Starting phenix.real_space_refine on Fri Sep 19 05:29:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m16_30038/09_2025/6m16_30038_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m16_30038/09_2025/6m16_30038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m16_30038/09_2025/6m16_30038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m16_30038/09_2025/6m16_30038.map" model { file = "/net/cci-nas-00/data/ceres_data/6m16_30038/09_2025/6m16_30038_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m16_30038/09_2025/6m16_30038_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 14835 2.51 5 N 3888 2.21 5 O 4572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23433 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 7534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7534 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 924} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7534 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 924} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7534 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 924} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "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: 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: "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: 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: "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: 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: "O" 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: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.47, per 1000 atoms: 0.23 Number of scatterers: 23433 At special positions: 0 Unit cell: (125.198, 128.381, 164.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 4572 8.00 N 3888 7.00 C 14835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 246 " distance=2.02 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 460 " distance=2.04 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 614 " distance=2.02 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 708 " distance=2.04 Simple disulfide: pdb=" SG CYS B 886 " - pdb=" SG CYS B 897 " distance=2.02 Simple disulfide: pdb=" SG CYS B 936 " - pdb=" SG CYS B 945 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 58 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 460 " distance=2.04 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 603 " distance=2.02 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 708 " distance=2.04 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 897 " distance=2.02 Simple disulfide: pdb=" SG CYS A 936 " - pdb=" SG CYS A 945 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 58 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 411 " - pdb=" SG CYS C 460 " distance=2.04 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 526 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 614 " distance=2.02 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 603 " distance=2.02 Simple disulfide: pdb=" SG CYS C 698 " - pdb=" SG CYS C 708 " distance=2.04 Simple disulfide: pdb=" SG CYS C 886 " - pdb=" SG CYS C 897 " distance=2.02 Simple disulfide: pdb=" SG CYS C 936 " - pdb=" SG CYS C 945 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1205 " - " ASN A 154 " " NAG A1208 " - " ASN A 514 " " NAG A1209 " - " ASN A 520 " " NAG A1217 " - " ASN A 992 " " NAG B1205 " - " ASN B 154 " " NAG B1208 " - " ASN B 514 " " NAG B1209 " - " ASN B 520 " " NAG B1217 " - " ASN B 992 " " NAG C1205 " - " ASN C 154 " " NAG C1208 " - " ASN C 514 " " NAG C1209 " - " ASN C 520 " " NAG C1217 " - " ASN C 992 " " NAG D 1 " - " ASN B 39 " " NAG E 1 " - " ASN B 654 " " NAG F 1 " - " ASN B 973 " " NAG G 1 " - " ASN B 957 " " NAG H 1 " - " ASN A 39 " " NAG I 1 " - " ASN A 654 " " NAG J 1 " - " ASN A 973 " " NAG K 1 " - " ASN A 957 " " NAG L 1 " - " ASN C 39 " " NAG M 1 " - " ASN C 654 " " NAG N 1 " - " ASN C 973 " " NAG O 1 " - " ASN C 957 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 900.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5358 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 39 sheets defined 23.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.738A pdb=" N LEU B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 316 through 321 removed outlier: 4.260A pdb=" N HIS B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.918A pdb=" N ASP B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 496' Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 612 through 640 removed outlier: 3.538A pdb=" N LYS B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 618 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.580A pdb=" N PHE B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 removed outlier: 3.504A pdb=" N PHE B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 702 Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 751 through 763 Processing helix chain 'B' and resid 770 through 787 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 796 through 818 removed outlier: 3.568A pdb=" N ALA B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 812 " --> pdb=" O GLN B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 830 through 836 removed outlier: 3.569A pdb=" N SER B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 886 removed outlier: 3.775A pdb=" N LEU B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 857 " --> pdb=" O GLY B 853 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.738A pdb=" N LEU A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 27 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN A 28 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.259A pdb=" N HIS A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.918A pdb=" N ASP A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 496' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 612 through 640 removed outlier: 3.537A pdb=" N LYS A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 618 " --> pdb=" O CYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.580A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 removed outlier: 3.505A pdb=" N PHE A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 702 Processing helix chain 'A' and resid 723 through 727 Processing helix chain 'A' and resid 751 through 763 Processing helix chain 'A' and resid 770 through 787 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.568A pdb=" N ALA A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 812 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 830 through 836 removed outlier: 3.569A pdb=" N SER A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 886 removed outlier: 3.775A pdb=" N LEU A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 removed outlier: 3.739A pdb=" N LEU C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 27 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 28 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 316 through 321 removed outlier: 4.260A pdb=" N HIS C 319 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 removed outlier: 3.918A pdb=" N ASP C 496 " --> pdb=" O ALA C 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 492 through 496' Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'C' and resid 612 through 640 removed outlier: 3.537A pdb=" N LYS C 616 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 618 " --> pdb=" O CYS C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 removed outlier: 3.580A pdb=" N PHE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 removed outlier: 3.505A pdb=" N PHE C 681 " --> pdb=" O GLU C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 702 Processing helix chain 'C' and resid 723 through 727 Processing helix chain 'C' and resid 751 through 763 Processing helix chain 'C' and resid 770 through 787 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 796 through 818 removed outlier: 3.568A pdb=" N ALA C 801 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 812 " --> pdb=" O GLN C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 821 No H-bonds generated for 'chain 'C' and resid 819 through 821' Processing helix chain 'C' and resid 830 through 836 removed outlier: 3.569A pdb=" N SER C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 886 removed outlier: 3.775A pdb=" N LEU C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 877 " --> pdb=" O ARG C 873 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 881 " --> pdb=" O ARG C 877 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.858A pdb=" N LEU C 439 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 444 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG C 446 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 426 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 46 removed outlier: 3.745A pdb=" N ARG B 232 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.524A pdb=" N PHE B 211 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 73 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 165 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN B 188 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.820A pdb=" N LEU B 125 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU B 150 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.514A pdb=" N VAL B 257 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B 469 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER B 259 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 467 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.546A pdb=" N TYR B 426 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG B 446 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 444 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 439 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR B 440 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 277 through 278 removed outlier: 7.703A pdb=" N SER B 277 " --> pdb=" O ILE B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 296 through 298 removed outlier: 7.071A pdb=" N ILE B 383 " --> pdb=" O ASN B 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB1, first strand: chain 'B' and resid 393 through 394 removed outlier: 4.111A pdb=" N GLN A 188 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 165 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 73 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 211 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 516 through 523 removed outlier: 6.654A pdb=" N SER B 516 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG B 546 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ALA B 518 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN B 925 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS B 572 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 574 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 921 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 576 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR B 919 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU B 578 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 917 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 580 " --> pdb=" O MET B 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET B 915 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 921 " --> pdb=" O HIS B 902 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS B 902 " --> pdb=" O LEU B 921 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN B 925 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS B 572 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 574 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 921 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 576 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR B 919 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU B 578 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 917 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 580 " --> pdb=" O MET B 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET B 915 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 932 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU B 953 " --> pdb=" O THR B 932 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 587 through 590 removed outlier: 3.841A pdb=" N GLN B 710 " --> pdb=" O VAL B 717 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 979 through 982 removed outlier: 3.752A pdb=" N CYS B 945 " --> pdb=" O VAL B 982 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 41 through 46 removed outlier: 3.744A pdb=" N ARG A 232 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.820A pdb=" N LEU A 125 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU A 150 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 256 through 262 removed outlier: 5.514A pdb=" N VAL A 257 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 469 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER A 259 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 467 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.545A pdb=" N TYR A 426 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG A 446 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 444 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 439 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR A 440 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 277 through 278 removed outlier: 7.702A pdb=" N SER A 277 " --> pdb=" O ILE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 296 through 298 removed outlier: 7.071A pdb=" N ILE A 383 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AC5, first strand: chain 'A' and resid 393 through 394 removed outlier: 4.106A pdb=" N GLN C 188 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 165 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 73 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 211 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 516 through 523 removed outlier: 6.654A pdb=" N SER A 516 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARG A 546 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ALA A 518 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN A 925 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS A 572 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 574 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 921 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 576 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 919 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 578 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE A 917 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 580 " --> pdb=" O MET A 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 915 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 921 " --> pdb=" O HIS A 902 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS A 902 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN A 925 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS A 572 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 574 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 921 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 576 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 919 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 578 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE A 917 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE A 580 " --> pdb=" O MET A 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 915 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 932 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A 953 " --> pdb=" O THR A 932 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 587 through 590 removed outlier: 3.841A pdb=" N GLN A 710 " --> pdb=" O VAL A 717 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 979 through 982 removed outlier: 3.752A pdb=" N CYS A 945 " --> pdb=" O VAL A 982 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.745A pdb=" N ARG C 232 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.821A pdb=" N LEU C 125 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU C 150 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 256 through 262 removed outlier: 5.514A pdb=" N VAL C 257 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR C 469 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER C 259 " --> pdb=" O VAL C 467 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 467 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 277 through 278 removed outlier: 7.703A pdb=" N SER C 277 " --> pdb=" O ILE C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 296 through 298 removed outlier: 7.071A pdb=" N ILE C 383 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AD8, first strand: chain 'C' and resid 516 through 523 removed outlier: 6.654A pdb=" N SER C 516 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG C 546 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N ALA C 518 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN C 925 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS C 572 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 574 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 921 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU C 576 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C 919 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU C 578 " --> pdb=" O PHE C 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C 917 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE C 580 " --> pdb=" O MET C 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET C 915 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU C 921 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS C 902 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 564 through 581 removed outlier: 6.405A pdb=" N ASN C 925 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS C 572 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 574 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 921 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU C 576 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C 919 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU C 578 " --> pdb=" O PHE C 917 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE C 917 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE C 580 " --> pdb=" O MET C 915 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET C 915 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 932 " --> pdb=" O LEU C 953 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 953 " --> pdb=" O THR C 932 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 587 through 590 removed outlier: 3.841A pdb=" N GLN C 710 " --> pdb=" O VAL C 717 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 979 through 982 removed outlier: 3.751A pdb=" N CYS C 945 " --> pdb=" O VAL C 982 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2055 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: 5.46 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6529 1.33 - 1.45: 5755 1.45 - 1.58: 11497 1.58 - 1.70: 0 1.70 - 1.83: 186 Bond restraints: 23967 Sorted by residual: bond pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.11e-02 8.12e+03 8.45e+00 bond pdb=" C LEU C 499 " pdb=" N PRO C 500 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.11e-02 8.12e+03 8.40e+00 bond pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.11e-02 8.12e+03 8.35e+00 bond pdb=" CG1 ILE A 742 " pdb=" CD1 ILE A 742 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.88e+00 bond pdb=" CG1 ILE B 742 " pdb=" CD1 ILE B 742 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.86e+00 ... (remaining 23962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 31150 2.32 - 4.63: 1321 4.63 - 6.95: 121 6.95 - 9.26: 27 9.26 - 11.58: 6 Bond angle restraints: 32625 Sorted by residual: angle pdb=" N VAL A 120 " pdb=" CA VAL A 120 " pdb=" C VAL A 120 " ideal model delta sigma weight residual 108.12 114.19 -6.07 1.34e+00 5.57e-01 2.05e+01 angle pdb=" N VAL B 120 " pdb=" CA VAL B 120 " pdb=" C VAL B 120 " ideal model delta sigma weight residual 108.12 114.19 -6.07 1.34e+00 5.57e-01 2.05e+01 angle pdb=" N VAL C 120 " pdb=" CA VAL C 120 " pdb=" C VAL C 120 " ideal model delta sigma weight residual 108.12 114.19 -6.07 1.34e+00 5.57e-01 2.05e+01 angle pdb=" N ASP B 598 " pdb=" CA ASP B 598 " pdb=" C ASP B 598 " ideal model delta sigma weight residual 111.02 115.88 -4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N ASP C 598 " pdb=" CA ASP C 598 " pdb=" C ASP C 598 " ideal model delta sigma weight residual 111.02 115.87 -4.85 1.22e+00 6.72e-01 1.58e+01 ... (remaining 32620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.23: 14322 20.23 - 40.46: 408 40.46 - 60.69: 93 60.69 - 80.92: 72 80.92 - 101.15: 24 Dihedral angle restraints: 14919 sinusoidal: 6540 harmonic: 8379 Sorted by residual: dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual -86.00 -15.49 -70.51 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS B 19 " pdb=" SG CYS B 19 " pdb=" SG CYS B 58 " pdb=" CB CYS B 58 " ideal model delta sinusoidal sigma weight residual -86.00 -15.54 -70.46 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 58 " pdb=" CB CYS C 58 " ideal model delta sinusoidal sigma weight residual -86.00 -15.56 -70.44 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3296 0.095 - 0.191: 472 0.191 - 0.286: 30 0.286 - 0.381: 3 0.381 - 0.476: 6 Chirality restraints: 3807 Sorted by residual: chirality pdb=" C1 NAG B1208 " pdb=" ND2 ASN B 514 " pdb=" C2 NAG B1208 " pdb=" O5 NAG B1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" C1 NAG A1208 " pdb=" ND2 ASN A 514 " pdb=" C2 NAG A1208 " pdb=" O5 NAG A1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 514 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 ... (remaining 3804 not shown) Planarity restraints: 4146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 681 " 0.018 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE A 681 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 681 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 681 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 681 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 681 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 681 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 681 " -0.017 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE B 681 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 681 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE B 681 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 681 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 681 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 681 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 681 " -0.017 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE C 681 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 681 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 681 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 681 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE C 681 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 681 " -0.003 2.00e-02 2.50e+03 ... (remaining 4143 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 30 1.90 - 2.65: 356 2.65 - 3.40: 28894 3.40 - 4.15: 55185 4.15 - 4.90: 99016 Nonbonded interactions: 183481 Sorted by model distance: nonbonded pdb=" ND2 ASN A 337 " pdb=" N LEU C 838 " model vdw 1.146 3.200 nonbonded pdb=" ND2 ASN B 337 " pdb=" N LEU A 838 " model vdw 1.147 3.200 nonbonded pdb=" N LEU B 838 " pdb=" ND2 ASN C 337 " model vdw 1.153 3.200 nonbonded pdb=" OD1 ASN A 337 " pdb=" C LEU C 838 " model vdw 1.156 3.270 nonbonded pdb=" OE2 GLU A 822 " pdb=" CA GLY C 611 " model vdw 1.157 3.440 ... (remaining 183476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.270 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.011 0.109 24051 Z= 0.459 Angle : 1.084 11.577 32832 Z= 0.594 Chirality : 0.069 0.476 3807 Planarity : 0.008 0.070 4122 Dihedral : 12.541 101.147 9426 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.52 % Favored : 92.37 % Rotamer: Outliers : 0.36 % Allowed : 2.16 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.10 (0.12), residues: 2871 helix: -4.24 (0.09), residues: 591 sheet: -2.02 (0.18), residues: 627 loop : -2.45 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 877 TYR 0.037 0.004 TYR A 479 PHE 0.055 0.005 PHE A 681 TRP 0.045 0.004 TRP B 752 HIS 0.018 0.004 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.01074 (23967) covalent geometry : angle 1.06520 (32625) SS BOND : bond 0.00761 ( 45) SS BOND : angle 2.54388 ( 90) hydrogen bonds : bond 0.29320 ( 742) hydrogen bonds : angle 9.51690 ( 2055) link_BETA1-4 : bond 0.01013 ( 15) link_BETA1-4 : angle 3.25173 ( 45) link_NAG-ASN : bond 0.00492 ( 24) link_NAG-ASN : angle 2.68632 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 323 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.6706 (t70) cc_final: 0.6370 (p0) REVERT: B 523 MET cc_start: 0.8538 (mtp) cc_final: 0.8321 (mtp) REVERT: A 173 ASN cc_start: 0.8166 (m110) cc_final: 0.7938 (m-40) REVERT: A 200 ASN cc_start: 0.7750 (t0) cc_final: 0.7522 (t0) REVERT: A 386 TRP cc_start: 0.6548 (p-90) cc_final: 0.6296 (p-90) REVERT: A 390 ASP cc_start: 0.6516 (t70) cc_final: 0.6241 (p0) REVERT: A 660 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9280 (mt) REVERT: A 712 HIS cc_start: 0.8070 (m90) cc_final: 0.7741 (m-70) REVERT: A 749 MET cc_start: 0.8973 (mtm) cc_final: 0.8664 (mtp) REVERT: C 173 ASN cc_start: 0.8324 (m110) cc_final: 0.8112 (m-40) REVERT: C 390 ASP cc_start: 0.6773 (t70) cc_final: 0.6424 (p0) REVERT: C 767 GLN cc_start: 0.7948 (tp40) cc_final: 0.7687 (tt0) outliers start: 9 outliers final: 2 residues processed: 332 average time/residue: 0.6232 time to fit residues: 236.4303 Evaluate side-chains 198 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain A residue 660 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 188 GLN B 328 ASN B 334 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 767 GLN ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN B 925 ASN B 987 ASN A 34 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 328 ASN A 334 ASN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 525 ASN A 767 GLN A 783 GLN A 807 ASN A 894 ASN A 909 ASN A 925 ASN A 987 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 188 GLN C 200 ASN C 328 ASN C 334 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN C 437 ASN C 525 ASN ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 ASN C 909 ASN C 925 ASN C 987 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.160171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106645 restraints weight = 28514.463| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.23 r_work: 0.2986 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24051 Z= 0.151 Angle : 0.699 10.065 32832 Z= 0.361 Chirality : 0.046 0.316 3807 Planarity : 0.005 0.056 4122 Dihedral : 9.689 66.369 4404 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.64 % Allowed : 6.81 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.14), residues: 2871 helix: -1.44 (0.18), residues: 594 sheet: -1.42 (0.20), residues: 582 loop : -2.01 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 249 TYR 0.017 0.002 TYR C 610 PHE 0.019 0.002 PHE C 976 TRP 0.022 0.001 TRP C 110 HIS 0.005 0.001 HIS C 902 Details of bonding type rmsd covalent geometry : bond 0.00338 (23967) covalent geometry : angle 0.67867 (32625) SS BOND : bond 0.00497 ( 45) SS BOND : angle 2.61960 ( 90) hydrogen bonds : bond 0.06129 ( 742) hydrogen bonds : angle 5.40139 ( 2055) link_BETA1-4 : bond 0.00530 ( 15) link_BETA1-4 : angle 1.90429 ( 45) link_NAG-ASN : bond 0.00342 ( 24) link_NAG-ASN : angle 1.77129 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 ARG cc_start: 0.7302 (ttp-110) cc_final: 0.7053 (ttm110) REVERT: B 390 ASP cc_start: 0.6969 (t70) cc_final: 0.6430 (p0) REVERT: B 523 MET cc_start: 0.9079 (mtp) cc_final: 0.8827 (mtp) REVERT: A 173 ASN cc_start: 0.8370 (m110) cc_final: 0.8025 (m-40) REVERT: A 276 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6822 (mtm) REVERT: A 386 TRP cc_start: 0.6392 (p-90) cc_final: 0.6024 (p-90) REVERT: A 390 ASP cc_start: 0.6608 (t70) cc_final: 0.6263 (p0) REVERT: A 660 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9245 (mt) REVERT: A 749 MET cc_start: 0.9239 (mtm) cc_final: 0.8901 (mtp) REVERT: A 838 LEU cc_start: 0.8576 (mt) cc_final: 0.8024 (mp) REVERT: C 124 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6840 (ttm110) REVERT: C 173 ASN cc_start: 0.8527 (m110) cc_final: 0.8211 (m-40) REVERT: C 299 PHE cc_start: 0.6990 (m-80) cc_final: 0.6580 (m-80) REVERT: C 338 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6852 (ttt-90) REVERT: C 390 ASP cc_start: 0.6995 (t70) cc_final: 0.6295 (p0) REVERT: C 749 MET cc_start: 0.9172 (mtm) cc_final: 0.8754 (mtm) REVERT: C 838 LEU cc_start: 0.8608 (mt) cc_final: 0.8034 (mt) outliers start: 41 outliers final: 15 residues processed: 279 average time/residue: 0.5292 time to fit residues: 172.8563 Evaluate side-chains 215 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 814 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 239 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 chunk 230 optimal weight: 0.7980 chunk 217 optimal weight: 0.0770 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 85 optimal weight: 0.0470 chunk 186 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 77 GLN B 328 ASN B 337 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 77 GLN A 200 ASN A 328 ASN C 77 GLN C 328 ASN C 337 ASN C 767 GLN ** C 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.162328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109744 restraints weight = 28704.670| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.13 r_work: 0.3013 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24051 Z= 0.109 Angle : 0.589 9.801 32832 Z= 0.304 Chirality : 0.044 0.294 3807 Planarity : 0.004 0.052 4122 Dihedral : 7.355 58.556 4400 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.88 % Allowed : 8.13 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.15), residues: 2871 helix: 0.27 (0.22), residues: 591 sheet: -1.14 (0.22), residues: 534 loop : -1.61 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 124 TYR 0.015 0.001 TYR A 636 PHE 0.024 0.001 PHE A 494 TRP 0.025 0.001 TRP C 110 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00235 (23967) covalent geometry : angle 0.57284 (32625) SS BOND : bond 0.00316 ( 45) SS BOND : angle 1.86328 ( 90) hydrogen bonds : bond 0.04523 ( 742) hydrogen bonds : angle 4.81574 ( 2055) link_BETA1-4 : bond 0.00536 ( 15) link_BETA1-4 : angle 1.79994 ( 45) link_NAG-ASN : bond 0.00359 ( 24) link_NAG-ASN : angle 1.77572 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 252 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7493 (p0) REVERT: B 338 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7151 (ttt180) REVERT: B 390 ASP cc_start: 0.6817 (t70) cc_final: 0.6325 (p0) REVERT: B 523 MET cc_start: 0.9054 (mtp) cc_final: 0.8802 (mtp) REVERT: B 712 HIS cc_start: 0.8554 (m90) cc_final: 0.8209 (m90) REVERT: A 173 ASN cc_start: 0.8273 (m110) cc_final: 0.7988 (m-40) REVERT: A 185 LEU cc_start: 0.8700 (tp) cc_final: 0.7958 (mp) REVERT: A 281 GLU cc_start: 0.6765 (mp0) cc_final: 0.6451 (mp0) REVERT: A 386 TRP cc_start: 0.6285 (p-90) cc_final: 0.5997 (p-90) REVERT: A 390 ASP cc_start: 0.6323 (t70) cc_final: 0.6038 (p0) REVERT: A 749 MET cc_start: 0.9173 (mtm) cc_final: 0.8878 (mtp) REVERT: A 915 MET cc_start: 0.9171 (ttm) cc_final: 0.8857 (tpp) REVERT: C 173 ASN cc_start: 0.8521 (m110) cc_final: 0.8237 (m-40) REVERT: C 390 ASP cc_start: 0.6814 (t70) cc_final: 0.6189 (p0) REVERT: C 608 PHE cc_start: 0.8496 (t80) cc_final: 0.8175 (t80) outliers start: 47 outliers final: 18 residues processed: 268 average time/residue: 0.4877 time to fit residues: 154.1654 Evaluate side-chains 220 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 738 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 257 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 114 optimal weight: 0.0470 chunk 216 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 218 optimal weight: 0.0370 chunk 251 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 807 ASN B 894 ASN A 34 HIS A 437 ASN A 899 GLN C 34 HIS C 337 ASN C 807 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108485 restraints weight = 28542.493| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.20 r_work: 0.2999 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24051 Z= 0.124 Angle : 0.583 9.776 32832 Z= 0.301 Chirality : 0.044 0.289 3807 Planarity : 0.004 0.052 4122 Dihedral : 6.373 57.192 4398 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.84 % Allowed : 9.58 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.16), residues: 2871 helix: 0.88 (0.22), residues: 591 sheet: -0.88 (0.22), residues: 528 loop : -1.45 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 249 TYR 0.017 0.001 TYR C 636 PHE 0.021 0.001 PHE C 613 TRP 0.022 0.001 TRP C 110 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00284 (23967) covalent geometry : angle 0.56316 (32625) SS BOND : bond 0.00704 ( 45) SS BOND : angle 2.37207 ( 90) hydrogen bonds : bond 0.04520 ( 742) hydrogen bonds : angle 4.70780 ( 2055) link_BETA1-4 : bond 0.00465 ( 15) link_BETA1-4 : angle 1.62271 ( 45) link_NAG-ASN : bond 0.00324 ( 24) link_NAG-ASN : angle 1.61778 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 252 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 338 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7153 (ttt180) REVERT: B 390 ASP cc_start: 0.6813 (t70) cc_final: 0.6380 (p0) REVERT: B 420 THR cc_start: 0.8858 (t) cc_final: 0.8624 (t) REVERT: B 712 HIS cc_start: 0.8631 (m90) cc_final: 0.8263 (m90) REVERT: A 173 ASN cc_start: 0.8264 (m110) cc_final: 0.7995 (m-40) REVERT: A 185 LEU cc_start: 0.8706 (tp) cc_final: 0.7932 (mp) REVERT: A 276 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6750 (mtm) REVERT: A 281 GLU cc_start: 0.6723 (mp0) cc_final: 0.6342 (mp0) REVERT: A 386 TRP cc_start: 0.6295 (p-90) cc_final: 0.5993 (p-90) REVERT: A 390 ASP cc_start: 0.6267 (t70) cc_final: 0.6014 (p0) REVERT: A 420 THR cc_start: 0.9000 (t) cc_final: 0.8776 (t) REVERT: A 608 PHE cc_start: 0.8491 (t80) cc_final: 0.8233 (t80) REVERT: A 715 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8972 (mm) REVERT: A 749 MET cc_start: 0.9168 (mtm) cc_final: 0.8954 (mtp) REVERT: A 915 MET cc_start: 0.9194 (ttm) cc_final: 0.8870 (tpp) REVERT: C 124 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6973 (ttm110) REVERT: C 173 ASN cc_start: 0.8527 (m110) cc_final: 0.8234 (m-40) REVERT: C 276 MET cc_start: 0.7077 (mtm) cc_final: 0.6762 (mtt) REVERT: C 390 ASP cc_start: 0.6663 (t70) cc_final: 0.6217 (p0) REVERT: C 436 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: C 608 PHE cc_start: 0.8457 (t80) cc_final: 0.8160 (t80) outliers start: 46 outliers final: 24 residues processed: 246 average time/residue: 0.4939 time to fit residues: 143.2675 Evaluate side-chains 219 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 76 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN B 899 GLN A 34 HIS C 34 HIS C 899 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110683 restraints weight = 28311.243| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.09 r_work: 0.3032 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 24051 Z= 0.114 Angle : 0.544 9.738 32832 Z= 0.283 Chirality : 0.043 0.285 3807 Planarity : 0.004 0.050 4122 Dihedral : 5.921 57.615 4398 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.36 % Allowed : 9.54 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.16), residues: 2871 helix: 1.32 (0.22), residues: 594 sheet: -0.83 (0.22), residues: 540 loop : -1.29 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 249 TYR 0.015 0.001 TYR C 636 PHE 0.014 0.001 PHE C 347 TRP 0.010 0.001 TRP C 386 HIS 0.003 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00270 (23967) covalent geometry : angle 0.52996 (32625) SS BOND : bond 0.00437 ( 45) SS BOND : angle 1.94413 ( 90) hydrogen bonds : bond 0.04179 ( 742) hydrogen bonds : angle 4.50907 ( 2055) link_BETA1-4 : bond 0.00449 ( 15) link_BETA1-4 : angle 1.29223 ( 45) link_NAG-ASN : bond 0.00280 ( 24) link_NAG-ASN : angle 1.42388 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.6180 (ttp80) REVERT: B 185 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7824 (mp) REVERT: B 252 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7496 (p0) REVERT: B 338 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7131 (ttt180) REVERT: B 390 ASP cc_start: 0.6680 (t70) cc_final: 0.6270 (p0) REVERT: B 402 ASN cc_start: 0.6152 (OUTLIER) cc_final: 0.5926 (t0) REVERT: B 712 HIS cc_start: 0.8620 (m90) cc_final: 0.8246 (m90) REVERT: A 20 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: A 124 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.7020 (ttp-110) REVERT: A 173 ASN cc_start: 0.8218 (m110) cc_final: 0.7986 (m-40) REVERT: A 185 LEU cc_start: 0.8692 (tp) cc_final: 0.7914 (mp) REVERT: A 276 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6792 (mtm) REVERT: A 281 GLU cc_start: 0.6695 (mp0) cc_final: 0.6403 (mp0) REVERT: A 338 ARG cc_start: 0.7422 (ttt90) cc_final: 0.7142 (tmt-80) REVERT: A 386 TRP cc_start: 0.6266 (p-90) cc_final: 0.5932 (p-90) REVERT: A 402 ASN cc_start: 0.6771 (m-40) cc_final: 0.6457 (p0) REVERT: A 420 THR cc_start: 0.8838 (t) cc_final: 0.8635 (t) REVERT: A 435 TYR cc_start: 0.8771 (m-80) cc_final: 0.8516 (m-80) REVERT: A 749 MET cc_start: 0.9122 (mtm) cc_final: 0.8885 (mtp) REVERT: A 915 MET cc_start: 0.9186 (ttm) cc_final: 0.8878 (tpp) REVERT: C 20 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: C 173 ASN cc_start: 0.8469 (m110) cc_final: 0.8229 (m-40) REVERT: C 276 MET cc_start: 0.7096 (mtm) cc_final: 0.6850 (mtt) REVERT: C 402 ASN cc_start: 0.6631 (m-40) cc_final: 0.6401 (p0) REVERT: C 436 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: C 547 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8718 (mtm) REVERT: C 608 PHE cc_start: 0.8443 (t80) cc_final: 0.8161 (t80) outliers start: 59 outliers final: 27 residues processed: 250 average time/residue: 0.5045 time to fit residues: 147.9025 Evaluate side-chains 226 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 915 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 31 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN A 34 HIS C 34 HIS C 328 ASN C 429 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104093 restraints weight = 28607.578| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.15 r_work: 0.2967 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 24051 Z= 0.195 Angle : 0.630 9.930 32832 Z= 0.324 Chirality : 0.046 0.293 3807 Planarity : 0.004 0.050 4122 Dihedral : 6.119 56.950 4398 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.72 % Allowed : 9.66 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.16), residues: 2871 helix: 1.15 (0.22), residues: 600 sheet: -0.54 (0.23), residues: 507 loop : -1.39 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 249 TYR 0.020 0.002 TYR C 636 PHE 0.021 0.002 PHE C 432 TRP 0.011 0.001 TRP C 386 HIS 0.005 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00469 (23967) covalent geometry : angle 0.61084 (32625) SS BOND : bond 0.00627 ( 45) SS BOND : angle 2.47965 ( 90) hydrogen bonds : bond 0.05364 ( 742) hydrogen bonds : angle 4.65259 ( 2055) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.31652 ( 45) link_NAG-ASN : bond 0.00241 ( 24) link_NAG-ASN : angle 1.72739 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: B 185 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7841 (mp) REVERT: B 252 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7438 (p0) REVERT: B 303 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7724 (mt) REVERT: B 338 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7293 (ttt180) REVERT: B 402 ASN cc_start: 0.6123 (OUTLIER) cc_final: 0.5889 (t0) REVERT: B 712 HIS cc_start: 0.8621 (m90) cc_final: 0.8244 (m90) REVERT: A 20 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: A 124 ARG cc_start: 0.7422 (ttp-110) cc_final: 0.7195 (ttp-110) REVERT: A 173 ASN cc_start: 0.8272 (m110) cc_final: 0.7946 (m-40) REVERT: A 185 LEU cc_start: 0.8727 (tp) cc_final: 0.7946 (mp) REVERT: A 281 GLU cc_start: 0.6798 (mp0) cc_final: 0.6388 (mp0) REVERT: A 338 ARG cc_start: 0.7471 (ttt90) cc_final: 0.7239 (ttt-90) REVERT: A 386 TRP cc_start: 0.6209 (p-90) cc_final: 0.5794 (p-90) REVERT: A 402 ASN cc_start: 0.6792 (m-40) cc_final: 0.6438 (p0) REVERT: A 420 THR cc_start: 0.8866 (t) cc_final: 0.8630 (t) REVERT: C 20 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 124 ARG cc_start: 0.7387 (ttp-110) cc_final: 0.6205 (tpp80) REVERT: C 173 ASN cc_start: 0.8458 (m110) cc_final: 0.8194 (m-40) REVERT: C 303 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7673 (mt) REVERT: C 338 ARG cc_start: 0.7350 (tmt-80) cc_final: 0.6952 (tmt-80) REVERT: C 420 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8596 (t) REVERT: C 436 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.6718 (m-80) REVERT: C 608 PHE cc_start: 0.8493 (t80) cc_final: 0.8248 (t80) outliers start: 68 outliers final: 33 residues processed: 243 average time/residue: 0.4915 time to fit residues: 140.3986 Evaluate side-chains 228 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 848 ASP Chi-restraints excluded: chain C residue 915 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 232 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 264 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 281 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 194 optimal weight: 0.3980 chunk 272 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN B 615 GLN A 34 HIS C 34 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110721 restraints weight = 28382.460| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3021 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 24051 Z= 0.117 Angle : 0.553 9.786 32832 Z= 0.288 Chirality : 0.043 0.290 3807 Planarity : 0.004 0.051 4122 Dihedral : 5.847 57.874 4398 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.16 % Allowed : 10.58 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2871 helix: 1.56 (0.22), residues: 600 sheet: -0.46 (0.23), residues: 507 loop : -1.33 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 249 TYR 0.015 0.001 TYR C 172 PHE 0.016 0.001 PHE C 494 TRP 0.013 0.001 TRP C 115 HIS 0.004 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00274 (23967) covalent geometry : angle 0.54065 (32625) SS BOND : bond 0.00454 ( 45) SS BOND : angle 1.85318 ( 90) hydrogen bonds : bond 0.04330 ( 742) hydrogen bonds : angle 4.47080 ( 2055) link_BETA1-4 : bond 0.00442 ( 15) link_BETA1-4 : angle 1.14564 ( 45) link_NAG-ASN : bond 0.00272 ( 24) link_NAG-ASN : angle 1.45207 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: B 185 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7906 (mp) REVERT: B 252 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 712 HIS cc_start: 0.8629 (m90) cc_final: 0.8271 (m90) REVERT: A 20 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 124 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.7159 (ttp-110) REVERT: A 185 LEU cc_start: 0.8725 (tp) cc_final: 0.8014 (mp) REVERT: A 276 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6993 (mtm) REVERT: A 281 GLU cc_start: 0.6760 (mp0) cc_final: 0.6431 (mp0) REVERT: A 386 TRP cc_start: 0.6348 (p-90) cc_final: 0.5928 (p-90) REVERT: A 402 ASN cc_start: 0.6777 (m-40) cc_final: 0.6554 (p0) REVERT: A 420 THR cc_start: 0.8854 (t) cc_final: 0.8653 (t) REVERT: A 749 MET cc_start: 0.9204 (mtm) cc_final: 0.8839 (mtp) REVERT: A 915 MET cc_start: 0.9221 (ttm) cc_final: 0.8956 (tpp) REVERT: C 20 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: C 115 TRP cc_start: 0.5021 (t-100) cc_final: 0.4792 (t-100) REVERT: C 193 GLN cc_start: 0.8321 (mp-120) cc_final: 0.7803 (mp10) REVERT: C 216 ASP cc_start: 0.7790 (t0) cc_final: 0.7361 (t70) REVERT: C 407 LYS cc_start: 0.8051 (pmtt) cc_final: 0.7597 (tttm) REVERT: C 436 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: C 608 PHE cc_start: 0.8559 (t80) cc_final: 0.8273 (t80) outliers start: 54 outliers final: 29 residues processed: 233 average time/residue: 0.5124 time to fit residues: 140.5856 Evaluate side-chains 226 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 915 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 37 optimal weight: 0.0000 chunk 152 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN B 615 GLN A 34 HIS C 34 HIS C 402 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107891 restraints weight = 28477.113| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.12 r_work: 0.3007 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 24051 Z= 0.134 Angle : 0.565 9.773 32832 Z= 0.293 Chirality : 0.043 0.289 3807 Planarity : 0.004 0.050 4122 Dihedral : 5.792 57.424 4398 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.88 % Allowed : 11.38 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2871 helix: 1.64 (0.22), residues: 600 sheet: -0.49 (0.23), residues: 513 loop : -1.31 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 249 TYR 0.016 0.001 TYR C 636 PHE 0.016 0.001 PHE B 211 TRP 0.012 0.001 TRP A 129 HIS 0.004 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00322 (23967) covalent geometry : angle 0.55096 (32625) SS BOND : bond 0.00627 ( 45) SS BOND : angle 1.97509 ( 90) hydrogen bonds : bond 0.04495 ( 742) hydrogen bonds : angle 4.46686 ( 2055) link_BETA1-4 : bond 0.00401 ( 15) link_BETA1-4 : angle 1.16135 ( 45) link_NAG-ASN : bond 0.00255 ( 24) link_NAG-ASN : angle 1.48689 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: B 124 ARG cc_start: 0.7348 (ttp-110) cc_final: 0.6097 (tpp80) REVERT: B 185 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7861 (mp) REVERT: B 200 ASN cc_start: 0.7892 (t0) cc_final: 0.7692 (t0) REVERT: B 252 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7397 (p0) REVERT: B 276 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6599 (mtm) REVERT: A 20 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: A 124 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7106 (ttp-110) REVERT: A 159 THR cc_start: 0.5419 (OUTLIER) cc_final: 0.5166 (m) REVERT: A 185 LEU cc_start: 0.8708 (tp) cc_final: 0.7919 (mp) REVERT: A 276 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6900 (mtm) REVERT: A 281 GLU cc_start: 0.6719 (mp0) cc_final: 0.6373 (mp0) REVERT: A 386 TRP cc_start: 0.6327 (p-90) cc_final: 0.5942 (p-90) REVERT: A 402 ASN cc_start: 0.6760 (m-40) cc_final: 0.6462 (p0) REVERT: A 420 THR cc_start: 0.8853 (t) cc_final: 0.8637 (t) REVERT: A 749 MET cc_start: 0.9210 (mtm) cc_final: 0.8921 (mtp) REVERT: A 915 MET cc_start: 0.9206 (ttm) cc_final: 0.8921 (tpp) REVERT: C 20 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 124 ARG cc_start: 0.7359 (ttp-110) cc_final: 0.6185 (tpp80) REVERT: C 216 ASP cc_start: 0.7766 (t0) cc_final: 0.7315 (t70) REVERT: C 328 ASN cc_start: 0.8282 (t160) cc_final: 0.8045 (t0) REVERT: C 338 ARG cc_start: 0.7145 (tmt-80) cc_final: 0.6724 (tmt-80) REVERT: C 436 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: C 608 PHE cc_start: 0.8510 (t80) cc_final: 0.8225 (t80) outliers start: 47 outliers final: 32 residues processed: 227 average time/residue: 0.5326 time to fit residues: 142.3650 Evaluate side-chains 238 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 915 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 121 optimal weight: 0.0770 chunk 169 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 232 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 328 ASN B 337 ASN A 34 HIS C 34 HIS C 402 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113040 restraints weight = 28459.742| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.16 r_work: 0.3017 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 24051 Z= 0.105 Angle : 0.532 9.728 32832 Z= 0.277 Chirality : 0.042 0.284 3807 Planarity : 0.004 0.051 4122 Dihedral : 5.613 59.522 4398 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.00 % Allowed : 11.46 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2871 helix: 1.89 (0.22), residues: 603 sheet: -0.37 (0.23), residues: 507 loop : -1.27 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 249 TYR 0.014 0.001 TYR B 636 PHE 0.018 0.001 PHE C 494 TRP 0.012 0.001 TRP C 386 HIS 0.004 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00242 (23967) covalent geometry : angle 0.52167 (32625) SS BOND : bond 0.00443 ( 45) SS BOND : angle 1.58719 ( 90) hydrogen bonds : bond 0.03889 ( 742) hydrogen bonds : angle 4.34592 ( 2055) link_BETA1-4 : bond 0.00442 ( 15) link_BETA1-4 : angle 1.09469 ( 45) link_NAG-ASN : bond 0.00285 ( 24) link_NAG-ASN : angle 1.32603 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: B 185 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 200 ASN cc_start: 0.7947 (t0) cc_final: 0.7722 (t0) REVERT: B 252 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7402 (p0) REVERT: B 276 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6561 (mtm) REVERT: B 296 ARG cc_start: 0.6656 (mtt90) cc_final: 0.5218 (mtm-85) REVERT: B 855 MET cc_start: 0.9235 (mtp) cc_final: 0.8907 (mtp) REVERT: A 20 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: A 159 THR cc_start: 0.5348 (OUTLIER) cc_final: 0.5097 (m) REVERT: A 185 LEU cc_start: 0.8710 (tp) cc_final: 0.7955 (mp) REVERT: A 281 GLU cc_start: 0.6521 (mp0) cc_final: 0.6301 (mp0) REVERT: A 386 TRP cc_start: 0.6296 (p-90) cc_final: 0.5911 (p-90) REVERT: A 402 ASN cc_start: 0.6693 (m-40) cc_final: 0.6489 (p0) REVERT: A 420 THR cc_start: 0.8858 (t) cc_final: 0.8642 (t) REVERT: A 749 MET cc_start: 0.9238 (mtm) cc_final: 0.8926 (mtp) REVERT: A 840 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7422 (tptm) REVERT: A 915 MET cc_start: 0.9245 (ttm) cc_final: 0.8971 (tpp) REVERT: C 20 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: C 124 ARG cc_start: 0.7321 (ttp-110) cc_final: 0.6199 (tpp80) REVERT: C 338 ARG cc_start: 0.7146 (tmt-80) cc_final: 0.6731 (tmt-80) REVERT: C 436 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: C 608 PHE cc_start: 0.8539 (t80) cc_final: 0.8231 (t80) REVERT: C 712 HIS cc_start: 0.8670 (m90) cc_final: 0.8426 (m90) REVERT: C 840 LYS cc_start: 0.7842 (mmpt) cc_final: 0.7306 (tptm) outliers start: 50 outliers final: 29 residues processed: 235 average time/residue: 0.5224 time to fit residues: 144.0684 Evaluate side-chains 233 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 915 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 22 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 337 ASN A 34 HIS C 34 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.106414 restraints weight = 28583.568| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.17 r_work: 0.2947 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 24051 Z= 0.226 Angle : 0.656 9.853 32832 Z= 0.337 Chirality : 0.047 0.290 3807 Planarity : 0.005 0.054 4122 Dihedral : 5.957 57.584 4398 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.84 % Allowed : 11.62 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.16), residues: 2871 helix: 1.32 (0.21), residues: 615 sheet: -0.77 (0.22), residues: 549 loop : -1.36 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 338 TYR 0.025 0.002 TYR C 636 PHE 0.024 0.002 PHE C 432 TRP 0.016 0.002 TRP C 129 HIS 0.005 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00551 (23967) covalent geometry : angle 0.63871 (32625) SS BOND : bond 0.00579 ( 45) SS BOND : angle 2.36710 ( 90) hydrogen bonds : bond 0.05546 ( 742) hydrogen bonds : angle 4.60650 ( 2055) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.28501 ( 45) link_NAG-ASN : bond 0.00220 ( 24) link_NAG-ASN : angle 1.74965 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: B 185 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7942 (mp) REVERT: B 252 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7464 (p0) REVERT: B 276 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6585 (mtm) REVERT: B 296 ARG cc_start: 0.6775 (mtt90) cc_final: 0.5462 (mtm-85) REVERT: A 20 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: A 159 THR cc_start: 0.5487 (OUTLIER) cc_final: 0.5223 (m) REVERT: A 185 LEU cc_start: 0.8733 (tp) cc_final: 0.7988 (mp) REVERT: A 281 GLU cc_start: 0.6811 (mp0) cc_final: 0.6414 (mp0) REVERT: A 386 TRP cc_start: 0.6278 (p-90) cc_final: 0.5918 (p-90) REVERT: A 402 ASN cc_start: 0.6738 (m-40) cc_final: 0.6488 (p0) REVERT: A 420 THR cc_start: 0.8901 (t) cc_final: 0.8675 (t) REVERT: A 808 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: C 20 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 338 ARG cc_start: 0.7478 (tmt-80) cc_final: 0.7135 (tmt-80) REVERT: C 436 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: C 608 PHE cc_start: 0.8562 (t80) cc_final: 0.8341 (t80) outliers start: 46 outliers final: 29 residues processed: 228 average time/residue: 0.5176 time to fit residues: 139.1332 Evaluate side-chains 229 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 808 GLN Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 915 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 286 optimal weight: 0.3980 chunk 267 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 214 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 203 optimal weight: 0.0670 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 200 ASN B 337 ASN A 34 HIS A 852 ASN C 34 HIS C 852 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112527 restraints weight = 28348.375| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.08 r_work: 0.3066 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 24051 Z= 0.103 Angle : 0.537 9.730 32832 Z= 0.280 Chirality : 0.043 0.286 3807 Planarity : 0.004 0.051 4122 Dihedral : 5.604 58.886 4398 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.36 % Allowed : 12.30 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2871 helix: 1.92 (0.22), residues: 603 sheet: -0.38 (0.23), residues: 516 loop : -1.26 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 124 TYR 0.020 0.001 TYR C 636 PHE 0.016 0.001 PHE B 211 TRP 0.013 0.001 TRP C 129 HIS 0.003 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00236 (23967) covalent geometry : angle 0.52813 (32625) SS BOND : bond 0.00417 ( 45) SS BOND : angle 1.48083 ( 90) hydrogen bonds : bond 0.03828 ( 742) hydrogen bonds : angle 4.35401 ( 2055) link_BETA1-4 : bond 0.00488 ( 15) link_BETA1-4 : angle 1.06153 ( 45) link_NAG-ASN : bond 0.00300 ( 24) link_NAG-ASN : angle 1.29138 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8340.73 seconds wall clock time: 142 minutes 26.97 seconds (8546.97 seconds total)