3.68239 ( 69) link_NAG-ASN : bond 0.00990 ( 31) link_NAG-ASN : angle 5.58724 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 472 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 248 MET cc_start: 0.6853 (mmm) cc_final: 0.6522 (mtt) REVERT: A 325 ASP cc_start: 0.8626 (m-30) cc_final: 0.8378 (m-30) REVERT: A 431 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8262 (tpm170) REVERT: A 669 ASP cc_start: 0.7671 (m-30) cc_final: 0.7243 (m-30) REVERT: B 106 ILE cc_start: 0.9114 (mt) cc_final: 0.8904 (mm) REVERT: B 107 PHE cc_start: 0.9046 (m-80) cc_final: 0.8762 (m-80) REVERT: B 249 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 340 MET cc_start: 0.6297 (mmm) cc_final: 0.5934 (mmm) REVERT: B 481 ARG cc_start: 0.7161 (ttm-80) cc_final: 0.6714 (mtp-110) REVERT: B 482 LEU cc_start: 0.8030 (mt) cc_final: 0.7726 (tt) REVERT: B 613 TRP cc_start: 0.8163 (t-100) cc_final: 0.7830 (t-100) REVERT: B 627 MET cc_start: 0.5979 (ttp) cc_final: 0.5743 (tmm) REVERT: B 861 MET cc_start: 0.4773 (mmp) cc_final: 0.3634 (tmm) REVERT: C 79 ASP cc_start: 0.8416 (t0) cc_final: 0.8089 (t70) REVERT: C 82 LYS cc_start: 0.8543 (mttp) cc_final: 0.8271 (mmmt) REVERT: C 98 GLN cc_start: 0.7968 (mt0) cc_final: 0.7750 (mt0) REVERT: C 323 MET cc_start: 0.9416 (tpt) cc_final: 0.9171 (tpp) REVERT: C 413 MET cc_start: 0.7993 (mmm) cc_final: 0.7325 (mmt) REVERT: C 572 LEU cc_start: 0.8586 (mt) cc_final: 0.7977 (mm) REVERT: C 698 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8137 (tppt) REVERT: D 316 MET cc_start: 0.8562 (ttp) cc_final: 0.8236 (ttp) REVERT: D 351 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8314 (mttm) REVERT: E 76 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.5650 (tt) REVERT: E 120 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.6816 (mtp-110) REVERT: E 124 MET cc_start: 0.6097 (mtp) cc_final: 0.5895 (mtp) REVERT: E 137 MET cc_start: 0.4476 (ptp) cc_final: 0.2791 (mtm) REVERT: E 334 LYS cc_start: 0.4978 (mmmm) cc_final: 0.4480 (mptt) REVERT: E 363 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.6196 (mp) REVERT: E 365 SER cc_start: 0.8451 (m) cc_final: 0.8182 (t) REVERT: E 378 MET cc_start: 0.2566 (mpt) cc_final: 0.1657 (mmp) outliers start: 102 outliers final: 49 residues processed: 535 average time/residue: 0.1675 time to fit residues: 148.8960 Evaluate side-chains 475 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 363 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 134 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 232 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN C 677 GLN D 335 GLN D 367 HIS E 56 HIS E 230 HIS E 305 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.158065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124797 restraints weight = 59020.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126197 restraints weight = 37157.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126802 restraints weight = 36175.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127625 restraints weight = 25219.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128633 restraints weight = 22956.885| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 31527 Z= 0.241 Angle : 0.857 19.477 42648 Z= 0.402 Chirality : 0.051 0.503 4822 Planarity : 0.005 0.068 5232 Dihedral : 16.385 151.830 5949 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.97 % Favored : 87.79 % Rotamer: Outliers : 4.15 % Allowed : 15.70 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.13), residues: 3669 helix: -0.05 (0.13), residues: 1535 sheet: -3.28 (0.21), residues: 458 loop : -3.21 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 184 TYR 0.023 0.002 TYR E 62 PHE 0.041 0.002 PHE C 359 TRP 0.046 0.002 TRP A 296 HIS 0.006 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00557 (31447) covalent geometry : angle 0.80196 (42423) SS BOND : bond 0.00802 ( 15) SS BOND : angle 2.24600 ( 30) hydrogen bonds : bond 0.04172 ( 970) hydrogen bonds : angle 4.60962 ( 2763) link_ALPHA1-3 : bond 0.01585 ( 5) link_ALPHA1-3 : angle 2.60565 ( 15) link_ALPHA1-6 : bond 0.00783 ( 5) link_ALPHA1-6 : angle 2.04619 ( 15) link_BETA1-3 : bond 0.00497 ( 1) link_BETA1-3 : angle 5.23814 ( 3) link_BETA1-4 : bond 0.01062 ( 23) link_BETA1-4 : angle 3.71059 ( 69) link_NAG-ASN : bond 0.00855 ( 31) link_NAG-ASN : angle 5.41359 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 426 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 218 MET cc_start: 0.6514 (mmm) cc_final: 0.6151 (mpp) REVERT: A 325 ASP cc_start: 0.8646 (m-30) cc_final: 0.8388 (m-30) REVERT: A 431 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8247 (tpm170) REVERT: A 458 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7358 (pmt100) REVERT: A 627 MET cc_start: 0.6245 (mmp) cc_final: 0.5966 (mtt) REVERT: A 669 ASP cc_start: 0.7600 (m-30) cc_final: 0.7144 (m-30) REVERT: B 106 ILE cc_start: 0.9162 (mt) cc_final: 0.8958 (mm) REVERT: B 476 PHE cc_start: 0.5861 (p90) cc_final: 0.5521 (p90) REVERT: B 481 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6706 (mtp-110) REVERT: B 482 LEU cc_start: 0.8071 (mt) cc_final: 0.7793 (tt) REVERT: B 627 MET cc_start: 0.6250 (ttp) cc_final: 0.5982 (tmm) REVERT: B 861 MET cc_start: 0.4662 (mmp) cc_final: 0.3543 (tmm) REVERT: C 79 ASP cc_start: 0.8453 (t0) cc_final: 0.8126 (t70) REVERT: C 82 LYS cc_start: 0.8802 (mttp) cc_final: 0.8475 (mmtt) REVERT: C 87 ASP cc_start: 0.8010 (t0) cc_final: 0.7784 (m-30) REVERT: C 98 GLN cc_start: 0.8129 (mt0) cc_final: 0.7928 (mt0) REVERT: C 214 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7423 (tt) REVERT: C 413 MET cc_start: 0.7938 (mmm) cc_final: 0.7307 (mmt) REVERT: C 482 LEU cc_start: 0.8403 (pt) cc_final: 0.8152 (mt) REVERT: C 572 LEU cc_start: 0.8416 (mt) cc_final: 0.8151 (mm) REVERT: C 698 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8092 (tppt) REVERT: C 733 TYR cc_start: 0.8200 (t80) cc_final: 0.7870 (t80) REVERT: C 770 MET cc_start: 0.7840 (tpp) cc_final: 0.7551 (tpp) REVERT: D 316 MET cc_start: 0.8598 (ttp) cc_final: 0.8340 (ttp) REVERT: D 351 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8424 (mttm) REVERT: D 361 SER cc_start: 0.8642 (t) cc_final: 0.8280 (t) REVERT: D 669 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8136 (t70) REVERT: E 120 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7607 (mtp-110) REVERT: E 137 MET cc_start: 0.4542 (ptp) cc_final: 0.2923 (mtm) REVERT: E 334 LYS cc_start: 0.5094 (mmmm) cc_final: 0.4621 (mptt) REVERT: E 363 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6226 (mp) REVERT: E 365 SER cc_start: 0.8609 (m) cc_final: 0.8228 (t) REVERT: E 378 MET cc_start: 0.2747 (mpt) cc_final: 0.1623 (mmp) outliers start: 133 outliers final: 85 residues processed: 515 average time/residue: 0.1645 time to fit residues: 141.6181 Evaluate side-chains 477 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 386 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 56 HIS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 363 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 353 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 97 optimal weight: 0.0060 chunk 343 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 341 optimal weight: 0.0020 chunk 110 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 591 ASN B 123 ASN B 495 ASN B 610 ASN C 141 ASN C 350 HIS ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 605 ASN E 230 HIS E 232 ASN E 305 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.162040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128932 restraints weight = 58383.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129813 restraints weight = 32908.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130893 restraints weight = 31184.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131403 restraints weight = 23240.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.132612 restraints weight = 21575.169| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31527 Z= 0.134 Angle : 0.771 19.496 42648 Z= 0.356 Chirality : 0.047 0.492 4822 Planarity : 0.005 0.081 5232 Dihedral : 15.567 142.081 5949 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.98 % Favored : 89.78 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3669 helix: 0.31 (0.13), residues: 1540 sheet: -3.07 (0.22), residues: 442 loop : -3.09 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 120 TYR 0.023 0.001 TYR D 521 PHE 0.035 0.001 PHE D 584 TRP 0.028 0.001 TRP A 296 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00293 (31447) covalent geometry : angle 0.71355 (42423) SS BOND : bond 0.00592 ( 15) SS BOND : angle 1.66964 ( 30) hydrogen bonds : bond 0.03365 ( 970) hydrogen bonds : angle 4.28483 ( 2763) link_ALPHA1-3 : bond 0.01844 ( 5) link_ALPHA1-3 : angle 2.53517 ( 15) link_ALPHA1-6 : bond 0.00946 ( 5) link_ALPHA1-6 : angle 2.09673 ( 15) link_BETA1-3 : bond 0.00496 ( 1) link_BETA1-3 : angle 5.26440 ( 3) link_BETA1-4 : bond 0.01019 ( 23) link_BETA1-4 : angle 3.51253 ( 69) link_NAG-ASN : bond 0.00949 ( 31) link_NAG-ASN : angle 5.22951 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 441 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8516 (m-30) cc_final: 0.8212 (m-30) REVERT: A 368 TRP cc_start: 0.7436 (t-100) cc_final: 0.7036 (t-100) REVERT: A 669 ASP cc_start: 0.7533 (m-30) cc_final: 0.7120 (m-30) REVERT: A 808 GLU cc_start: 0.7086 (pp20) cc_final: 0.5306 (tm-30) REVERT: B 476 PHE cc_start: 0.5790 (p90) cc_final: 0.5386 (p90) REVERT: B 482 LEU cc_start: 0.7992 (mt) cc_final: 0.7743 (tt) REVERT: B 627 MET cc_start: 0.6142 (ttp) cc_final: 0.5880 (tmm) REVERT: B 709 MET cc_start: 0.7865 (ptt) cc_final: 0.7589 (mtm) REVERT: B 861 MET cc_start: 0.4700 (mmp) cc_final: 0.3442 (tmm) REVERT: C 79 ASP cc_start: 0.8437 (t0) cc_final: 0.8128 (t70) REVERT: C 82 LYS cc_start: 0.8680 (mttp) cc_final: 0.8403 (mmtt) REVERT: C 98 GLN cc_start: 0.8072 (mt0) cc_final: 0.7843 (mt0) REVERT: C 413 MET cc_start: 0.7955 (mmm) cc_final: 0.7350 (mmt) REVERT: C 482 LEU cc_start: 0.8439 (pt) cc_final: 0.8232 (mt) REVERT: C 538 ILE cc_start: 0.9257 (mt) cc_final: 0.9008 (mm) REVERT: C 698 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8031 (tppt) REVERT: D 316 MET cc_start: 0.8529 (ttp) cc_final: 0.8201 (ttp) REVERT: D 351 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8381 (mttm) REVERT: E 76 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.5602 (tt) REVERT: E 120 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7598 (mmm-85) REVERT: E 137 MET cc_start: 0.4433 (ptp) cc_final: 0.2828 (mtm) REVERT: E 144 ASP cc_start: 0.5306 (p0) cc_final: 0.4018 (t0) REVERT: E 334 LYS cc_start: 0.5059 (mmmm) cc_final: 0.4590 (mptt) REVERT: E 363 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.6127 (mp) REVERT: E 365 SER cc_start: 0.8557 (m) cc_final: 0.8227 (t) REVERT: E 378 MET cc_start: 0.2642 (mpt) cc_final: 0.1533 (mmp) outliers start: 97 outliers final: 56 residues processed: 498 average time/residue: 0.1692 time to fit residues: 141.9325 Evaluate side-chains 452 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 363 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 205 optimal weight: 4.9990 chunk 321 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 308 optimal weight: 0.7980 chunk 306 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 362 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN E 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.164241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130460 restraints weight = 58773.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131635 restraints weight = 33867.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133244 restraints weight = 29835.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133347 restraints weight = 22896.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134377 restraints weight = 21514.183| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31527 Z= 0.137 Angle : 0.762 19.301 42648 Z= 0.352 Chirality : 0.047 0.498 4822 Planarity : 0.004 0.083 5232 Dihedral : 15.006 130.041 5949 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.41 % Favored : 89.34 % Rotamer: Outliers : 3.03 % Allowed : 17.76 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3669 helix: 0.52 (0.13), residues: 1536 sheet: -2.95 (0.23), residues: 434 loop : -3.05 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 184 TYR 0.018 0.001 TYR D 521 PHE 0.034 0.001 PHE D 584 TRP 0.038 0.001 TRP A 296 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00306 (31447) covalent geometry : angle 0.70823 (42423) SS BOND : bond 0.00692 ( 15) SS BOND : angle 1.36768 ( 30) hydrogen bonds : bond 0.03307 ( 970) hydrogen bonds : angle 4.21946 ( 2763) link_ALPHA1-3 : bond 0.01671 ( 5) link_ALPHA1-3 : angle 2.58539 ( 15) link_ALPHA1-6 : bond 0.00885 ( 5) link_ALPHA1-6 : angle 2.02374 ( 15) link_BETA1-3 : bond 0.00643 ( 1) link_BETA1-3 : angle 5.14667 ( 3) link_BETA1-4 : bond 0.00974 ( 23) link_BETA1-4 : angle 3.48139 ( 69) link_NAG-ASN : bond 0.00899 ( 31) link_NAG-ASN : angle 5.05214 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 420 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.7561 (mm) cc_final: 0.7340 (mm) REVERT: A 325 ASP cc_start: 0.8599 (m-30) cc_final: 0.8281 (m-30) REVERT: A 368 TRP cc_start: 0.7447 (t-100) cc_final: 0.7055 (t-100) REVERT: A 458 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6787 (pmt100) REVERT: A 669 ASP cc_start: 0.7552 (m-30) cc_final: 0.7207 (m-30) REVERT: A 808 GLU cc_start: 0.6914 (pp20) cc_final: 0.5114 (tm-30) REVERT: B 476 PHE cc_start: 0.5823 (p90) cc_final: 0.5357 (p90) REVERT: B 482 LEU cc_start: 0.7984 (mt) cc_final: 0.7712 (tt) REVERT: B 627 MET cc_start: 0.6233 (ttp) cc_final: 0.5987 (tmm) REVERT: B 709 MET cc_start: 0.7897 (ptt) cc_final: 0.7609 (mtm) REVERT: B 861 MET cc_start: 0.4709 (mmp) cc_final: 0.3439 (tmm) REVERT: C 79 ASP cc_start: 0.8438 (t0) cc_final: 0.8127 (t70) REVERT: C 82 LYS cc_start: 0.8698 (mttp) cc_final: 0.8393 (mmtt) REVERT: C 98 GLN cc_start: 0.8135 (mt0) cc_final: 0.7918 (mt0) REVERT: C 323 MET cc_start: 0.9453 (tpt) cc_final: 0.9249 (tpp) REVERT: C 402 ILE cc_start: 0.8534 (pt) cc_final: 0.7942 (pt) REVERT: C 413 MET cc_start: 0.7937 (mmm) cc_final: 0.7246 (mmt) REVERT: C 482 LEU cc_start: 0.8443 (pt) cc_final: 0.8233 (mt) REVERT: C 572 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8114 (mm) REVERT: C 698 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8018 (tppt) REVERT: D 50 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6636 (mtm) REVERT: D 316 MET cc_start: 0.8511 (ttp) cc_final: 0.8159 (ttp) REVERT: D 351 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8454 (mttm) REVERT: E 76 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5758 (tt) REVERT: E 120 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7627 (mmm-85) REVERT: E 137 MET cc_start: 0.4563 (ptp) cc_final: 0.2932 (mtm) REVERT: E 144 ASP cc_start: 0.5278 (p0) cc_final: 0.4053 (t0) REVERT: E 334 LYS cc_start: 0.5118 (mmmm) cc_final: 0.4630 (mptt) REVERT: E 363 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.6057 (mp) REVERT: E 365 SER cc_start: 0.8571 (m) cc_final: 0.8255 (t) REVERT: E 378 MET cc_start: 0.2626 (mpt) cc_final: 0.1620 (mmp) outliers start: 97 outliers final: 64 residues processed: 481 average time/residue: 0.1635 time to fit residues: 132.0188 Evaluate side-chains 462 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 393 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 363 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 206 optimal weight: 0.0980 chunk 361 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 199 optimal weight: 0.3980 chunk 219 optimal weight: 0.8980 chunk 318 optimal weight: 0.0060 chunk 66 optimal weight: 0.0020 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN B 123 ASN C 136 HIS ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN E 61 ASN E 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.168073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134617 restraints weight = 58398.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136192 restraints weight = 32225.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136549 restraints weight = 32186.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137571 restraints weight = 23381.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138496 restraints weight = 20840.068| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31527 Z= 0.125 Angle : 0.756 19.087 42648 Z= 0.348 Chirality : 0.046 0.492 4822 Planarity : 0.004 0.089 5232 Dihedral : 14.308 119.483 5949 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.76 % Favored : 90.00 % Rotamer: Outliers : 2.40 % Allowed : 18.88 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.14), residues: 3669 helix: 0.80 (0.14), residues: 1528 sheet: -2.70 (0.24), residues: 431 loop : -2.91 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 300 TYR 0.017 0.001 TYR C 195 PHE 0.036 0.001 PHE D 584 TRP 0.025 0.001 TRP A 296 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00269 (31447) covalent geometry : angle 0.70516 (42423) SS BOND : bond 0.00473 ( 15) SS BOND : angle 1.26748 ( 30) hydrogen bonds : bond 0.03071 ( 970) hydrogen bonds : angle 4.09579 ( 2763) link_ALPHA1-3 : bond 0.01858 ( 5) link_ALPHA1-3 : angle 2.58340 ( 15) link_ALPHA1-6 : bond 0.00915 ( 5) link_ALPHA1-6 : angle 1.94538 ( 15) link_BETA1-3 : bond 0.00689 ( 1) link_BETA1-3 : angle 5.11109 ( 3) link_BETA1-4 : bond 0.00965 ( 23) link_BETA1-4 : angle 3.39211 ( 69) link_NAG-ASN : bond 0.00937 ( 31) link_NAG-ASN : angle 4.87739 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 430 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7050 (mm) REVERT: A 325 ASP cc_start: 0.8552 (m-30) cc_final: 0.8209 (m-30) REVERT: A 368 TRP cc_start: 0.7433 (t-100) cc_final: 0.7046 (t-100) REVERT: A 458 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6740 (pmt100) REVERT: A 627 MET cc_start: 0.6227 (mmp) cc_final: 0.5901 (mtt) REVERT: A 669 ASP cc_start: 0.7479 (m-30) cc_final: 0.7081 (m-30) REVERT: A 808 GLU cc_start: 0.6865 (pp20) cc_final: 0.5165 (tm-30) REVERT: A 872 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5864 (pp30) REVERT: B 94 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8243 (mmmm) REVERT: B 270 ARG cc_start: 0.8907 (ptm-80) cc_final: 0.8446 (ttp-110) REVERT: B 482 LEU cc_start: 0.7991 (mt) cc_final: 0.7679 (tt) REVERT: B 709 MET cc_start: 0.7884 (ptt) cc_final: 0.7599 (mtm) REVERT: B 861 MET cc_start: 0.4814 (mmp) cc_final: 0.3520 (tmm) REVERT: C 79 ASP cc_start: 0.8416 (t0) cc_final: 0.8139 (t70) REVERT: C 82 LYS cc_start: 0.8647 (mttp) cc_final: 0.8400 (mmtt) REVERT: C 98 GLN cc_start: 0.8171 (mt0) cc_final: 0.7946 (mt0) REVERT: C 323 MET cc_start: 0.9440 (tpt) cc_final: 0.9205 (tpp) REVERT: C 402 ILE cc_start: 0.8523 (pt) cc_final: 0.7929 (pt) REVERT: C 413 MET cc_start: 0.7865 (mmm) cc_final: 0.7207 (mmt) REVERT: C 563 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 572 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (mm) REVERT: C 698 LYS cc_start: 0.8676 (mmmt) cc_final: 0.7996 (tppt) REVERT: D 50 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6635 (mtm) REVERT: D 148 SER cc_start: 0.9413 (t) cc_final: 0.9165 (p) REVERT: D 316 MET cc_start: 0.8482 (ttp) cc_final: 0.8187 (ttp) REVERT: D 351 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8449 (mttm) REVERT: E 64 ASP cc_start: 0.6895 (m-30) cc_final: 0.6566 (m-30) REVERT: E 76 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.5928 (tt) REVERT: E 120 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7541 (mmm-85) REVERT: E 137 MET cc_start: 0.4533 (ptp) cc_final: 0.2889 (mtm) REVERT: E 144 ASP cc_start: 0.5069 (p0) cc_final: 0.4033 (t0) REVERT: E 334 LYS cc_start: 0.5141 (mmmm) cc_final: 0.4656 (mptt) REVERT: E 365 SER cc_start: 0.8599 (m) cc_final: 0.8310 (t) REVERT: E 378 MET cc_start: 0.2668 (mpt) cc_final: 0.1931 (mmp) outliers start: 77 outliers final: 48 residues processed: 480 average time/residue: 0.1576 time to fit residues: 127.8234 Evaluate side-chains 454 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 398 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 241 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 137 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 304 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN C 232 HIS ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.167358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134243 restraints weight = 58669.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135090 restraints weight = 33606.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135838 restraints weight = 32450.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136494 restraints weight = 24535.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137769 restraints weight = 22428.640| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31527 Z= 0.144 Angle : 0.769 18.823 42648 Z= 0.352 Chirality : 0.047 0.502 4822 Planarity : 0.004 0.093 5232 Dihedral : 13.864 117.408 5949 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.06 % Favored : 89.70 % Rotamer: Outliers : 2.22 % Allowed : 19.13 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3669 helix: 0.87 (0.14), residues: 1533 sheet: -2.74 (0.23), residues: 452 loop : -2.90 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 712 TYR 0.020 0.001 TYR C 195 PHE 0.033 0.001 PHE D 584 TRP 0.019 0.001 TRP A 296 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00327 (31447) covalent geometry : angle 0.71976 (42423) SS BOND : bond 0.00562 ( 15) SS BOND : angle 1.15724 ( 30) hydrogen bonds : bond 0.03210 ( 970) hydrogen bonds : angle 4.14708 ( 2763) link_ALPHA1-3 : bond 0.01785 ( 5) link_ALPHA1-3 : angle 2.56874 ( 15) link_ALPHA1-6 : bond 0.01023 ( 5) link_ALPHA1-6 : angle 1.94884 ( 15) link_BETA1-3 : bond 0.00585 ( 1) link_BETA1-3 : angle 4.98940 ( 3) link_BETA1-4 : bond 0.00922 ( 23) link_BETA1-4 : angle 3.38022 ( 69) link_NAG-ASN : bond 0.00842 ( 31) link_NAG-ASN : angle 4.84007 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 415 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8564 (m-30) cc_final: 0.8238 (m-30) REVERT: A 368 TRP cc_start: 0.7484 (t-100) cc_final: 0.7118 (t-100) REVERT: A 388 ASP cc_start: 0.7195 (m-30) cc_final: 0.6688 (p0) REVERT: A 458 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6730 (pmt100) REVERT: A 627 MET cc_start: 0.6319 (mmp) cc_final: 0.6009 (mtt) REVERT: A 669 ASP cc_start: 0.7541 (m-30) cc_final: 0.7106 (m-30) REVERT: A 808 GLU cc_start: 0.6866 (pp20) cc_final: 0.5196 (tm-30) REVERT: B 94 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8411 (mmmm) REVERT: B 340 MET cc_start: 0.6168 (tpp) cc_final: 0.5650 (mmm) REVERT: B 476 PHE cc_start: 0.6192 (p90) cc_final: 0.5577 (p90) REVERT: B 482 LEU cc_start: 0.8002 (mt) cc_final: 0.7667 (tt) REVERT: B 861 MET cc_start: 0.4707 (mmp) cc_final: 0.3473 (tmm) REVERT: C 50 MET cc_start: 0.5770 (mtm) cc_final: 0.5515 (mtm) REVERT: C 79 ASP cc_start: 0.8405 (t0) cc_final: 0.8119 (t70) REVERT: C 82 LYS cc_start: 0.8668 (mttp) cc_final: 0.8432 (mmtt) REVERT: C 323 MET cc_start: 0.9459 (tpt) cc_final: 0.9217 (tpp) REVERT: C 413 MET cc_start: 0.7933 (mmm) cc_final: 0.7397 (mmt) REVERT: C 568 LEU cc_start: 0.8895 (tt) cc_final: 0.8557 (tt) REVERT: C 572 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8139 (mm) REVERT: C 698 LYS cc_start: 0.8619 (mmmt) cc_final: 0.7977 (tppt) REVERT: C 810 LYS cc_start: 0.5117 (OUTLIER) cc_final: 0.4738 (tttt) REVERT: D 316 MET cc_start: 0.8486 (ttp) cc_final: 0.8231 (ttp) REVERT: D 351 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8465 (mttm) REVERT: D 361 SER cc_start: 0.8666 (t) cc_final: 0.8299 (t) REVERT: D 804 CYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5544 (t) REVERT: E 76 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6099 (tm) REVERT: E 120 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7541 (mmm-85) REVERT: E 137 MET cc_start: 0.4619 (ptp) cc_final: 0.2951 (mtm) REVERT: E 144 ASP cc_start: 0.5115 (p0) cc_final: 0.4280 (t0) REVERT: E 334 LYS cc_start: 0.5153 (mmmm) cc_final: 0.4683 (mptt) REVERT: E 365 SER cc_start: 0.8644 (m) cc_final: 0.8328 (t) REVERT: E 378 MET cc_start: 0.2876 (mpt) cc_final: 0.1742 (mmp) outliers start: 71 outliers final: 53 residues processed: 463 average time/residue: 0.1736 time to fit residues: 135.2787 Evaluate side-chains 451 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 219 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 204 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 chunk 207 optimal weight: 0.0570 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.164830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132227 restraints weight = 57557.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133958 restraints weight = 31026.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.134202 restraints weight = 31081.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135293 restraints weight = 22476.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.136039 restraints weight = 19946.910| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31527 Z= 0.128 Angle : 0.749 18.566 42648 Z= 0.346 Chirality : 0.046 0.502 4822 Planarity : 0.005 0.101 5232 Dihedral : 13.442 114.073 5949 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.43 % Favored : 90.32 % Rotamer: Outliers : 2.09 % Allowed : 19.41 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3669 helix: 1.00 (0.14), residues: 1532 sheet: -2.42 (0.25), residues: 420 loop : -2.82 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 300 TYR 0.035 0.001 TYR E 66 PHE 0.035 0.001 PHE D 584 TRP 0.014 0.001 TRP E 326 HIS 0.004 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00285 (31447) covalent geometry : angle 0.70376 (42423) SS BOND : bond 0.00478 ( 15) SS BOND : angle 1.11173 ( 30) hydrogen bonds : bond 0.03128 ( 970) hydrogen bonds : angle 4.11621 ( 2763) link_ALPHA1-3 : bond 0.01713 ( 5) link_ALPHA1-3 : angle 2.53415 ( 15) link_ALPHA1-6 : bond 0.00836 ( 5) link_ALPHA1-6 : angle 1.72996 ( 15) link_BETA1-3 : bond 0.00561 ( 1) link_BETA1-3 : angle 4.81225 ( 3) link_BETA1-4 : bond 0.00919 ( 23) link_BETA1-4 : angle 3.30672 ( 69) link_NAG-ASN : bond 0.00853 ( 31) link_NAG-ASN : angle 4.57097 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 415 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7023 (mmm) cc_final: 0.6801 (mmt) REVERT: A 325 ASP cc_start: 0.8508 (m-30) cc_final: 0.8125 (m-30) REVERT: A 368 TRP cc_start: 0.7497 (t-100) cc_final: 0.7281 (t-100) REVERT: A 388 ASP cc_start: 0.7350 (m-30) cc_final: 0.6777 (p0) REVERT: A 458 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6691 (pmt100) REVERT: A 627 MET cc_start: 0.6305 (mmp) cc_final: 0.6001 (mtt) REVERT: A 808 GLU cc_start: 0.6819 (pp20) cc_final: 0.5256 (tm-30) REVERT: B 94 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8273 (mmmm) REVERT: B 251 TYR cc_start: 0.7999 (m-80) cc_final: 0.7672 (m-80) REVERT: B 340 MET cc_start: 0.6055 (tpp) cc_final: 0.5568 (mmm) REVERT: B 476 PHE cc_start: 0.6205 (p90) cc_final: 0.5470 (p90) REVERT: B 482 LEU cc_start: 0.7953 (mt) cc_final: 0.7633 (tt) REVERT: B 587 TYR cc_start: 0.6415 (t80) cc_final: 0.6155 (t80) REVERT: B 861 MET cc_start: 0.4841 (mmp) cc_final: 0.3548 (tmm) REVERT: C 50 MET cc_start: 0.5515 (mtm) cc_final: 0.5186 (mtm) REVERT: C 79 ASP cc_start: 0.8383 (t0) cc_final: 0.8115 (t70) REVERT: C 82 LYS cc_start: 0.8629 (mttp) cc_final: 0.8419 (mmtt) REVERT: C 414 THR cc_start: 0.7510 (t) cc_final: 0.6973 (p) REVERT: C 540 ILE cc_start: 0.9093 (mt) cc_final: 0.8825 (mt) REVERT: C 563 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8421 (tp) REVERT: C 568 LEU cc_start: 0.8902 (tt) cc_final: 0.8589 (tt) REVERT: C 572 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 698 LYS cc_start: 0.8614 (mmmt) cc_final: 0.7965 (tppt) REVERT: C 810 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.4645 (tttt) REVERT: D 316 MET cc_start: 0.8538 (ttp) cc_final: 0.8274 (ttp) REVERT: D 351 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8526 (mttm) REVERT: E 76 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.5987 (tm) REVERT: E 120 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7598 (mmm-85) REVERT: E 137 MET cc_start: 0.4558 (ptp) cc_final: 0.2905 (mtm) REVERT: E 144 ASP cc_start: 0.5351 (p0) cc_final: 0.4749 (t0) REVERT: E 148 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6646 (tp30) REVERT: E 334 LYS cc_start: 0.5205 (mmmm) cc_final: 0.4724 (mptt) REVERT: E 365 SER cc_start: 0.8612 (m) cc_final: 0.8279 (t) REVERT: E 378 MET cc_start: 0.2869 (mpt) cc_final: 0.2099 (mmp) outliers start: 67 outliers final: 52 residues processed: 457 average time/residue: 0.1686 time to fit residues: 129.7327 Evaluate side-chains 444 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 386 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 241 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 91 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 97 optimal weight: 0.4980 chunk 310 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN D 335 GLN E 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.164883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130997 restraints weight = 58425.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132598 restraints weight = 34893.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133248 restraints weight = 31991.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133909 restraints weight = 24141.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134661 restraints weight = 22060.307| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31527 Z= 0.163 Angle : 0.775 18.263 42648 Z= 0.360 Chirality : 0.047 0.512 4822 Planarity : 0.005 0.092 5232 Dihedral : 13.278 112.916 5949 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.17 % Favored : 89.59 % Rotamer: Outliers : 2.12 % Allowed : 20.10 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3669 helix: 0.96 (0.14), residues: 1537 sheet: -2.70 (0.23), residues: 466 loop : -2.82 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 184 TYR 0.019 0.001 TYR A 195 PHE 0.033 0.002 PHE D 584 TRP 0.015 0.001 TRP A 296 HIS 0.005 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00380 (31447) covalent geometry : angle 0.73064 (42423) SS BOND : bond 0.00550 ( 15) SS BOND : angle 1.26191 ( 30) hydrogen bonds : bond 0.03321 ( 970) hydrogen bonds : angle 4.21517 ( 2763) link_ALPHA1-3 : bond 0.01674 ( 5) link_ALPHA1-3 : angle 2.53692 ( 15) link_ALPHA1-6 : bond 0.00687 ( 5) link_ALPHA1-6 : angle 1.53463 ( 15) link_BETA1-3 : bond 0.00344 ( 1) link_BETA1-3 : angle 4.68178 ( 3) link_BETA1-4 : bond 0.00923 ( 23) link_BETA1-4 : angle 3.34598 ( 69) link_NAG-ASN : bond 0.00788 ( 31) link_NAG-ASN : angle 4.60150 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5382.52 seconds wall clock time: 93 minutes 49.59 seconds (5629.59 seconds total)