Starting phenix.real_space_refine on Fri Feb 6 21:10:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4o_48900/02_2026/9n4o_48900.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4o_48900/02_2026/9n4o_48900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4o_48900/02_2026/9n4o_48900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4o_48900/02_2026/9n4o_48900.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4o_48900/02_2026/9n4o_48900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4o_48900/02_2026/9n4o_48900.cif" } resolution = 3.6 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= -0.027 sd= 1.104 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 144 5.16 5 C 17720 2.51 5 N 4371 2.21 5 O 5253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s 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: 27503 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" 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: "B" 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: "C" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "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: 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: "L" 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: "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: 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: "Q" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 264 Unusual residues: {'NAG': 4, 'POV': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 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: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 264 Unusual residues: {'NAG': 4, 'POV': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 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 Time building chain proxies: 6.30, per 1000 atoms: 0.23 Number of scatterers: 27503 At special positions: 0 Unit cell: (131.14, 155.21, 210.82, 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 144 16.00 P 15 15.00 O 5253 8.00 N 4371 7.00 C 17720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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=2.53 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=2.53 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=2.53 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=2.53 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 K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA K 3 " - " MAN K 5 " " BMA P 3 " - " MAN P 5 " BETA1-3 " NAG F 2 " - " BMA F 3 " " BMA N 3 " - " BMA N 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1003 " - " ASN A 67 " " NAG A1004 " - " ASN A 73 " " NAG A1005 " - " ASN A 423 " " NAG A1006 " - " ASN A 751 " " NAG B1003 " - " ASN B 67 " " NAG B1004 " - " ASN B 73 " " NAG B1005 " - " ASN B 430 " " NAG B1006 " - " ASN B 751 " " NAG C1005 " - " ASN C 73 " " NAG C1006 " - " ASN C 412 " " NAG C1007 " - " ASN C 430 " " NAG C1008 " - " ASN C 751 " " NAG D1006 " - " ASN D 67 " " NAG D1007 " - " ASN D 73 " " NAG D1008 " - " ASN D 546 " " NAG D1009 " - " ASN D 751 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 412 " " NAG H 1 " - " ASN A 430 " " NAG I 1 " - " ASN A 546 " " NAG J 1 " - " ASN B 275 " " NAG K 1 " - " ASN B 378 " " NAG L 1 " - " ASN B 412 " " NAG M 1 " - " ASN B 423 " " NAG N 1 " - " ASN B 546 " " NAG O 1 " - " ASN C 275 " " NAG P 1 " - " ASN C 378 " " NAG Q 1 " - " ASN C 546 " " NAG R 1 " - " ASN D 275 " " NAG S 1 " - " ASN D 378 " " NAG T 1 " - " ASN D 412 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 56 sheets defined 43.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.507A pdb=" N VAL A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.778A pdb=" N LEU A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 71 " --> pdb=" O ARG A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 71' Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.737A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.844A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.961A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.722A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.850A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.730A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 3.510A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 removed outlier: 3.686A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.660A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.749A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 557 " --> pdb=" O SER A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.543A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.537A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 645 " --> pdb=" O TRP A 641 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.841A 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 697 removed outlier: 3.688A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.667A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.089A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.531A pdb=" N LYS A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.732A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 3.508A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.778A pdb=" N LEU B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 71 " --> pdb=" O ARG B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 67 through 71' Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.738A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.844A pdb=" N ARG B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.961A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.722A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.851A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.729A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 removed outlier: 3.509A pdb=" N ILE B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.686A pdb=" N GLU B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.660A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.749A pdb=" N LEU B 556 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 557 " --> pdb=" O SER B 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 557' Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.544A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 659 removed outlier: 3.537A pdb=" N ILE B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 645 " --> pdb=" O TRP B 641 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) removed outlier: 3.752A 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 697 removed outlier: 3.688A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.667A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 739 through 746 Processing helix chain 'B' and resid 773 through 788 removed outlier: 4.089A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 783 " --> pdb=" O THR B 779 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.531A pdb=" N LYS B 797 " --> pdb=" O MET B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.732A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 850 " --> pdb=" O SER B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.507A pdb=" N VAL C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.778A pdb=" N LEU C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU C 71 " --> pdb=" O ARG C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 71' Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.738A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.844A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.961A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 removed outlier: 3.723A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.852A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 297 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.729A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 365 removed outlier: 3.510A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 474 removed outlier: 3.686A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.660A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.749A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 557 " --> pdb=" O SER C 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 557' Processing helix chain 'C' and resid 560 through 585 removed outlier: 3.543A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.536A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP C 641 " --> pdb=" O GLY C 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 645 " --> pdb=" O TRP C 641 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 689 through 697 Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.667A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.089A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 787 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.531A pdb=" N LYS C 797 " --> pdb=" O MET C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 813 removed outlier: 4.545A pdb=" N SER C 813 " --> pdb=" O LYS C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 821 through 850 removed outlier: 3.732A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 removed outlier: 3.508A pdb=" N VAL D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.779A pdb=" N LEU D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU D 71 " --> pdb=" O ARG D 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 67 through 71' Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 111 through 124 removed outlier: 3.738A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 167 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.843A pdb=" N ARG D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 180 through 185' Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 220 removed outlier: 3.961A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.722A pdb=" N ALA D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 297 removed outlier: 3.851A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.730A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 365 removed outlier: 3.510A pdb=" N ILE D 363 " --> pdb=" O PHE D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.687A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.660A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.749A pdb=" N LEU D 556 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 557 " --> pdb=" O SER D 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 553 through 557' Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.543A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 662 removed outlier: 3.537A pdb=" N ILE D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 645 " --> pdb=" O TRP D 641 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.688A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.666A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 773 through 788 removed outlier: 4.089A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 778 " --> pdb=" O TYR D 774 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.531A pdb=" N LYS D 797 " --> pdb=" O MET D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.732A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 848 " --> pdb=" O TYR D 844 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 850 " --> pdb=" O SER D 846 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 83 removed outlier: 6.055A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 8.352A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.601A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 removed outlier: 3.508A pdb=" N VAL A 226 " --> pdb=" O HIS A 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.871A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AB1, first strand: chain 'A' and resid 489 through 491 removed outlier: 3.752A pdb=" N ALA A 490 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 499 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.577A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.818A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 684 through 685 removed outlier: 5.563A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 83 removed outlier: 6.055A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 105 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 129 through 131 removed outlier: 8.351A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.600A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.507A pdb=" N VAL B 226 " --> pdb=" O HIS B 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 367 through 369 Processing sheet with id=AC2, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AC4, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.871A pdb=" N THR B 437 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC6, first strand: chain 'B' and resid 489 through 491 removed outlier: 3.752A pdb=" N ALA B 490 " --> pdb=" O ASN B 499 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 499 " --> pdb=" O ALA B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.577A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 736 through 738 removed outlier: 3.818A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 684 through 685 removed outlier: 5.563A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 76 through 83 removed outlier: 6.055A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 105 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 129 through 131 removed outlier: 8.351A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.600A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.508A pdb=" N VAL C 226 " --> pdb=" O HIS C 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 367 through 369 Processing sheet with id=AD7, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AD8, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AD9, first strand: chain 'C' and resid 436 through 437 removed outlier: 3.871A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AE2, first strand: chain 'C' and resid 489 through 491 removed outlier: 3.751A pdb=" N ALA C 490 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 499 " --> pdb=" O ALA C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AE4, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.577A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 736 through 738 removed outlier: 3.818A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 684 through 685 removed outlier: 5.563A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 76 through 83 removed outlier: 6.054A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA D 105 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 129 through 131 removed outlier: 8.351A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.600A pdb=" N TYR D 176 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 225 through 226 removed outlier: 3.509A pdb=" N VAL D 226 " --> pdb=" O HIS D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AF3, first strand: chain 'D' and resid 392 through 394 Processing sheet with id=AF4, first strand: chain 'D' and resid 404 through 406 Processing sheet with id=AF5, first strand: chain 'D' and resid 436 through 437 removed outlier: 3.871A pdb=" N THR D 437 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AF7, first strand: chain 'D' and resid 489 through 491 removed outlier: 3.752A pdb=" N ALA D 490 " --> pdb=" O ASN D 499 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 499 " --> pdb=" O ALA D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AF9, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.577A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 736 through 738 removed outlier: 3.818A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 684 through 685 removed outlier: 5.563A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 860 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4327 1.32 - 1.44: 7587 1.44 - 1.57: 15878 1.57 - 1.70: 44 1.70 - 1.83: 248 Bond restraints: 28084 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.572 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.561 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C1 NAG C1007 " pdb=" O5 NAG C1007 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.514 -0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 28079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 37409 4.82 - 9.64: 411 9.64 - 14.46: 70 14.46 - 19.28: 5 19.28 - 24.10: 1 Bond angle restraints: 37896 Sorted by residual: angle pdb=" O CYS D 804 " pdb=" C CYS D 804 " pdb=" N PRO D 805 " ideal model delta sigma weight residual 121.32 109.49 11.83 1.15e+00 7.56e-01 1.06e+02 angle pdb=" C SER A 429 " pdb=" N ASN A 430 " pdb=" CA ASN A 430 " ideal model delta sigma weight residual 120.63 131.79 -11.16 1.61e+00 3.86e-01 4.80e+01 angle pdb=" CA LEU A 428 " pdb=" CB LEU A 428 " pdb=" CG LEU A 428 " ideal model delta sigma weight residual 116.30 140.40 -24.10 3.50e+00 8.16e-02 4.74e+01 angle pdb=" N VAL A 601 " pdb=" CA VAL A 601 " pdb=" C VAL A 601 " ideal model delta sigma weight residual 113.20 106.66 6.54 9.60e-01 1.09e+00 4.64e+01 angle pdb=" N VAL D 601 " pdb=" CA VAL D 601 " pdb=" C VAL D 601 " ideal model delta sigma weight residual 113.20 106.66 6.54 9.60e-01 1.09e+00 4.64e+01 ... (remaining 37891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 16870 35.90 - 71.80: 574 71.80 - 107.70: 239 107.70 - 143.59: 38 143.59 - 179.49: 3 Dihedral angle restraints: 17724 sinusoidal: 8240 harmonic: 9484 Sorted by residual: dihedral pdb=" CA GLU B 415 " pdb=" C GLU B 415 " pdb=" N SER B 416 " pdb=" CA SER B 416 " ideal model delta harmonic sigma weight residual -180.00 -104.07 -75.93 0 5.00e+00 4.00e-02 2.31e+02 dihedral pdb=" CA PRO B 805 " pdb=" C PRO B 805 " pdb=" N GLU B 806 " pdb=" CA GLU B 806 " ideal model delta harmonic sigma weight residual 180.00 119.79 60.21 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA CYS D 804 " pdb=" C CYS D 804 " pdb=" N PRO D 805 " pdb=" CA PRO D 805 " ideal model delta harmonic sigma weight residual -180.00 -121.01 -58.99 0 5.00e+00 4.00e-02 1.39e+02 ... (remaining 17721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 4188 0.138 - 0.277: 99 0.277 - 0.415: 20 0.415 - 0.553: 8 0.553 - 0.691: 5 Chirality restraints: 4320 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 412 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG A1005 " pdb=" ND2 ASN A 423 " pdb=" C2 NAG A1005 " pdb=" O5 NAG A1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 4317 not shown) Planarity restraints: 4689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 804 " 0.081 2.00e-02 2.50e+03 1.54e-01 2.38e+02 pdb=" C CYS D 804 " -0.267 2.00e-02 2.50e+03 pdb=" O CYS D 804 " 0.102 2.00e-02 2.50e+03 pdb=" N PRO D 805 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 415 " -0.053 2.00e-02 2.50e+03 1.07e-01 1.15e+02 pdb=" C GLU A 415 " 0.186 2.00e-02 2.50e+03 pdb=" O GLU A 415 " -0.071 2.00e-02 2.50e+03 pdb=" N SER A 416 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 804 " -0.049 2.00e-02 2.50e+03 9.73e-02 9.47e+01 pdb=" C CYS B 804 " 0.168 2.00e-02 2.50e+03 pdb=" O CYS B 804 " -0.063 2.00e-02 2.50e+03 pdb=" N PRO B 805 " -0.057 2.00e-02 2.50e+03 ... (remaining 4686 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1670 2.72 - 3.27: 25255 3.27 - 3.81: 42332 3.81 - 4.36: 52099 4.36 - 4.90: 86894 Nonbonded interactions: 208250 Sorted by model distance: nonbonded pdb=" OE2 GLU B 787 " pdb=" OG1 THR C 520 " model vdw 2.178 3.040 nonbonded pdb=" OG SER A 632 " pdb=" OE1 GLU B 841 " model vdw 2.269 3.040 nonbonded pdb=" O LEU A 758 " pdb=" NH2 ARG D 712 " model vdw 2.282 3.120 nonbonded pdb=" OG SER D 554 " pdb=" O ASN D 819 " model vdw 2.290 3.040 nonbonded pdb=" OG SER C 554 " pdb=" O ASN C 819 " model vdw 2.290 3.040 ... (remaining 208245 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 1002 or resid 1006)) selection = (chain 'B' and (resid 33 through 1002 or resid 1006)) selection = (chain 'C' and (resid 33 through 1002 or resid 1006)) selection = (chain 'D' and (resid 33 through 1002 or resid 1006)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'S' } 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.550 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.500 28153 Z= 0.499 Angle : 1.419 24.100 38095 Z= 0.704 Chirality : 0.064 0.691 4320 Planarity : 0.008 0.154 4657 Dihedral : 20.790 179.492 11604 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.87 % Favored : 89.68 % Rotamer: Outliers : 0.56 % Allowed : 3.66 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.51 % 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: -5.91 (0.10), residues: 3264 helix: -4.51 (0.05), residues: 1354 sheet: -2.87 (0.26), residues: 276 loop : -3.59 (0.12), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 663 TYR 0.023 0.002 TYR D 733 PHE 0.017 0.002 PHE B 107 TRP 0.021 0.003 TRP A 353 HIS 0.009 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00781 (28084) covalent geometry : angle 1.32546 (37896) SS BOND : bond 0.35356 ( 8) SS BOND : angle 2.49274 ( 16) hydrogen bonds : bond 0.30828 ( 860) hydrogen bonds : angle 10.00457 ( 2493) link_ALPHA1-3 : bond 0.01010 ( 3) link_ALPHA1-3 : angle 2.16585 ( 9) link_ALPHA1-6 : bond 0.00708 ( 3) link_ALPHA1-6 : angle 1.60948 ( 9) link_BETA1-3 : bond 0.00854 ( 2) link_BETA1-3 : angle 5.72484 ( 6) link_BETA1-4 : bond 0.02228 ( 21) link_BETA1-4 : angle 6.48051 ( 63) link_NAG-ASN : bond 0.01392 ( 32) link_NAG-ASN : angle 8.60990 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 852 time to evaluate : 1.087 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 HIS cc_start: 0.5888 (t-90) cc_final: 0.5675 (m-70) REVERT: A 360 MET cc_start: 0.7450 (tpt) cc_final: 0.7099 (tpt) REVERT: A 411 LEU cc_start: 0.8003 (mt) cc_final: 0.6905 (mt) REVERT: B 257 THR cc_start: 0.7895 (m) cc_final: 0.7531 (p) REVERT: B 335 GLN cc_start: 0.8362 (tt0) cc_final: 0.8102 (mt0) REVERT: B 499 ASN cc_start: 0.7816 (p0) cc_final: 0.7448 (p0) REVERT: B 566 TYR cc_start: 0.7734 (m-10) cc_final: 0.7437 (m-80) REVERT: B 576 CYS cc_start: 0.7837 (m) cc_final: 0.7372 (m) REVERT: B 708 PHE cc_start: 0.7138 (t80) cc_final: 0.6640 (t80) REVERT: C 216 LYS cc_start: 0.7055 (ttmt) cc_final: 0.6638 (tttt) REVERT: C 298 MET cc_start: 0.7324 (mmt) cc_final: 0.6571 (tmm) REVERT: C 499 ASN cc_start: 0.8876 (p0) cc_final: 0.8672 (p0) REVERT: C 565 MET cc_start: 0.7418 (mtm) cc_final: 0.7155 (tpt) REVERT: C 589 TRP cc_start: 0.7508 (m100) cc_final: 0.7248 (m-10) REVERT: C 718 VAL cc_start: 0.8227 (p) cc_final: 0.7914 (p) REVERT: C 843 LEU cc_start: 0.7706 (mt) cc_final: 0.7471 (pp) REVERT: D 298 MET cc_start: 0.7639 (mmt) cc_final: 0.7070 (mtm) REVERT: D 616 VAL cc_start: 0.9145 (t) cc_final: 0.8935 (m) REVERT: D 620 MET cc_start: 0.8566 (mmt) cc_final: 0.8350 (mmm) REVERT: D 680 ILE cc_start: 0.7865 (mp) cc_final: 0.7598 (mt) REVERT: D 769 PRO cc_start: 0.3695 (Cg_exo) cc_final: 0.2825 (Cg_endo) REVERT: D 779 THR cc_start: 0.8874 (m) cc_final: 0.8636 (m) outliers start: 16 outliers final: 3 residues processed: 866 average time/residue: 0.2078 time to fit residues: 273.6293 Evaluate side-chains 459 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 456 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain D residue 67 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 339 GLN A 348 ASN A 596 ASN A 622 GLN A 721 ASN A 747 GLN B 65 ASN B 123 ASN B 339 GLN B 348 ASN B 593 HIS B 596 ASN B 622 GLN C 65 ASN C 123 ASN C 136 HIS C 137 GLN C 339 GLN C 348 ASN C 423 ASN C 596 ASN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN D 65 ASN D 123 ASN D 339 GLN D 348 ASN D 596 ASN D 622 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142979 restraints weight = 46347.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143144 restraints weight = 28767.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144001 restraints weight = 30000.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145310 restraints weight = 20157.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146410 restraints weight = 17664.036| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28153 Z= 0.166 Angle : 0.894 19.963 38095 Z= 0.411 Chirality : 0.052 0.482 4320 Planarity : 0.006 0.073 4657 Dihedral : 22.945 151.036 5434 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.45 % Rotamer: Outliers : 2.25 % Allowed : 12.54 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.35 % 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: -4.32 (0.11), residues: 3264 helix: -2.44 (0.10), residues: 1370 sheet: -2.64 (0.28), residues: 300 loop : -3.33 (0.13), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 202 TYR 0.024 0.002 TYR A 764 PHE 0.032 0.002 PHE A 693 TRP 0.018 0.002 TRP A 706 HIS 0.007 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00357 (28084) covalent geometry : angle 0.82212 (37896) SS BOND : bond 0.00315 ( 8) SS BOND : angle 1.60916 ( 16) hydrogen bonds : bond 0.05930 ( 860) hydrogen bonds : angle 5.48047 ( 2493) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 2.34146 ( 9) link_ALPHA1-6 : bond 0.00968 ( 3) link_ALPHA1-6 : angle 2.40232 ( 9) link_BETA1-3 : bond 0.01084 ( 2) link_BETA1-3 : angle 3.95003 ( 6) link_BETA1-4 : bond 0.01639 ( 21) link_BETA1-4 : angle 4.78316 ( 63) link_NAG-ASN : bond 0.01014 ( 32) link_NAG-ASN : angle 5.72002 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 493 time to evaluate : 1.059 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: A 111 HIS cc_start: 0.6353 (t-90) cc_final: 0.5810 (m-70) REVERT: A 270 ARG cc_start: 0.5426 (tpp80) cc_final: 0.5167 (mmm-85) REVERT: A 360 MET cc_start: 0.7751 (tpt) cc_final: 0.7426 (tpt) REVERT: B 245 MET cc_start: 0.8621 (mmm) cc_final: 0.8313 (tpp) REVERT: B 262 PHE cc_start: 0.8100 (t80) cc_final: 0.7734 (p90) REVERT: B 358 ARG cc_start: 0.6474 (tpm170) cc_final: 0.5926 (tpm170) REVERT: B 390 ASP cc_start: 0.8088 (m-30) cc_final: 0.7876 (m-30) REVERT: B 499 ASN cc_start: 0.7654 (p0) cc_final: 0.7392 (p0) REVERT: B 576 CYS cc_start: 0.7946 (m) cc_final: 0.7605 (m) REVERT: B 620 MET cc_start: 0.8701 (mmt) cc_final: 0.8162 (mmt) REVERT: B 708 PHE cc_start: 0.7277 (t80) cc_final: 0.6926 (t80) REVERT: B 755 ILE cc_start: 0.8990 (pp) cc_final: 0.8660 (pt) REVERT: C 216 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6956 (tttt) REVERT: C 298 MET cc_start: 0.7190 (mmt) cc_final: 0.6866 (ttp) REVERT: C 583 ARG cc_start: 0.6518 (mmt180) cc_final: 0.4627 (tpt-90) REVERT: C 589 TRP cc_start: 0.7686 (m100) cc_final: 0.7329 (m-10) REVERT: C 658 PHE cc_start: 0.8066 (t80) cc_final: 0.7155 (t80) REVERT: C 674 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8400 (tt) REVERT: C 793 MET cc_start: 0.7606 (tmm) cc_final: 0.7336 (tmm) REVERT: D 90 GLU cc_start: 0.7126 (tt0) cc_final: 0.6893 (tt0) REVERT: D 298 MET cc_start: 0.7402 (mmt) cc_final: 0.6988 (mtm) REVERT: D 316 MET cc_start: 0.7767 (ttp) cc_final: 0.7495 (ttp) REVERT: D 467 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7021 (tp) REVERT: D 620 MET cc_start: 0.8562 (mmt) cc_final: 0.8281 (mmm) REVERT: D 674 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (tm) REVERT: D 680 ILE cc_start: 0.8009 (mp) cc_final: 0.7772 (mt) REVERT: D 733 TYR cc_start: 0.8158 (t80) cc_final: 0.7933 (t80) outliers start: 64 outliers final: 40 residues processed: 538 average time/residue: 0.1912 time to fit residues: 162.1934 Evaluate side-chains 421 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 676 LYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 222 optimal weight: 0.6980 chunk 266 optimal weight: 4.9990 chunk 313 optimal weight: 0.6980 chunk 263 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 247 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 GLN B 98 GLN B 367 HIS C 622 GLN D 136 HIS D 508 HIS D 747 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138160 restraints weight = 47073.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139747 restraints weight = 34049.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140282 restraints weight = 33284.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141684 restraints weight = 21710.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142399 restraints weight = 18928.839| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28153 Z= 0.159 Angle : 0.846 20.064 38095 Z= 0.383 Chirality : 0.051 0.501 4320 Planarity : 0.005 0.072 4657 Dihedral : 20.325 152.006 5434 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.13 % Favored : 90.81 % Rotamer: Outliers : 3.06 % Allowed : 14.01 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.19 % 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: -3.18 (0.13), residues: 3264 helix: -1.00 (0.13), residues: 1373 sheet: -2.49 (0.27), residues: 319 loop : -3.11 (0.13), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 727 TYR 0.022 0.002 TYR D 44 PHE 0.024 0.002 PHE C 658 TRP 0.024 0.002 TRP D 798 HIS 0.011 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00342 (28084) covalent geometry : angle 0.78195 (37896) SS BOND : bond 0.00161 ( 8) SS BOND : angle 1.09160 ( 16) hydrogen bonds : bond 0.04371 ( 860) hydrogen bonds : angle 4.86015 ( 2493) link_ALPHA1-3 : bond 0.01346 ( 3) link_ALPHA1-3 : angle 2.59196 ( 9) link_ALPHA1-6 : bond 0.01250 ( 3) link_ALPHA1-6 : angle 2.54417 ( 9) link_BETA1-3 : bond 0.01399 ( 2) link_BETA1-3 : angle 3.69548 ( 6) link_BETA1-4 : bond 0.01402 ( 21) link_BETA1-4 : angle 4.52823 ( 63) link_NAG-ASN : bond 0.01460 ( 32) link_NAG-ASN : angle 5.20128 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 418 time to evaluate : 1.015 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 216 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7164 (mmmt) REVERT: A 220 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7650 (mtm180) REVERT: A 488 TYR cc_start: 0.4051 (m-10) cc_final: 0.3804 (m-10) REVERT: B 335 GLN cc_start: 0.8224 (tt0) cc_final: 0.7954 (tt0) REVERT: B 390 ASP cc_start: 0.8162 (m-30) cc_final: 0.7935 (m-30) REVERT: B 499 ASN cc_start: 0.7707 (p0) cc_final: 0.7477 (p0) REVERT: B 576 CYS cc_start: 0.7865 (m) cc_final: 0.7656 (m) REVERT: B 620 MET cc_start: 0.8725 (mmt) cc_final: 0.8176 (mmt) REVERT: B 708 PHE cc_start: 0.7322 (t80) cc_final: 0.7027 (t80) REVERT: B 733 TYR cc_start: 0.6486 (t80) cc_final: 0.6085 (t80) REVERT: C 276 MET cc_start: 0.7700 (mmm) cc_final: 0.7477 (mtm) REVERT: C 298 MET cc_start: 0.7143 (mmt) cc_final: 0.6883 (ttt) REVERT: C 316 MET cc_start: 0.7520 (tpt) cc_final: 0.7039 (tpt) REVERT: C 323 MET cc_start: 0.8119 (tpp) cc_final: 0.7804 (tpp) REVERT: C 583 ARG cc_start: 0.6591 (mmt180) cc_final: 0.4774 (tpt-90) REVERT: C 620 MET cc_start: 0.8200 (mmt) cc_final: 0.7987 (mmt) REVERT: C 674 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (tt) REVERT: D 90 GLU cc_start: 0.7149 (tt0) cc_final: 0.6915 (tt0) REVERT: D 298 MET cc_start: 0.7355 (mmt) cc_final: 0.6962 (mtm) REVERT: D 360 MET cc_start: 0.8964 (tpt) cc_final: 0.8680 (tpt) REVERT: D 680 ILE cc_start: 0.8272 (mp) cc_final: 0.7993 (mt) outliers start: 87 outliers final: 57 residues processed: 477 average time/residue: 0.1684 time to fit residues: 130.3813 Evaluate side-chains 424 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 366 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 706 TRP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 469 GLU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 73 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 308 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.173334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134672 restraints weight = 46867.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133821 restraints weight = 33655.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135840 restraints weight = 30989.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136075 restraints weight = 23357.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137921 restraints weight = 21543.110| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 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 = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28153 Z= 0.139 Angle : 0.815 20.490 38095 Z= 0.361 Chirality : 0.049 0.493 4320 Planarity : 0.004 0.071 4657 Dihedral : 18.458 146.129 5434 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 2.89 % Allowed : 15.46 % Favored : 81.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.16 % 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: -2.55 (0.14), residues: 3264 helix: -0.23 (0.14), residues: 1389 sheet: -2.40 (0.28), residues: 320 loop : -3.00 (0.14), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 431 TYR 0.016 0.001 TYR B 566 PHE 0.023 0.001 PHE C 842 TRP 0.014 0.001 TRP D 798 HIS 0.010 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00300 (28084) covalent geometry : angle 0.74111 (37896) SS BOND : bond 0.00151 ( 8) SS BOND : angle 1.99348 ( 16) hydrogen bonds : bond 0.03628 ( 860) hydrogen bonds : angle 4.47919 ( 2493) link_ALPHA1-3 : bond 0.01484 ( 3) link_ALPHA1-3 : angle 2.63735 ( 9) link_ALPHA1-6 : bond 0.01527 ( 3) link_ALPHA1-6 : angle 2.59571 ( 9) link_BETA1-3 : bond 0.01333 ( 2) link_BETA1-3 : angle 3.43977 ( 6) link_BETA1-4 : bond 0.01438 ( 21) link_BETA1-4 : angle 4.48068 ( 63) link_NAG-ASN : bond 0.00991 ( 32) link_NAG-ASN : angle 5.54716 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 403 time to evaluate : 0.909 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 216 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7467 (mmmt) REVERT: A 220 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: A 270 ARG cc_start: 0.6370 (mmm-85) cc_final: 0.5684 (mtp-110) REVERT: A 755 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7318 (mt) REVERT: B 335 GLN cc_start: 0.8196 (tt0) cc_final: 0.7830 (tt0) REVERT: B 576 CYS cc_start: 0.7944 (m) cc_final: 0.7677 (m) REVERT: B 620 MET cc_start: 0.8739 (mmt) cc_final: 0.8256 (mmt) REVERT: B 708 PHE cc_start: 0.7352 (t80) cc_final: 0.7082 (t80) REVERT: B 810 LYS cc_start: 0.6970 (ptpp) cc_final: 0.6465 (ttpp) REVERT: C 50 MET cc_start: 0.6901 (mtt) cc_final: 0.6697 (mtm) REVERT: C 233 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 262 PHE cc_start: 0.7883 (p90) cc_final: 0.7429 (t80) REVERT: C 298 MET cc_start: 0.7458 (mmt) cc_final: 0.6980 (ttt) REVERT: C 316 MET cc_start: 0.7696 (tpt) cc_final: 0.7247 (tpt) REVERT: C 323 MET cc_start: 0.8149 (tpp) cc_final: 0.7906 (tpp) REVERT: C 583 ARG cc_start: 0.6699 (mmt180) cc_final: 0.4781 (tpt170) REVERT: C 616 VAL cc_start: 0.9132 (t) cc_final: 0.8932 (p) REVERT: C 627 MET cc_start: 0.7703 (mmm) cc_final: 0.7475 (mmm) REVERT: D 90 GLU cc_start: 0.7179 (tt0) cc_final: 0.6901 (tt0) REVERT: D 200 LYS cc_start: 0.8277 (ttmp) cc_final: 0.7956 (mtpp) REVERT: D 298 MET cc_start: 0.7540 (mmt) cc_final: 0.7004 (mtm) REVERT: D 345 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7574 (tp) REVERT: D 360 MET cc_start: 0.8993 (tpt) cc_final: 0.8511 (tpt) REVERT: D 680 ILE cc_start: 0.8415 (mp) cc_final: 0.8102 (mt) outliers start: 82 outliers final: 58 residues processed: 460 average time/residue: 0.1637 time to fit residues: 123.0533 Evaluate side-chains 421 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 361 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 706 TRP Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 469 GLU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 69 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 128 optimal weight: 0.0020 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128631 restraints weight = 47267.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130003 restraints weight = 33362.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130257 restraints weight = 34891.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131892 restraints weight = 22427.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132540 restraints weight = 19030.853| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28153 Z= 0.209 Angle : 0.860 20.280 38095 Z= 0.387 Chirality : 0.051 0.639 4320 Planarity : 0.005 0.072 4657 Dihedral : 17.544 147.271 5434 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.68 % Favored : 90.26 % Rotamer: Outliers : 3.45 % Allowed : 15.85 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.16 % 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: -2.36 (0.14), residues: 3264 helix: 0.07 (0.14), residues: 1402 sheet: -2.51 (0.26), residues: 351 loop : -3.01 (0.14), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 431 TYR 0.024 0.002 TYR A 542 PHE 0.026 0.002 PHE A 693 TRP 0.034 0.002 TRP A 368 HIS 0.009 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00486 (28084) covalent geometry : angle 0.79555 (37896) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.48006 ( 16) hydrogen bonds : bond 0.03777 ( 860) hydrogen bonds : angle 4.47973 ( 2493) link_ALPHA1-3 : bond 0.01461 ( 3) link_ALPHA1-3 : angle 2.68553 ( 9) link_ALPHA1-6 : bond 0.01380 ( 3) link_ALPHA1-6 : angle 2.24917 ( 9) link_BETA1-3 : bond 0.01255 ( 2) link_BETA1-3 : angle 3.20135 ( 6) link_BETA1-4 : bond 0.01299 ( 21) link_BETA1-4 : angle 4.41416 ( 63) link_NAG-ASN : bond 0.00991 ( 32) link_NAG-ASN : angle 5.37974 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 387 time to evaluate : 1.055 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 194 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6744 (mtm180) REVERT: A 270 ARG cc_start: 0.6472 (mmm-85) cc_final: 0.5806 (mtp85) REVERT: A 755 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.7501 (mt) REVERT: B 158 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: B 170 LYS cc_start: 0.8103 (mppt) cc_final: 0.7741 (mmtt) REVERT: B 260 ASP cc_start: 0.8307 (m-30) cc_final: 0.7990 (m-30) REVERT: B 335 GLN cc_start: 0.8098 (tt0) cc_final: 0.7733 (tt0) REVERT: B 576 CYS cc_start: 0.7709 (m) cc_final: 0.7475 (m) REVERT: B 620 MET cc_start: 0.8824 (mmt) cc_final: 0.8422 (mmt) REVERT: C 280 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7298 (ttp80) REVERT: C 298 MET cc_start: 0.7345 (mmt) cc_final: 0.6968 (ttt) REVERT: C 323 MET cc_start: 0.8379 (tpp) cc_final: 0.7894 (tpp) REVERT: C 793 MET cc_start: 0.7922 (tmm) cc_final: 0.7500 (tmm) REVERT: D 90 GLU cc_start: 0.7310 (tt0) cc_final: 0.7040 (tt0) REVERT: D 99 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8016 (mt) REVERT: D 298 MET cc_start: 0.7491 (mmt) cc_final: 0.7057 (mtm) REVERT: D 345 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7366 (tp) REVERT: D 390 ASP cc_start: 0.7914 (m-30) cc_final: 0.7570 (m-30) REVERT: D 622 GLN cc_start: 0.8254 (mm110) cc_final: 0.8044 (mm-40) outliers start: 98 outliers final: 65 residues processed: 455 average time/residue: 0.1702 time to fit residues: 126.2157 Evaluate side-chains 416 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 348 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 706 TRP Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 755 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 300 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 0.0770 chunk 174 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS D 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.170376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132183 restraints weight = 46867.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133634 restraints weight = 31248.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133993 restraints weight = 31293.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134752 restraints weight = 21675.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136200 restraints weight = 19549.149| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28153 Z= 0.130 Angle : 0.787 19.689 38095 Z= 0.351 Chirality : 0.047 0.484 4320 Planarity : 0.004 0.064 4657 Dihedral : 16.814 147.458 5434 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.84 % Favored : 92.13 % Rotamer: Outliers : 3.20 % Allowed : 16.90 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.02 (0.14), residues: 3264 helix: 0.39 (0.14), residues: 1403 sheet: -2.27 (0.28), residues: 316 loop : -2.90 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 800 TYR 0.028 0.001 TYR D 521 PHE 0.029 0.001 PHE C 842 TRP 0.017 0.001 TRP A 368 HIS 0.009 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00284 (28084) covalent geometry : angle 0.71497 (37896) SS BOND : bond 0.00212 ( 8) SS BOND : angle 0.94010 ( 16) hydrogen bonds : bond 0.03221 ( 860) hydrogen bonds : angle 4.31060 ( 2493) link_ALPHA1-3 : bond 0.01406 ( 3) link_ALPHA1-3 : angle 2.78122 ( 9) link_ALPHA1-6 : bond 0.01571 ( 3) link_ALPHA1-6 : angle 2.19072 ( 9) link_BETA1-3 : bond 0.01355 ( 2) link_BETA1-3 : angle 3.01318 ( 6) link_BETA1-4 : bond 0.01357 ( 21) link_BETA1-4 : angle 4.41322 ( 63) link_NAG-ASN : bond 0.00862 ( 32) link_NAG-ASN : angle 5.39029 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 375 time to evaluate : 1.496 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: A 298 MET cc_start: 0.6419 (tmm) cc_final: 0.6098 (tmm) REVERT: A 501 MET cc_start: 0.7639 (tmm) cc_final: 0.7321 (tmm) REVERT: A 755 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7319 (mt) REVERT: B 71 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6059 (pp) REVERT: B 170 LYS cc_start: 0.8006 (mppt) cc_final: 0.7641 (mmtt) REVERT: B 335 GLN cc_start: 0.8055 (tt0) cc_final: 0.7673 (tt0) REVERT: B 360 MET cc_start: 0.7682 (tpt) cc_final: 0.7480 (tpt) REVERT: B 589 TRP cc_start: 0.6502 (m100) cc_final: 0.6251 (m100) REVERT: B 606 PHE cc_start: 0.8696 (m-80) cc_final: 0.8398 (m-10) REVERT: B 620 MET cc_start: 0.8724 (mmt) cc_final: 0.8372 (mmt) REVERT: C 262 PHE cc_start: 0.7723 (p90) cc_final: 0.7212 (t80) REVERT: C 298 MET cc_start: 0.7374 (mmt) cc_final: 0.6995 (ttt) REVERT: C 323 MET cc_start: 0.8352 (tpp) cc_final: 0.7933 (tpp) REVERT: D 90 GLU cc_start: 0.7208 (tt0) cc_final: 0.6969 (tt0) REVERT: D 298 MET cc_start: 0.7478 (mmt) cc_final: 0.7066 (mtm) REVERT: D 390 ASP cc_start: 0.7843 (m-30) cc_final: 0.7466 (m-30) REVERT: D 620 MET cc_start: 0.8471 (mmt) cc_final: 0.8202 (mmm) outliers start: 91 outliers final: 62 residues processed: 438 average time/residue: 0.1671 time to fit residues: 119.3042 Evaluate side-chains 401 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 337 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 157 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 316 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.165331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127081 restraints weight = 46976.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127478 restraints weight = 32248.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127960 restraints weight = 34291.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128716 restraints weight = 23072.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129621 restraints weight = 20409.457| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28153 Z= 0.187 Angle : 0.817 19.455 38095 Z= 0.369 Chirality : 0.049 0.484 4320 Planarity : 0.004 0.076 4657 Dihedral : 16.392 147.280 5434 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.59 % Rotamer: Outliers : 3.13 % Allowed : 17.57 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.96 (0.14), residues: 3264 helix: 0.53 (0.14), residues: 1401 sheet: -2.36 (0.28), residues: 333 loop : -2.93 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 66 TYR 0.021 0.002 TYR D 44 PHE 0.031 0.002 PHE C 262 TRP 0.024 0.002 TRP A 706 HIS 0.009 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00438 (28084) covalent geometry : angle 0.75150 (37896) SS BOND : bond 0.00261 ( 8) SS BOND : angle 0.99757 ( 16) hydrogen bonds : bond 0.03443 ( 860) hydrogen bonds : angle 4.37123 ( 2493) link_ALPHA1-3 : bond 0.01479 ( 3) link_ALPHA1-3 : angle 2.75846 ( 9) link_ALPHA1-6 : bond 0.01390 ( 3) link_ALPHA1-6 : angle 2.11580 ( 9) link_BETA1-3 : bond 0.01192 ( 2) link_BETA1-3 : angle 2.96260 ( 6) link_BETA1-4 : bond 0.01335 ( 21) link_BETA1-4 : angle 4.43257 ( 63) link_NAG-ASN : bond 0.00909 ( 32) link_NAG-ASN : angle 5.23283 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 367 time to evaluate : 1.114 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 298 MET cc_start: 0.6632 (tmm) cc_final: 0.6369 (tmm) REVERT: A 367 HIS cc_start: 0.6821 (m90) cc_final: 0.6430 (m90) REVERT: A 793 MET cc_start: 0.8135 (ppp) cc_final: 0.7839 (ppp) REVERT: B 130 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 170 LYS cc_start: 0.8128 (mppt) cc_final: 0.7712 (mmtt) REVERT: B 260 ASP cc_start: 0.8263 (m-30) cc_final: 0.7950 (m-30) REVERT: B 335 GLN cc_start: 0.8069 (tt0) cc_final: 0.7698 (tt0) REVERT: B 620 MET cc_start: 0.8797 (mmt) cc_final: 0.8471 (mmt) REVERT: C 323 MET cc_start: 0.8457 (tpp) cc_final: 0.7990 (tpp) REVERT: C 793 MET cc_start: 0.7882 (tmm) cc_final: 0.7588 (tmm) REVERT: D 90 GLU cc_start: 0.7276 (tt0) cc_final: 0.7023 (tt0) REVERT: D 187 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7198 (tt0) REVERT: D 298 MET cc_start: 0.7625 (mmt) cc_final: 0.7151 (mtm) REVERT: D 390 ASP cc_start: 0.7915 (m-30) cc_final: 0.7581 (m-30) outliers start: 89 outliers final: 68 residues processed: 436 average time/residue: 0.1551 time to fit residues: 112.0445 Evaluate side-chains 410 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 341 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 237 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.165547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128161 restraints weight = 47151.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130044 restraints weight = 34353.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130041 restraints weight = 36019.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131445 restraints weight = 22901.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132145 restraints weight = 19649.074| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28153 Z= 0.160 Angle : 0.798 19.146 38095 Z= 0.361 Chirality : 0.049 0.470 4320 Planarity : 0.004 0.069 4657 Dihedral : 15.844 147.753 5434 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.27 % Favored : 91.70 % Rotamer: Outliers : 2.99 % Allowed : 18.17 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.82 (0.14), residues: 3264 helix: 0.66 (0.14), residues: 1398 sheet: -2.15 (0.28), residues: 325 loop : -2.89 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 349 TYR 0.023 0.001 TYR B 774 PHE 0.031 0.002 PHE A 315 TRP 0.024 0.001 TRP A 706 HIS 0.012 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00365 (28084) covalent geometry : angle 0.73089 (37896) SS BOND : bond 0.01017 ( 8) SS BOND : angle 1.35638 ( 16) hydrogen bonds : bond 0.03261 ( 860) hydrogen bonds : angle 4.30638 ( 2493) link_ALPHA1-3 : bond 0.01561 ( 3) link_ALPHA1-3 : angle 2.95053 ( 9) link_ALPHA1-6 : bond 0.01501 ( 3) link_ALPHA1-6 : angle 2.16660 ( 9) link_BETA1-3 : bond 0.01342 ( 2) link_BETA1-3 : angle 2.86974 ( 6) link_BETA1-4 : bond 0.01418 ( 21) link_BETA1-4 : angle 4.41182 ( 63) link_NAG-ASN : bond 0.00960 ( 32) link_NAG-ASN : angle 5.20239 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 367 time to evaluate : 1.054 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 216 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7238 (mmtp) REVERT: A 298 MET cc_start: 0.6443 (tmm) cc_final: 0.6150 (tmm) REVERT: A 367 HIS cc_start: 0.6750 (m90) cc_final: 0.6452 (m90) REVERT: A 501 MET cc_start: 0.7569 (tmm) cc_final: 0.7317 (tmm) REVERT: B 130 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8938 (mm) REVERT: B 170 LYS cc_start: 0.8192 (mppt) cc_final: 0.7763 (mmtt) REVERT: B 260 ASP cc_start: 0.8286 (m-30) cc_final: 0.7969 (m-30) REVERT: B 335 GLN cc_start: 0.8130 (tt0) cc_final: 0.7835 (tt0) REVERT: B 534 MET cc_start: 0.8477 (ttp) cc_final: 0.8222 (ptm) REVERT: B 620 MET cc_start: 0.8780 (mmt) cc_final: 0.8444 (mmt) REVERT: C 298 MET cc_start: 0.6862 (ttt) cc_final: 0.5656 (tmm) REVERT: C 316 MET cc_start: 0.8097 (tpt) cc_final: 0.7836 (mmm) REVERT: C 323 MET cc_start: 0.8501 (tpp) cc_final: 0.8074 (tpp) REVERT: C 569 LEU cc_start: 0.8967 (tt) cc_final: 0.8403 (mt) REVERT: D 90 GLU cc_start: 0.7209 (tt0) cc_final: 0.6989 (tt0) REVERT: D 187 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7108 (tt0) REVERT: D 298 MET cc_start: 0.7636 (mmt) cc_final: 0.7121 (mtm) REVERT: D 337 PHE cc_start: 0.8169 (t80) cc_final: 0.7689 (t80) REVERT: D 794 MET cc_start: 0.8305 (mpp) cc_final: 0.8024 (mpp) outliers start: 85 outliers final: 66 residues processed: 432 average time/residue: 0.1572 time to fit residues: 113.2535 Evaluate side-chains 402 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 835 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 66 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 280 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 chunk 1 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN D 819 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.167249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129495 restraints weight = 47096.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132315 restraints weight = 32221.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131769 restraints weight = 33656.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133253 restraints weight = 21467.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134573 restraints weight = 18304.744| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28153 Z= 0.130 Angle : 0.807 21.404 38095 Z= 0.362 Chirality : 0.052 1.322 4320 Planarity : 0.004 0.067 4657 Dihedral : 15.494 147.649 5432 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.49 % Favored : 91.48 % Rotamer: Outliers : 2.50 % Allowed : 18.98 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.66 (0.14), residues: 3264 helix: 0.77 (0.14), residues: 1398 sheet: -2.02 (0.29), residues: 318 loop : -2.80 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 194 TYR 0.025 0.001 TYR A 462 PHE 0.026 0.001 PHE C 842 TRP 0.017 0.001 TRP A 706 HIS 0.013 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00282 (28084) covalent geometry : angle 0.73127 (37896) SS BOND : bond 0.00289 ( 8) SS BOND : angle 0.88741 ( 16) hydrogen bonds : bond 0.03156 ( 860) hydrogen bonds : angle 4.22638 ( 2493) link_ALPHA1-3 : bond 0.01716 ( 3) link_ALPHA1-3 : angle 3.05745 ( 9) link_ALPHA1-6 : bond 0.01585 ( 3) link_ALPHA1-6 : angle 2.28450 ( 9) link_BETA1-3 : bond 0.01275 ( 2) link_BETA1-3 : angle 2.89671 ( 6) link_BETA1-4 : bond 0.01276 ( 21) link_BETA1-4 : angle 4.31669 ( 63) link_NAG-ASN : bond 0.00875 ( 32) link_NAG-ASN : angle 5.76130 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 358 time to evaluate : 1.020 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 216 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7150 (mmtp) REVERT: A 298 MET cc_start: 0.6460 (tmm) cc_final: 0.6176 (tmm) REVERT: A 319 ASP cc_start: 0.7476 (m-30) cc_final: 0.7196 (m-30) REVERT: A 367 HIS cc_start: 0.6725 (m90) cc_final: 0.6477 (m90) REVERT: A 501 MET cc_start: 0.7502 (tmm) cc_final: 0.7168 (tmm) REVERT: B 71 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6063 (pp) REVERT: B 130 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8879 (mm) REVERT: B 170 LYS cc_start: 0.8091 (mppt) cc_final: 0.7708 (mmtt) REVERT: B 260 ASP cc_start: 0.8265 (m-30) cc_final: 0.7956 (m-30) REVERT: B 335 GLN cc_start: 0.8117 (tt0) cc_final: 0.7815 (tt0) REVERT: B 534 MET cc_start: 0.8472 (ttp) cc_final: 0.8208 (ptm) REVERT: B 620 MET cc_start: 0.8775 (mmt) cc_final: 0.8436 (mmt) REVERT: B 669 ASP cc_start: 0.7981 (t70) cc_final: 0.7554 (t0) REVERT: C 316 MET cc_start: 0.8053 (tpt) cc_final: 0.7735 (mmm) REVERT: C 323 MET cc_start: 0.8455 (tpp) cc_final: 0.8016 (tpp) REVERT: C 336 GLN cc_start: 0.7167 (mt0) cc_final: 0.6911 (mt0) REVERT: C 569 LEU cc_start: 0.8955 (tt) cc_final: 0.8384 (mt) REVERT: D 187 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7064 (tt0) REVERT: D 298 MET cc_start: 0.7613 (mmt) cc_final: 0.7124 (mtm) REVERT: D 337 PHE cc_start: 0.8183 (t80) cc_final: 0.7717 (t80) REVERT: D 620 MET cc_start: 0.8767 (tpp) cc_final: 0.8491 (mmm) outliers start: 71 outliers final: 59 residues processed: 411 average time/residue: 0.1641 time to fit residues: 111.7472 Evaluate side-chains 395 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 446 PHE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 186 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.167383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130007 restraints weight = 46919.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131816 restraints weight = 33504.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131954 restraints weight = 35055.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133367 restraints weight = 22543.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134491 restraints weight = 19422.877| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28153 Z= 0.134 Angle : 0.813 26.022 38095 Z= 0.365 Chirality : 0.048 0.541 4320 Planarity : 0.004 0.067 4657 Dihedral : 15.079 147.127 5432 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.36 % Favored : 91.61 % Rotamer: Outliers : 2.29 % Allowed : 19.40 % Favored : 78.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.56 (0.15), residues: 3264 helix: 0.85 (0.14), residues: 1397 sheet: -1.94 (0.29), residues: 319 loop : -2.74 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 133 TYR 0.018 0.001 TYR A 462 PHE 0.032 0.001 PHE D 579 TRP 0.028 0.001 TRP A 706 HIS 0.013 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00296 (28084) covalent geometry : angle 0.73521 (37896) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.93618 ( 16) hydrogen bonds : bond 0.03087 ( 860) hydrogen bonds : angle 4.18745 ( 2493) link_ALPHA1-3 : bond 0.01847 ( 3) link_ALPHA1-3 : angle 3.11592 ( 9) link_ALPHA1-6 : bond 0.01484 ( 3) link_ALPHA1-6 : angle 2.23239 ( 9) link_BETA1-3 : bond 0.01197 ( 2) link_BETA1-3 : angle 2.91848 ( 6) link_BETA1-4 : bond 0.01213 ( 21) link_BETA1-4 : angle 4.18064 ( 63) link_NAG-ASN : bond 0.00859 ( 32) link_NAG-ASN : angle 5.96109 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 0.923 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 276 MET cc_start: 0.6667 (mtt) cc_final: 0.6416 (mtt) REVERT: A 298 MET cc_start: 0.6413 (tmm) cc_final: 0.6078 (tmm) REVERT: A 367 HIS cc_start: 0.6692 (m90) cc_final: 0.6488 (m90) REVERT: B 71 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.5985 (pp) REVERT: B 260 ASP cc_start: 0.8273 (m-30) cc_final: 0.7972 (m-30) REVERT: B 335 GLN cc_start: 0.8103 (tt0) cc_final: 0.7798 (tt0) REVERT: B 534 MET cc_start: 0.8492 (ttp) cc_final: 0.8218 (ptm) REVERT: B 620 MET cc_start: 0.8777 (mmt) cc_final: 0.8411 (mmt) REVERT: B 669 ASP cc_start: 0.8019 (t70) cc_final: 0.7591 (t0) REVERT: C 316 MET cc_start: 0.8132 (tpt) cc_final: 0.7785 (mmm) REVERT: C 323 MET cc_start: 0.8535 (tpp) cc_final: 0.8090 (tpp) REVERT: C 372 THR cc_start: 0.7567 (p) cc_final: 0.7358 (p) REVERT: C 569 LEU cc_start: 0.8958 (tt) cc_final: 0.8385 (mt) REVERT: D 187 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7106 (tt0) REVERT: D 298 MET cc_start: 0.7636 (mmt) cc_final: 0.7133 (mtm) REVERT: D 337 PHE cc_start: 0.8170 (t80) cc_final: 0.7731 (t80) REVERT: D 620 MET cc_start: 0.8790 (tpp) cc_final: 0.8445 (tpp) outliers start: 65 outliers final: 54 residues processed: 388 average time/residue: 0.1580 time to fit residues: 103.7071 Evaluate side-chains 385 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 330 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 478 TYR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 834 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 59 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126922 restraints weight = 46830.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127112 restraints weight = 33575.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128220 restraints weight = 32660.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129088 restraints weight = 23409.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130543 restraints weight = 21101.298| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28153 Z= 0.170 Angle : 0.804 18.698 38095 Z= 0.366 Chirality : 0.048 0.456 4320 Planarity : 0.004 0.066 4657 Dihedral : 15.108 146.448 5432 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.01 % Favored : 90.93 % Rotamer: Outliers : 2.29 % Allowed : 19.44 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.62 (0.15), residues: 3264 helix: 0.79 (0.14), residues: 1404 sheet: -2.03 (0.29), residues: 320 loop : -2.75 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 349 TYR 0.022 0.002 TYR D 44 PHE 0.029 0.002 PHE D 579 TRP 0.039 0.001 TRP A 706 HIS 0.013 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00395 (28084) covalent geometry : angle 0.74485 (37896) SS BOND : bond 0.00288 ( 8) SS BOND : angle 1.06742 ( 16) hydrogen bonds : bond 0.03257 ( 860) hydrogen bonds : angle 4.26438 ( 2493) link_ALPHA1-3 : bond 0.01818 ( 3) link_ALPHA1-3 : angle 3.05732 ( 9) link_ALPHA1-6 : bond 0.01571 ( 3) link_ALPHA1-6 : angle 2.28603 ( 9) link_BETA1-3 : bond 0.01180 ( 2) link_BETA1-3 : angle 2.88799 ( 6) link_BETA1-4 : bond 0.01148 ( 21) link_BETA1-4 : angle 4.10905 ( 63) link_NAG-ASN : bond 0.00742 ( 32) link_NAG-ASN : angle 4.93565 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5050.78 seconds wall clock time: 88 minutes 9.96 seconds (5289.96 seconds total)