Starting phenix.real_space_refine on Sat Feb 7 00:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr8_62522/02_2026/9kr8_62522.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr8_62522/02_2026/9kr8_62522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kr8_62522/02_2026/9kr8_62522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr8_62522/02_2026/9kr8_62522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kr8_62522/02_2026/9kr8_62522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr8_62522/02_2026/9kr8_62522.map" } resolution = 2.39 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= -0.001 sd= 0.168 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 150 5.16 5 C 17961 2.51 5 N 4551 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28356 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 9036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9036 Classifications: {'peptide': 1163} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1105} Chain breaks: 2 Chain: "B" Number of atoms: 9036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9036 Classifications: {'peptide': 1163} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1105} Chain breaks: 2 Chain: "C" Number of atoms: 9036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9036 Classifications: {'peptide': 1163} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1105} Chain breaks: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {'NAG': 11, 'OLA': 1, 'PLM': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {'NAG': 11, 'OLA': 1, 'PLM': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {'NAG': 11, 'OLA': 1, 'PLM': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.14, per 1000 atoms: 0.25 Number of scatterers: 28356 At special positions: 0 Unit cell: (153.267, 153.267, 170.659, 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 150 16.00 O 5694 8.00 N 4551 7.00 C 17961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 222 " distance=2.04 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 357 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 583 " distance=2.04 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 532 " distance=2.04 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 648 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 733 " distance=2.02 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 825 " distance=2.04 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 814 " distance=2.05 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 922 " distance=2.04 Simple disulfide: pdb=" SG CYS A1103 " - pdb=" SG CYS A1114 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 222 " distance=2.04 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 357 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 486 " distance=2.04 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 583 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 652 " distance=2.04 Simple disulfide: pdb=" SG CYS B 618 " - pdb=" SG CYS B 648 " distance=2.04 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 825 " distance=2.04 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 814 " distance=2.05 Simple disulfide: pdb=" SG CYS B 909 " - pdb=" SG CYS B 922 " distance=2.04 Simple disulfide: pdb=" SG CYS B1103 " - pdb=" SG CYS B1114 " distance=2.04 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 245 " distance=2.04 Simple disulfide: pdb=" SG CYS C 347 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 486 " distance=2.04 Simple disulfide: pdb=" SG CYS C 445 " - pdb=" SG CYS C 583 " distance=2.04 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 532 " distance=2.04 Simple disulfide: pdb=" SG CYS C 601 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS C 618 " - pdb=" SG CYS C 648 " distance=2.04 Simple disulfide: pdb=" SG CYS C 677 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 733 " distance=2.04 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 825 " distance=2.04 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 814 " distance=2.05 Simple disulfide: pdb=" SG CYS C 909 " - pdb=" SG CYS C 922 " distance=2.04 Simple disulfide: pdb=" SG CYS C1103 " - pdb=" SG CYS C1114 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A3002 " - " ASN A 73 " " NAG A3003 " - " ASN A 111 " " NAG A3004 " - " ASN A 132 " " NAG A3005 " - " ASN A 167 " " NAG A3006 " - " ASN A 244 " " NAG A3007 " - " ASN A 495 " " NAG A3008 " - " ASN A 590 " " NAG A3009 " - " ASN A 617 " " NAG A3010 " - " ASN A 716 " " NAG A3011 " - " ASN A 760 " " NAG A3012 " - " ASN A 771 " " NAG B2003 " - " ASN B 73 " " NAG B2004 " - " ASN B 111 " " NAG B2005 " - " ASN B 132 " " NAG B2006 " - " ASN B 167 " " NAG B2007 " - " ASN B 244 " " NAG B2008 " - " ASN B 495 " " NAG B2009 " - " ASN B 590 " " NAG B2010 " - " ASN B 617 " " NAG B2011 " - " ASN B 716 " " NAG B2012 " - " ASN B 760 " " NAG B2013 " - " ASN B 771 " " NAG C2003 " - " ASN C 73 " " NAG C2004 " - " ASN C 111 " " NAG C2005 " - " ASN C 132 " " NAG C2006 " - " ASN C 167 " " NAG C2007 " - " ASN C 244 " " NAG C2008 " - " ASN C 495 " " NAG C2009 " - " ASN C 590 " " NAG C2010 " - " ASN C 617 " " NAG C2011 " - " ASN C 716 " " NAG C2012 " - " ASN C 760 " " NAG C2013 " - " ASN C 771 " " NAG D 1 " - " ASN A 174 " " NAG E 1 " - " ASN A 250 " " NAG F 1 " - " ASN A 418 " " NAG G 1 " - " ASN A 782 " " NAG H 1 " - " ASN A 867 " " NAG I 1 " - " ASN A1145 " " NAG J 1 " - " ASN A1172 " " NAG K 1 " - " ASN A1214 " " NAG L 1 " - " ASN B 174 " " NAG M 1 " - " ASN B 250 " " NAG N 1 " - " ASN B 418 " " NAG O 1 " - " ASN B 782 " " NAG P 1 " - " ASN B 867 " " NAG Q 1 " - " ASN B1145 " " NAG R 1 " - " ASN B1172 " " NAG S 1 " - " ASN B1214 " " NAG T 1 " - " ASN C 174 " " NAG U 1 " - " ASN C 250 " " NAG V 1 " - " ASN C 418 " " NAG W 1 " - " ASN C 782 " " NAG X 1 " - " ASN C 867 " " NAG Y 1 " - " ASN C1145 " " NAG Z 1 " - " ASN C1172 " " NAG a 1 " - " ASN C1214 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 56 sheets defined 25.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.836A pdb=" N PHE A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 45 " --> pdb=" O PRO A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.808A pdb=" N TYR A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 457 through 465 removed outlier: 5.349A pdb=" N SER A 462 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.720A pdb=" N GLN A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.522A pdb=" N LEU A 588 " --> pdb=" O MET A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 802 through 809 Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 821 through 848 removed outlier: 3.508A pdb=" N LYS A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 828 " --> pdb=" O PHE A 824 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 829 " --> pdb=" O CYS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 removed outlier: 3.750A pdb=" N THR A 852 " --> pdb=" O SER A 849 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 853 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 853' Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 885 through 893 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.648A pdb=" N VAL A 926 " --> pdb=" O CYS A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 951 Processing helix chain 'A' and resid 968 through 979 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 990 through 1003 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.879A pdb=" N THR A1007 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1036 removed outlier: 3.718A pdb=" N LEU A1030 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A1036 " --> pdb=" O LYS A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1039 No H-bonds generated for 'chain 'A' and resid 1037 through 1039' Processing helix chain 'A' and resid 1047 through 1055 removed outlier: 3.564A pdb=" N ILE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1104 removed outlier: 3.705A pdb=" N ALA A1062 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A1067 " --> pdb=" O GLN A1063 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.956A pdb=" N TYR B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 457 through 465 removed outlier: 5.455A pdb=" N SER B 462 " --> pdb=" O ASP B 459 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 476 removed outlier: 3.609A pdb=" N GLN B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.517A pdb=" N LEU B 588 " --> pdb=" O MET B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.568A pdb=" N VAL B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 681' Processing helix chain 'B' and resid 802 through 809 Processing helix chain 'B' and resid 811 through 819 Processing helix chain 'B' and resid 821 through 848 removed outlier: 3.515A pdb=" N LYS B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 829 " --> pdb=" O CYS B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.743A pdb=" N THR B 852 " --> pdb=" O SER B 849 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 853 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 849 through 853' Processing helix chain 'B' and resid 885 through 893 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 922 through 928 removed outlier: 3.788A pdb=" N VAL B 926 " --> pdb=" O CYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 951 removed outlier: 3.510A pdb=" N GLU B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 Processing helix chain 'B' and resid 983 through 990 Processing helix chain 'B' and resid 990 through 1003 Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1013 through 1036 removed outlier: 3.674A pdb=" N LEU B1030 " --> pdb=" O ASN B1026 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B1036 " --> pdb=" O LYS B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1039 No H-bonds generated for 'chain 'B' and resid 1037 through 1039' Processing helix chain 'B' and resid 1047 through 1055 removed outlier: 3.554A pdb=" N ILE B1051 " --> pdb=" O SER B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1104 removed outlier: 3.777A pdb=" N ALA B1062 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B1066 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B1067 " --> pdb=" O GLN B1063 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 230 through 239 removed outlier: 3.948A pdb=" N TYR C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.521A pdb=" N LEU C 425 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 426 " --> pdb=" O LEU C 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 426' Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 457 through 465 removed outlier: 5.455A pdb=" N SER C 462 " --> pdb=" O ASP C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 removed outlier: 3.642A pdb=" N GLN C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 802 through 809 Processing helix chain 'C' and resid 811 through 819 Processing helix chain 'C' and resid 821 through 848 removed outlier: 3.668A pdb=" N LYS C 827 " --> pdb=" O GLN C 823 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 828 " --> pdb=" O PHE C 824 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 829 " --> pdb=" O CYS C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 853 removed outlier: 3.671A pdb=" N THR C 852 " --> pdb=" O SER C 849 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 853 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 849 through 853' Processing helix chain 'C' and resid 885 through 893 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 922 through 928 removed outlier: 3.831A pdb=" N VAL C 926 " --> pdb=" O CYS C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 removed outlier: 3.505A pdb=" N GLU C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 979 Processing helix chain 'C' and resid 983 through 990 Processing helix chain 'C' and resid 990 through 1003 Processing helix chain 'C' and resid 1004 through 1009 removed outlier: 3.538A pdb=" N THR C1007 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1036 removed outlier: 3.731A pdb=" N LEU C1030 " --> pdb=" O ASN C1026 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1039 No H-bonds generated for 'chain 'C' and resid 1037 through 1039' Processing helix chain 'C' and resid 1047 through 1055 Processing helix chain 'C' and resid 1056 through 1104 removed outlier: 3.760A pdb=" N ALA C1062 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C1066 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C1067 " --> pdb=" O GLN C1063 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C1084 " --> pdb=" O ALA C1080 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C1094 " --> pdb=" O ALA C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1224 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.856A pdb=" N VAL A 63 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N HIS A 288 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 273 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 291 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 271 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TRP A 261 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 4.015A pdb=" N LYS A 343 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.659A pdb=" N GLY A 135 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 317 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 367 through 374 removed outlier: 4.480A pdb=" N VAL A 657 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER A 373 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 655 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 673 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA9, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.644A pdb=" N SER A 448 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 485 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 433 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A 487 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 431 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 489 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 415 through 416 removed outlier: 6.576A pdb=" N CYS A 415 " --> pdb=" O CYS A 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.530A pdb=" N THR A 555 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS A 511 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 553 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 545 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 601 through 606 removed outlier: 4.726A pdb=" N VAL A 637 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 629 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 721 removed outlier: 3.794A pdb=" N SER A 717 " --> pdb=" O ILE A 756 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 758 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET A 719 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1118 through 1127 removed outlier: 6.095A pdb=" N HIS A1119 " --> pdb=" O TYR A1138 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A1138 " --> pdb=" O HIS A1119 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR A1147 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A1169 " --> pdb=" O ALA A1149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1127 removed outlier: 6.095A pdb=" N HIS A1119 " --> pdb=" O TYR A1138 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A1138 " --> pdb=" O HIS A1119 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 782 " --> pdb=" O THR A1141 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS A1143 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN A1145 " --> pdb=" O ALA A 778 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA A 778 " --> pdb=" O ASN A1145 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A1147 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 776 " --> pdb=" O THR A1147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 798 through 801 removed outlier: 4.578A pdb=" N LYS A 798 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AB9, first strand: chain 'A' and resid 964 through 965 removed outlier: 6.978A pdb=" N VAL B 776 " --> pdb=" O THR B1147 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1147 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 778 " --> pdb=" O ASN B1145 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1145 " --> pdb=" O ALA B 778 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS B1143 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 782 " --> pdb=" O THR B1141 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B1138 " --> pdb=" O HIS B1119 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N HIS B1119 " --> pdb=" O TYR B1138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 964 through 965 removed outlier: 6.978A pdb=" N VAL B 776 " --> pdb=" O THR B1147 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1147 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 778 " --> pdb=" O ASN B1145 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1145 " --> pdb=" O ALA B 778 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS B1143 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 782 " --> pdb=" O THR B1141 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR B1147 " --> pdb=" O LEU B1171 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B1169 " --> pdb=" O ALA B1149 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY B1189 " --> pdb=" O HIS B1194 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B1194 " --> pdb=" O GLY B1189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1203 through 1206 removed outlier: 4.348A pdb=" N CYS A1161 " --> pdb=" O VAL A1206 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.867A pdb=" N VAL B 63 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N HIS B 288 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 273 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 291 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 271 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TRP B 261 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 260 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 74 through 82 removed outlier: 4.058A pdb=" N LYS B 343 " --> pdb=" O ASN B 334 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 117 through 118 removed outlier: 6.419A pdb=" N LEU B 188 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 249 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 190 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 247 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR B 192 " --> pdb=" O CYS B 245 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 245 " --> pdb=" O TYR B 192 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'B' and resid 214 through 216 removed outlier: 6.305A pdb=" N LEU B 214 " --> pdb=" O SER B 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 222 through 223 removed outlier: 4.347A pdb=" N VAL B 223 " --> pdb=" O SER B 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 367 through 371 removed outlier: 4.390A pdb=" N VAL B 657 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AD2, first strand: chain 'B' and resid 408 through 412 removed outlier: 3.664A pdb=" N SER B 448 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 430 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 491 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL B 428 " --> pdb=" O THR B 491 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 415 through 416 removed outlier: 6.622A pdb=" N CYS B 415 " --> pdb=" O CYS B 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.516A pdb=" N THR B 555 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS B 511 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR B 553 " --> pdb=" O CYS B 511 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 545 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 601 through 606 removed outlier: 4.460A pdb=" N TYR B 646 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 637 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 629 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 714 through 721 removed outlier: 6.972A pdb=" N PHE B 754 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER B 717 " --> pdb=" O PHE B 754 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 756 " --> pdb=" O SER B 717 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N MET B 719 " --> pdb=" O ILE B 756 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 799 through 801 Processing sheet with id=AD8, first strand: chain 'B' and resid 862 through 863 Processing sheet with id=AD9, first strand: chain 'B' and resid 964 through 965 removed outlier: 6.386A pdb=" N SER C1142 " --> pdb=" O THR C 781 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE C 783 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE C 785 " --> pdb=" O TYR C1138 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR C1138 " --> pdb=" O PHE C 785 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 787 " --> pdb=" O VAL C1136 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C1136 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN C 789 " --> pdb=" O PHE C1134 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE C1134 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE C 791 " --> pdb=" O TYR C1132 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1132 " --> pdb=" O PHE C 791 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU C 793 " --> pdb=" O GLY C1130 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY C1130 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY C1130 " --> pdb=" O ASN C1126 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN C1126 " --> pdb=" O GLY C1130 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR C1132 " --> pdb=" O ALA C1124 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA C1124 " --> pdb=" O TYR C1132 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE C1134 " --> pdb=" O SER C1122 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C1122 " --> pdb=" O PHE C1134 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C1136 " --> pdb=" O ILE C1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 964 through 965 removed outlier: 6.386A pdb=" N SER C1142 " --> pdb=" O THR C 781 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE C 783 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE C 785 " --> pdb=" O TYR C1138 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR C1138 " --> pdb=" O PHE C 785 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 787 " --> pdb=" O VAL C1136 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C1136 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN C 789 " --> pdb=" O PHE C1134 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE C1134 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE C 791 " --> pdb=" O TYR C1132 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1132 " --> pdb=" O PHE C 791 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU C 793 " --> pdb=" O GLY C1130 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY C1130 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE C1169 " --> pdb=" O ALA C1149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1152 through 1153 Processing sheet with id=AE3, first strand: chain 'B' and resid 1161 through 1164 removed outlier: 4.175A pdb=" N CYS B1161 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.812A pdb=" N VAL C 63 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N HIS C 288 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C 291 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 271 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TRP C 261 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 260 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 74 through 82 removed outlier: 4.055A pdb=" N LYS C 343 " --> pdb=" O ASN C 334 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.617A pdb=" N ALA C 100 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AE8, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AE9, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'C' and resid 214 through 216 removed outlier: 6.304A pdb=" N LEU C 214 " --> pdb=" O SER C 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 367 through 371 removed outlier: 4.406A pdb=" N VAL C 657 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.556A pdb=" N GLY C 399 " --> pdb=" O THR C 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.604A pdb=" N SER C 448 " --> pdb=" O GLN C 574 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 430 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR C 491 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL C 428 " --> pdb=" O THR C 491 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 415 through 416 removed outlier: 6.459A pdb=" N CYS C 415 " --> pdb=" O CYS C 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.585A pdb=" N THR C 555 " --> pdb=" O THR C 509 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS C 511 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 553 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 545 " --> pdb=" O GLY C 556 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 601 through 606 removed outlier: 4.647A pdb=" N VAL C 637 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL C 629 " --> pdb=" O VAL C 637 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 714 through 721 removed outlier: 6.678A pdb=" N PHE C 754 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER C 717 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE C 756 " --> pdb=" O SER C 717 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N MET C 719 " --> pdb=" O ILE C 756 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 799 through 801 Processing sheet with id=AG1, first strand: chain 'C' and resid 862 through 863 Processing sheet with id=AG2, first strand: chain 'C' and resid 1161 through 1164 removed outlier: 4.232A pdb=" N CYS C1161 " --> pdb=" O VAL C1206 " (cutoff:3.500A) 1091 hydrogen bonds defined for protein. 2904 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: 6.87 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7006 1.33 - 1.46: 8488 1.46 - 1.59: 13312 1.59 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 29007 Sorted by residual: bond pdb=" C ILE B 64 " pdb=" N TYR B 65 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.09e+01 bond pdb=" N ASN C 174 " pdb=" CA ASN C 174 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.91e+00 bond pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.70e+00 bond pdb=" CB PHE B 382 " pdb=" CG PHE B 382 " ideal model delta sigma weight residual 1.502 1.566 -0.064 2.30e-02 1.89e+03 7.65e+00 bond pdb=" C1 NAG A3012 " pdb=" O5 NAG A3012 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 ... (remaining 29002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 38584 2.89 - 5.77: 770 5.77 - 8.66: 98 8.66 - 11.55: 18 11.55 - 14.43: 7 Bond angle restraints: 39477 Sorted by residual: angle pdb=" N THR A 497 " pdb=" CA THR A 497 " pdb=" C THR A 497 " ideal model delta sigma weight residual 108.96 122.65 -13.69 1.49e+00 4.50e-01 8.44e+01 angle pdb=" C THR A 497 " pdb=" N THR A 498 " pdb=" CA THR A 498 " ideal model delta sigma weight residual 122.54 136.97 -14.43 1.65e+00 3.67e-01 7.65e+01 angle pdb=" N GLN B 494 " pdb=" CA GLN B 494 " pdb=" C GLN B 494 " ideal model delta sigma weight residual 111.71 119.72 -8.01 1.15e+00 7.56e-01 4.85e+01 angle pdb=" N ASN A 495 " pdb=" CA ASN A 495 " pdb=" C ASN A 495 " ideal model delta sigma weight residual 113.50 121.99 -8.49 1.23e+00 6.61e-01 4.76e+01 angle pdb=" C GLN C 853 " pdb=" N ASN C 854 " pdb=" CA ASN C 854 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 ... (remaining 39472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 16188 17.88 - 35.75: 1385 35.75 - 53.63: 505 53.63 - 71.50: 179 71.50 - 89.38: 61 Dihedral angle restraints: 18318 sinusoidal: 8100 harmonic: 10218 Sorted by residual: dihedral pdb=" CA GLN B 201 " pdb=" C GLN B 201 " pdb=" N ASN B 202 " pdb=" CA ASN B 202 " ideal model delta harmonic sigma weight residual -180.00 -121.91 -58.09 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA GLN A 201 " pdb=" C GLN A 201 " pdb=" N ASN A 202 " pdb=" CA ASN A 202 " ideal model delta harmonic sigma weight residual -180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA GLN C 201 " pdb=" C GLN C 201 " pdb=" N ASN C 202 " pdb=" CA ASN C 202 " ideal model delta harmonic sigma weight residual 180.00 -125.90 -54.10 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 18315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4651 0.305 - 0.610: 6 0.610 - 0.915: 0 0.915 - 1.220: 0 1.220 - 1.525: 2 Chirality restraints: 4659 Sorted by residual: chirality pdb=" C1 NAG B2008 " pdb=" ND2 ASN B 495 " pdb=" C2 NAG B2008 " pdb=" O5 NAG B2008 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb=" C1 NAG A3007 " pdb=" ND2 ASN A 495 " pdb=" C2 NAG A3007 " pdb=" O5 NAG A3007 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.53e+01 chirality pdb=" CA ASN C 495 " pdb=" N ASN C 495 " pdb=" C ASN C 495 " pdb=" CB ASN C 495 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 4656 not shown) Planarity restraints: 5061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 495 " 0.145 2.00e-02 2.50e+03 2.54e-01 8.08e+02 pdb=" CG ASN A 495 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 495 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 495 " -0.449 2.00e-02 2.50e+03 pdb=" C1 NAG A3007 " 0.293 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 495 " 0.132 2.00e-02 2.50e+03 2.00e-01 4.99e+02 pdb=" CG ASN B 495 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN B 495 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN B 495 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG B2008 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 495 " -0.028 2.00e-02 2.50e+03 7.50e-02 7.03e+01 pdb=" CG ASN C 495 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN C 495 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN C 495 " 0.135 2.00e-02 2.50e+03 pdb=" C1 NAG C2008 " -0.082 2.00e-02 2.50e+03 ... (remaining 5058 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 329 2.63 - 3.20: 22288 3.20 - 3.76: 42173 3.76 - 4.33: 61481 4.33 - 4.90: 98760 Nonbonded interactions: 225031 Sorted by model distance: nonbonded pdb=" O LEU B 496 " pdb=" OG1 THR B 497 " model vdw 2.062 3.040 nonbonded pdb=" O LEU C 496 " pdb=" OG1 THR C 497 " model vdw 2.082 3.040 nonbonded pdb=" O PRO A 83 " pdb=" OH TYR A 331 " model vdw 2.222 3.040 nonbonded pdb=" O THR B 400 " pdb=" CF PLM B2002 " model vdw 2.234 3.440 nonbonded pdb=" O GLU A 793 " pdb=" OG SER A1092 " model vdw 2.235 3.040 ... (remaining 225026 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 1228 or resid 3003 through 3012)) selection = (chain 'B' and (resid 39 through 1228 or resid 2003 through 2012)) selection = (chain 'C' and (resid 39 through 1228 or resid 2003 through 2012)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.240 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 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 : 0.009 0.153 29133 Z= 0.384 Angle : 1.138 44.874 39810 Z= 0.606 Chirality : 0.070 1.525 4659 Planarity : 0.008 0.078 5004 Dihedral : 16.882 89.378 11649 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.93 % Favored : 93.52 % Rotamer: Outliers : 10.13 % Allowed : 9.50 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.12), residues: 3471 helix: -1.79 (0.15), residues: 771 sheet: 0.18 (0.18), residues: 705 loop : -2.06 (0.12), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1085 TYR 0.033 0.003 TYR B 417 PHE 0.031 0.004 PHE A 382 TRP 0.021 0.002 TRP B 957 HIS 0.010 0.002 HIS C1135 Details of bonding type rmsd covalent geometry : bond 0.00846 (29007) covalent geometry : angle 1.06320 (39477) SS BOND : bond 0.00782 ( 45) SS BOND : angle 2.20529 ( 90) hydrogen bonds : bond 0.15805 ( 1025) hydrogen bonds : angle 6.57356 ( 2904) link_BETA1-4 : bond 0.00787 ( 24) link_BETA1-4 : angle 3.40823 ( 72) link_NAG-ASN : bond 0.02375 ( 57) link_NAG-ASN : angle 5.76495 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 305 poor density : 304 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.5809 (p0) REVERT: A 90 LYS cc_start: 0.7457 (tttt) cc_final: 0.7232 (tttp) REVERT: A 93 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6186 (mm) REVERT: A 196 HIS cc_start: 0.6931 (t70) cc_final: 0.6710 (t-170) REVERT: A 210 LYS cc_start: 0.2907 (OUTLIER) cc_final: 0.2509 (tppt) REVERT: A 230 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: A 239 TYR cc_start: 0.7429 (m-80) cc_final: 0.7089 (m-80) REVERT: A 243 ILE cc_start: 0.7867 (mt) cc_final: 0.7625 (mm) REVERT: A 282 PHE cc_start: 0.7905 (m-80) cc_final: 0.7535 (m-80) REVERT: A 396 MET cc_start: 0.8214 (ttp) cc_final: 0.7908 (ttm) REVERT: A 408 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6129 (mmmm) REVERT: A 421 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6687 (pttt) REVERT: A 446 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6781 (p90) REVERT: A 473 VAL cc_start: 0.7677 (t) cc_final: 0.7426 (p) REVERT: A 510 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6327 (mm-30) REVERT: A 585 MET cc_start: 0.7546 (mtt) cc_final: 0.6906 (mtt) REVERT: A 597 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7238 (pttp) REVERT: A 723 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: A 776 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7725 (p) REVERT: A 805 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6824 (tp40) REVERT: A 827 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6133 (mmtm) REVERT: A 848 SER cc_start: 0.7339 (OUTLIER) cc_final: 0.6812 (p) REVERT: A 870 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6968 (mmt) REVERT: A 884 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7513 (mtt-85) REVERT: A 903 MET cc_start: 0.7641 (ttp) cc_final: 0.7369 (ttm) REVERT: A 1000 GLN cc_start: 0.6695 (tt0) cc_final: 0.6426 (mt0) REVERT: A 1006 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: A 1028 MET cc_start: 0.6263 (tpt) cc_final: 0.5953 (tpp) REVERT: A 1031 SER cc_start: 0.7672 (m) cc_final: 0.7177 (p) REVERT: A 1059 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5884 (mm-30) REVERT: A 1095 LEU cc_start: 0.6321 (tp) cc_final: 0.5574 (mt) REVERT: A 1097 GLN cc_start: 0.6738 (tt0) cc_final: 0.6308 (tp40) REVERT: A 1166 ASP cc_start: 0.6895 (m-30) cc_final: 0.6685 (t0) REVERT: A 1180 ASP cc_start: 0.4532 (OUTLIER) cc_final: 0.3897 (t70) REVERT: A 1208 MET cc_start: 0.6875 (tmm) cc_final: 0.6616 (tmm) REVERT: B 59 LYS cc_start: 0.7291 (mtmt) cc_final: 0.7013 (mtpp) REVERT: B 108 PHE cc_start: -0.0053 (OUTLIER) cc_final: -0.0302 (t80) REVERT: B 230 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6053 (mt-10) REVERT: B 248 ARG cc_start: 0.7278 (mtt90) cc_final: 0.7069 (mtt90) REVERT: B 267 ASP cc_start: 0.6825 (p0) cc_final: 0.6569 (p0) REVERT: B 408 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6174 (mmmt) REVERT: B 446 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.5600 (p90) REVERT: B 510 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6108 (mm-30) REVERT: B 570 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6449 (mm) REVERT: B 624 ARG cc_start: 0.6206 (ptm160) cc_final: 0.5644 (ttt180) REVERT: B 625 ASN cc_start: 0.7295 (m-40) cc_final: 0.7079 (m-40) REVERT: B 712 MET cc_start: 0.7613 (mmm) cc_final: 0.6850 (mpt) REVERT: B 715 ILE cc_start: 0.8064 (tt) cc_final: 0.7863 (pt) REVERT: B 719 MET cc_start: 0.7240 (ttt) cc_final: 0.6847 (ttm) REVERT: B 790 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: B 812 LYS cc_start: 0.6706 (mttm) cc_final: 0.6384 (mttm) REVERT: B 883 TYR cc_start: 0.7337 (m-10) cc_final: 0.7091 (m-10) REVERT: B 941 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6227 (mp0) REVERT: B 992 LYS cc_start: 0.6602 (mtpt) cc_final: 0.6399 (mmmt) REVERT: B 1000 GLN cc_start: 0.7145 (pt0) cc_final: 0.6910 (pt0) REVERT: B 1011 THR cc_start: 0.8421 (p) cc_final: 0.8044 (m) REVERT: B 1061 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: B 1066 ARG cc_start: 0.6959 (mtt-85) cc_final: 0.6652 (mtp85) REVERT: B 1208 MET cc_start: 0.7430 (tmm) cc_final: 0.6897 (tmt) REVERT: C 42 ASP cc_start: 0.3255 (OUTLIER) cc_final: 0.2900 (t70) REVERT: C 59 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6684 (mmtm) REVERT: C 90 LYS cc_start: 0.6963 (tttt) cc_final: 0.6596 (tmtt) REVERT: C 121 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: C 133 LYS cc_start: 0.2459 (OUTLIER) cc_final: 0.1497 (mmtt) REVERT: C 163 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5533 (t80) REVERT: C 187 ILE cc_start: 0.7968 (mm) cc_final: 0.7619 (tp) REVERT: C 221 ASP cc_start: 0.3528 (OUTLIER) cc_final: 0.3290 (m-30) REVERT: C 237 LYS cc_start: 0.7485 (mttt) cc_final: 0.7276 (mttm) REVERT: C 282 PHE cc_start: 0.7791 (m-80) cc_final: 0.7499 (m-80) REVERT: C 446 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6904 (p90) REVERT: C 592 THR cc_start: 0.6903 (OUTLIER) cc_final: 0.6613 (p) REVERT: C 805 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6617 (tp40) REVERT: C 812 LYS cc_start: 0.6725 (mttm) cc_final: 0.6488 (tmmt) REVERT: C 823 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6088 (mm110) REVERT: C 853 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.4412 (tm-30) REVERT: C 884 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7582 (mtt180) REVERT: C 948 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6932 (mp) REVERT: C 972 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7842 (m) REVERT: C 991 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: C 1028 MET cc_start: 0.6497 (tpt) cc_final: 0.6281 (tpp) REVERT: C 1059 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5971 (mt-10) REVERT: C 1061 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6129 (tp30) REVERT: C 1063 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7765 (mm110) REVERT: C 1087 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5822 (mm-30) REVERT: C 1097 GLN cc_start: 0.6491 (tt0) cc_final: 0.6048 (tt0) REVERT: C 1196 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7282 (pt0) outliers start: 305 outliers final: 130 residues processed: 561 average time/residue: 0.6612 time to fit residues: 433.9041 Evaluate side-chains 428 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 255 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain A residue 884 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1154 ASN Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 LYS Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1092 SER Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1182 ASP Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 805 GLN Chi-restraints excluded: chain C residue 809 ASN Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 884 ARG Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1063 GLN Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1171 LEU Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain C residue 1224 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 285 ASN A 354 GLN A 414 ASN A 574 GLN A 809 ASN A 853 GLN A 856 GLN A 875 GLN A 911 GLN A1006 GLN A1063 GLN A1082 GLN A1107 GLN A1111 ASN A1154 ASN A1183 GLN A1217 ASN B 86 ASN B 285 ASN B 327 HIS B 354 GLN B 385 GLN B 414 ASN B 666 ASN B 805 GLN B 809 ASN B 856 GLN B 912 GLN B 915 GLN B 990 ASN B1039 ASN B1063 GLN B1082 GLN B1111 ASN B1154 ASN B1159 GLN B1183 GLN C 40 GLN C 48 HIS C 91 GLN C 285 ASN C 288 HIS C 354 GLN C 385 GLN C 414 ASN C 416 ASN C 574 GLN C 640 HIS C 809 ASN C 839 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 GLN C 904 GLN C 911 GLN C 915 GLN C 978 ASN C1039 ASN C1082 GLN C1107 GLN C1154 ASN C1173 GLN C1183 GLN C1217 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112200 restraints weight = 28479.935| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.51 r_work: 0.3158 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29133 Z= 0.210 Angle : 0.783 13.090 39810 Z= 0.409 Chirality : 0.049 0.278 4659 Planarity : 0.006 0.057 5004 Dihedral : 12.731 86.424 5907 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.79 % Favored : 93.98 % Rotamer: Outliers : 7.37 % Allowed : 12.75 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3471 helix: -0.21 (0.18), residues: 756 sheet: 0.24 (0.17), residues: 771 loop : -1.72 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 379 TYR 0.023 0.002 TYR B1138 PHE 0.028 0.002 PHE B 119 TRP 0.019 0.002 TRP A 957 HIS 0.007 0.001 HIS C1135 Details of bonding type rmsd covalent geometry : bond 0.00480 (29007) covalent geometry : angle 0.74632 (39477) SS BOND : bond 0.00572 ( 45) SS BOND : angle 1.86891 ( 90) hydrogen bonds : bond 0.07428 ( 1025) hydrogen bonds : angle 5.68561 ( 2904) link_BETA1-4 : bond 0.00447 ( 24) link_BETA1-4 : angle 1.87139 ( 72) link_NAG-ASN : bond 0.00587 ( 57) link_NAG-ASN : angle 3.28986 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 271 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7137 (p0) REVERT: A 210 LYS cc_start: 0.3013 (OUTLIER) cc_final: 0.2529 (tppt) REVERT: A 230 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 239 TYR cc_start: 0.7938 (m-80) cc_final: 0.7587 (m-80) REVERT: A 278 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6580 (pttt) REVERT: A 282 PHE cc_start: 0.8248 (m-80) cc_final: 0.7907 (m-80) REVERT: A 379 ARG cc_start: 0.7034 (mtt90) cc_final: 0.6816 (mtt-85) REVERT: A 421 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7397 (pttt) REVERT: A 446 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8035 (p90) REVERT: A 460 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8952 (mtp) REVERT: A 496 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 510 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8143 (mm-30) REVERT: A 585 MET cc_start: 0.8556 (mtt) cc_final: 0.8148 (mtt) REVERT: A 818 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 819 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8532 (mtpt) REVERT: A 839 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: A 859 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7916 (mm-40) REVERT: A 884 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7988 (mtt-85) REVERT: A 1000 GLN cc_start: 0.8186 (tt0) cc_final: 0.7947 (mt0) REVERT: A 1059 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 1081 GLN cc_start: 0.8779 (tt0) cc_final: 0.8579 (tm-30) REVERT: A 1095 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 1097 GLN cc_start: 0.8918 (tt0) cc_final: 0.8714 (tp40) REVERT: A 1166 ASP cc_start: 0.8209 (m-30) cc_final: 0.7929 (t0) REVERT: A 1180 ASP cc_start: 0.3696 (OUTLIER) cc_final: 0.3331 (t70) REVERT: B 59 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8134 (mtpm) REVERT: B 173 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7719 (pp) REVERT: B 230 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: B 390 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: B 408 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8616 (mmmt) REVERT: B 446 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.7351 (p90) REVERT: B 510 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8049 (mm-30) REVERT: B 570 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8606 (mm) REVERT: B 593 SER cc_start: 0.8459 (t) cc_final: 0.8046 (p) REVERT: B 624 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7470 (ttt180) REVERT: B 627 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6877 (ttp-170) REVERT: B 650 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8063 (ttp80) REVERT: B 712 MET cc_start: 0.9124 (mmm) cc_final: 0.8716 (mpt) REVERT: B 804 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8661 (ttmm) REVERT: B 812 LYS cc_start: 0.8159 (mttm) cc_final: 0.7920 (mttm) REVERT: B 883 TYR cc_start: 0.8002 (m-10) cc_final: 0.7787 (m-10) REVERT: B 941 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8087 (mp0) REVERT: B 992 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7955 (mmmt) REVERT: B 1011 THR cc_start: 0.8766 (p) cc_final: 0.8486 (m) REVERT: B 1061 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: B 1066 ARG cc_start: 0.8789 (mtt-85) cc_final: 0.8587 (mtp85) REVERT: B 1208 MET cc_start: 0.8555 (tmm) cc_final: 0.8025 (tmt) REVERT: C 59 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7291 (mmtm) REVERT: C 90 LYS cc_start: 0.7891 (tttt) cc_final: 0.7556 (tmtt) REVERT: C 117 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: C 133 LYS cc_start: 0.1402 (OUTLIER) cc_final: 0.0894 (mmtt) REVERT: C 163 TYR cc_start: 0.6000 (OUTLIER) cc_final: 0.4725 (t80) REVERT: C 187 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7825 (tp) REVERT: C 446 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8342 (p90) REVERT: C 593 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8348 (m) REVERT: C 812 LYS cc_start: 0.8240 (mttm) cc_final: 0.7854 (tmmt) REVERT: C 819 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8248 (tppp) REVERT: C 823 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7022 (mm-40) REVERT: C 903 MET cc_start: 0.8834 (ttp) cc_final: 0.8612 (ttp) REVERT: C 948 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8469 (mp) REVERT: C 1059 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: C 1061 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: C 1087 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8321 (mm-30) REVERT: C 1097 GLN cc_start: 0.8618 (tt0) cc_final: 0.8400 (tt0) outliers start: 222 outliers final: 110 residues processed: 458 average time/residue: 0.5778 time to fit residues: 312.6620 Evaluate side-chains 394 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 247 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 884 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1226 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 804 LYS Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1171 LEU Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1228 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 15 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 302 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 196 HIS A 285 ASN A 911 GLN A1111 ASN B 115 GLN B 354 GLN B 645 ASN B 912 GLN B1111 ASN C 115 GLN C 809 ASN C1063 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110785 restraints weight = 28765.022| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.58 r_work: 0.3138 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29133 Z= 0.255 Angle : 0.818 12.777 39810 Z= 0.426 Chirality : 0.052 0.280 4659 Planarity : 0.006 0.058 5004 Dihedral : 11.601 87.759 5784 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 7.10 % Allowed : 14.11 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 3471 helix: 0.10 (0.19), residues: 756 sheet: 0.24 (0.17), residues: 771 loop : -1.58 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 379 TYR 0.024 0.002 TYR B1138 PHE 0.030 0.003 PHE B 382 TRP 0.016 0.002 TRP A 957 HIS 0.008 0.002 HIS C1135 Details of bonding type rmsd covalent geometry : bond 0.00599 (29007) covalent geometry : angle 0.78132 (39477) SS BOND : bond 0.00719 ( 45) SS BOND : angle 2.16503 ( 90) hydrogen bonds : bond 0.07790 ( 1025) hydrogen bonds : angle 5.66731 ( 2904) link_BETA1-4 : bond 0.00427 ( 24) link_BETA1-4 : angle 1.98832 ( 72) link_NAG-ASN : bond 0.00573 ( 57) link_NAG-ASN : angle 3.26388 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 244 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 239 TYR cc_start: 0.7883 (m-80) cc_final: 0.7544 (m-80) REVERT: A 278 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6389 (pttp) REVERT: A 282 PHE cc_start: 0.8244 (m-80) cc_final: 0.7900 (m-80) REVERT: A 379 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6806 (mtt-85) REVERT: A 446 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8045 (p90) REVERT: A 510 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8189 (mm-30) REVERT: A 585 MET cc_start: 0.8572 (mtt) cc_final: 0.8169 (mtt) REVERT: A 683 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.5216 (ptt) REVERT: A 715 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 839 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: A 859 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7871 (mm-40) REVERT: A 862 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7845 (pp) REVERT: A 884 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: A 1000 GLN cc_start: 0.8158 (tt0) cc_final: 0.7907 (mt0) REVERT: A 1059 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 1095 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8157 (mt) REVERT: A 1180 ASP cc_start: 0.3357 (OUTLIER) cc_final: 0.3018 (t70) REVERT: B 59 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8177 (mtpm) REVERT: B 121 ASP cc_start: 0.8132 (m-30) cc_final: 0.7729 (m-30) REVERT: B 173 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7737 (pp) REVERT: B 198 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5840 (mtp85) REVERT: B 230 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: B 390 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: B 408 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8621 (mmmt) REVERT: B 430 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8548 (pt0) REVERT: B 446 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.7330 (p90) REVERT: B 510 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8150 (mm-30) REVERT: B 570 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 593 SER cc_start: 0.8635 (t) cc_final: 0.8150 (p) REVERT: B 624 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7428 (ttt180) REVERT: B 627 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.6945 (ttp-170) REVERT: B 650 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8094 (ttp80) REVERT: B 712 MET cc_start: 0.9114 (mmm) cc_final: 0.8706 (mpt) REVERT: B 804 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8595 (ttmm) REVERT: B 805 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8104 (tp-100) REVERT: B 812 LYS cc_start: 0.8175 (mttm) cc_final: 0.7946 (mttm) REVERT: B 883 TYR cc_start: 0.7984 (m-10) cc_final: 0.7781 (m-80) REVERT: B 941 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8097 (mp0) REVERT: B 992 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7961 (mmmt) REVERT: B 1011 THR cc_start: 0.8755 (p) cc_final: 0.8481 (m) REVERT: B 1063 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: B 1066 ARG cc_start: 0.8818 (mtt-85) cc_final: 0.8592 (mtp85) REVERT: B 1208 MET cc_start: 0.8547 (tmm) cc_final: 0.8009 (tmt) REVERT: C 59 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7188 (mmtm) REVERT: C 90 LYS cc_start: 0.7856 (tttt) cc_final: 0.7502 (tmtt) REVERT: C 117 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: C 133 LYS cc_start: 0.1446 (OUTLIER) cc_final: 0.0804 (mmtt) REVERT: C 163 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.4805 (t80) REVERT: C 187 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7808 (tp) REVERT: C 282 PHE cc_start: 0.8084 (m-80) cc_final: 0.7843 (m-80) REVERT: C 365 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: C 446 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8209 (p90) REVERT: C 593 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8407 (m) REVERT: C 812 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7893 (tmmt) REVERT: C 823 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7003 (mm-40) REVERT: C 903 MET cc_start: 0.8899 (ttp) cc_final: 0.8644 (ttp) REVERT: C 948 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 991 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: C 1059 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: C 1061 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: C 1087 GLU cc_start: 0.8683 (tp30) cc_final: 0.8357 (mm-30) REVERT: C 1097 GLN cc_start: 0.8635 (tt0) cc_final: 0.8416 (tt0) REVERT: C 1196 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8287 (pt0) outliers start: 214 outliers final: 116 residues processed: 422 average time/residue: 0.5835 time to fit residues: 289.7235 Evaluate side-chains 394 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 239 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 884 ARG Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1177 THR Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1226 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 804 LYS Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1224 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 813 LYS Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1171 LEU Chi-restraints excluded: chain C residue 1196 GLU Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 323 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 271 optimal weight: 0.7980 chunk 318 optimal weight: 0.0370 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 327 HIS A 911 GLN A 971 GLN A1111 ASN B 912 GLN B 978 ASN B1013 ASN B1111 ASN C 809 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116378 restraints weight = 28697.696| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.50 r_work: 0.3216 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29133 Z= 0.116 Angle : 0.623 12.533 39810 Z= 0.323 Chirality : 0.044 0.222 4659 Planarity : 0.004 0.058 5004 Dihedral : 10.225 88.046 5758 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.58 % Rotamer: Outliers : 4.58 % Allowed : 16.77 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3471 helix: 0.87 (0.20), residues: 738 sheet: 0.56 (0.17), residues: 756 loop : -1.31 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 379 TYR 0.019 0.001 TYR B1138 PHE 0.022 0.001 PHE C 119 TRP 0.015 0.001 TRP B 51 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00235 (29007) covalent geometry : angle 0.59127 (39477) SS BOND : bond 0.00526 ( 45) SS BOND : angle 1.22214 ( 90) hydrogen bonds : bond 0.05112 ( 1025) hydrogen bonds : angle 5.19928 ( 2904) link_BETA1-4 : bond 0.00403 ( 24) link_BETA1-4 : angle 1.59921 ( 72) link_NAG-ASN : bond 0.00451 ( 57) link_NAG-ASN : angle 2.80861 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 270 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7945 (m-80) cc_final: 0.7608 (m-80) REVERT: A 278 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6599 (pttt) REVERT: A 282 PHE cc_start: 0.8266 (m-80) cc_final: 0.7979 (m-80) REVERT: A 379 ARG cc_start: 0.6959 (mtt90) cc_final: 0.6726 (mtt-85) REVERT: A 389 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6296 (pp30) REVERT: A 421 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7165 (pttt) REVERT: A 441 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 446 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8201 (p90) REVERT: A 460 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8842 (mtp) REVERT: A 510 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8079 (mm-30) REVERT: A 585 MET cc_start: 0.8569 (mtt) cc_final: 0.8200 (mtt) REVERT: A 683 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5645 (ptt) REVERT: A 715 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7783 (tp) REVERT: A 818 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8526 (tp) REVERT: A 819 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8327 (mtpt) REVERT: A 991 GLN cc_start: 0.7791 (mt0) cc_final: 0.7583 (mt0) REVERT: A 1059 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 1095 LEU cc_start: 0.8581 (tp) cc_final: 0.8061 (mt) REVERT: A 1180 ASP cc_start: 0.3322 (OUTLIER) cc_final: 0.3010 (t70) REVERT: A 1208 MET cc_start: 0.8248 (tmm) cc_final: 0.8028 (tmm) REVERT: B 59 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7985 (mttm) REVERT: B 67 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 198 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5922 (mtm180) REVERT: B 230 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: B 390 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: B 408 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8548 (tmtm) REVERT: B 446 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.7353 (p90) REVERT: B 510 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7971 (mm-30) REVERT: B 624 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7432 (ttt180) REVERT: B 627 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.6755 (ttp-170) REVERT: B 712 MET cc_start: 0.8977 (mmm) cc_final: 0.8547 (mpt) REVERT: B 784 THR cc_start: 0.8601 (p) cc_final: 0.8293 (t) REVERT: B 812 LYS cc_start: 0.7997 (mttm) cc_final: 0.7743 (mttm) REVERT: B 894 LYS cc_start: 0.8695 (mmtm) cc_final: 0.8257 (mmmt) REVERT: B 941 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7990 (mp0) REVERT: B 948 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 992 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7977 (mmmt) REVERT: B 1107 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8191 (mm-40) REVERT: B 1208 MET cc_start: 0.8585 (tmm) cc_final: 0.8086 (tmt) REVERT: C 59 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7242 (mmtm) REVERT: C 90 LYS cc_start: 0.7821 (tttt) cc_final: 0.7561 (tmtt) REVERT: C 117 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: C 133 LYS cc_start: 0.1649 (OUTLIER) cc_final: 0.1250 (ptmt) REVERT: C 171 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6716 (ttm170) REVERT: C 191 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6741 (p90) REVERT: C 282 PHE cc_start: 0.8097 (m-80) cc_final: 0.7857 (m-80) REVERT: C 446 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8520 (p90) REVERT: C 510 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7896 (mm-30) REVERT: C 570 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8776 (mm) REVERT: C 593 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8356 (m) REVERT: C 756 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mt) REVERT: C 812 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7779 (tmmt) REVERT: C 823 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6894 (mm110) REVERT: C 918 ARG cc_start: 0.3501 (OUTLIER) cc_final: 0.1808 (ptt90) REVERT: C 948 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8417 (mp) REVERT: C 991 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: C 1061 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: C 1087 GLU cc_start: 0.8553 (tp30) cc_final: 0.8229 (mm-30) outliers start: 138 outliers final: 49 residues processed: 386 average time/residue: 0.6975 time to fit residues: 314.5165 Evaluate side-chains 330 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 247 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1159 GLN Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain A residue 1226 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1174 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 258 ASN A 839 GLN A1111 ASN B 520 ASN B 626 GLN B 911 GLN B 912 GLN B1111 ASN C 465 GLN C 809 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114459 restraints weight = 28671.920| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.32 r_work: 0.3197 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29133 Z= 0.151 Angle : 0.665 12.198 39810 Z= 0.345 Chirality : 0.046 0.218 4659 Planarity : 0.005 0.056 5004 Dihedral : 9.410 88.755 5679 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 4.65 % Allowed : 16.67 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3471 helix: 0.85 (0.20), residues: 756 sheet: 0.54 (0.17), residues: 768 loop : -1.20 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1218 TYR 0.021 0.002 TYR B1138 PHE 0.026 0.002 PHE B 191 TRP 0.011 0.001 TRP B 51 HIS 0.006 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00337 (29007) covalent geometry : angle 0.63330 (39477) SS BOND : bond 0.00493 ( 45) SS BOND : angle 1.54228 ( 90) hydrogen bonds : bond 0.05993 ( 1025) hydrogen bonds : angle 5.25846 ( 2904) link_BETA1-4 : bond 0.00372 ( 24) link_BETA1-4 : angle 1.64168 ( 72) link_NAG-ASN : bond 0.00458 ( 57) link_NAG-ASN : angle 2.79736 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 244 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7844 (m-80) cc_final: 0.7463 (m-80) REVERT: A 278 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6646 (pttt) REVERT: A 282 PHE cc_start: 0.8243 (m-80) cc_final: 0.7957 (m-80) REVERT: A 379 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6746 (mtt-85) REVERT: A 421 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7416 (pttt) REVERT: A 446 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8109 (p90) REVERT: A 460 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8875 (mtp) REVERT: A 510 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8040 (mm-30) REVERT: A 585 MET cc_start: 0.8563 (mtt) cc_final: 0.8132 (mtt) REVERT: A 683 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5664 (ptt) REVERT: A 818 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 1059 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 1095 LEU cc_start: 0.8622 (tp) cc_final: 0.8093 (mt) REVERT: A 1180 ASP cc_start: 0.3546 (OUTLIER) cc_final: 0.3193 (t70) REVERT: B 59 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8060 (mttm) REVERT: B 67 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7425 (p0) REVERT: B 198 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5948 (mtm180) REVERT: B 230 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: B 390 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: B 408 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8599 (tmtm) REVERT: B 446 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.7351 (p90) REVERT: B 510 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8042 (mm-30) REVERT: B 624 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7438 (ttt180) REVERT: B 712 MET cc_start: 0.8991 (mmm) cc_final: 0.8584 (mpt) REVERT: B 784 THR cc_start: 0.8607 (p) cc_final: 0.8263 (t) REVERT: B 805 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7970 (tp-100) REVERT: B 812 LYS cc_start: 0.8054 (mttm) cc_final: 0.7824 (mttm) REVERT: B 894 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8292 (mmmt) REVERT: B 941 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8102 (mp0) REVERT: B 948 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8594 (mt) REVERT: B 992 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7942 (mmmt) REVERT: B 1063 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: B 1208 MET cc_start: 0.8565 (tmm) cc_final: 0.8070 (tmt) REVERT: B 1218 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7661 (ptp-110) REVERT: C 59 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7261 (mmtm) REVERT: C 90 LYS cc_start: 0.7851 (tttt) cc_final: 0.7561 (tmtt) REVERT: C 117 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: C 133 LYS cc_start: 0.1656 (OUTLIER) cc_final: 0.1000 (mmtt) REVERT: C 187 ILE cc_start: 0.8126 (mm) cc_final: 0.7728 (tp) REVERT: C 191 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6694 (p90) REVERT: C 282 PHE cc_start: 0.8157 (m-80) cc_final: 0.7906 (m-80) REVERT: C 381 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: C 446 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8367 (p90) REVERT: C 593 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8362 (m) REVERT: C 756 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8444 (mt) REVERT: C 812 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7814 (tmmt) REVERT: C 823 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6935 (mm110) REVERT: C 918 ARG cc_start: 0.3602 (OUTLIER) cc_final: 0.1876 (ptt90) REVERT: C 948 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8427 (mp) REVERT: C 991 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: C 1087 GLU cc_start: 0.8609 (tp30) cc_final: 0.8292 (mm-30) outliers start: 140 outliers final: 72 residues processed: 358 average time/residue: 0.6214 time to fit residues: 260.1807 Evaluate side-chains 346 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 245 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1159 GLN Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1226 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1174 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 230 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 281 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 330 optimal weight: 0.0470 chunk 117 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 196 HIS A1111 ASN B 520 ASN B 911 GLN B 912 GLN B1111 ASN C 809 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114352 restraints weight = 28708.052| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.32 r_work: 0.3197 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29133 Z= 0.157 Angle : 0.665 12.205 39810 Z= 0.346 Chirality : 0.046 0.221 4659 Planarity : 0.005 0.058 5004 Dihedral : 9.169 87.411 5666 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 4.45 % Allowed : 16.97 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3471 helix: 0.99 (0.20), residues: 738 sheet: 0.56 (0.17), residues: 768 loop : -1.19 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.021 0.002 TYR B1138 PHE 0.027 0.002 PHE B 191 TRP 0.010 0.001 TRP B 51 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00354 (29007) covalent geometry : angle 0.63461 (39477) SS BOND : bond 0.00512 ( 45) SS BOND : angle 1.56641 ( 90) hydrogen bonds : bond 0.06084 ( 1025) hydrogen bonds : angle 5.26565 ( 2904) link_BETA1-4 : bond 0.00376 ( 24) link_BETA1-4 : angle 1.63234 ( 72) link_NAG-ASN : bond 0.00460 ( 57) link_NAG-ASN : angle 2.77580 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 251 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7824 (m-80) cc_final: 0.7449 (m-80) REVERT: A 278 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6531 (pttp) REVERT: A 282 PHE cc_start: 0.8235 (m-80) cc_final: 0.7937 (m-80) REVERT: A 421 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7336 (pttt) REVERT: A 446 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8114 (p90) REVERT: A 460 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8888 (mtp) REVERT: A 510 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8130 (mm-30) REVERT: A 585 MET cc_start: 0.8563 (mtt) cc_final: 0.8127 (mtt) REVERT: A 683 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5679 (ptt) REVERT: A 818 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8587 (tp) REVERT: A 819 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8439 (mtpt) REVERT: A 971 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7917 (mp-120) REVERT: A 1059 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 1095 LEU cc_start: 0.8602 (tp) cc_final: 0.8067 (mt) REVERT: B 59 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8060 (mttm) REVERT: B 67 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7442 (p0) REVERT: B 198 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5942 (mtm180) REVERT: B 230 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6910 (mt-10) REVERT: B 390 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: B 408 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8606 (tmtm) REVERT: B 446 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.7353 (p90) REVERT: B 510 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8029 (tp30) REVERT: B 570 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8571 (mm) REVERT: B 624 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7747 (ttm110) REVERT: B 712 MET cc_start: 0.8995 (mmm) cc_final: 0.8588 (mpt) REVERT: B 784 THR cc_start: 0.8604 (p) cc_final: 0.8262 (t) REVERT: B 805 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7979 (tp-100) REVERT: B 812 LYS cc_start: 0.8029 (mttm) cc_final: 0.7791 (mttm) REVERT: B 894 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8287 (mmmt) REVERT: B 948 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 992 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7981 (mmmt) REVERT: B 1063 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: B 1208 MET cc_start: 0.8544 (tmm) cc_final: 0.8062 (tmt) REVERT: C 59 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7266 (mmtm) REVERT: C 90 LYS cc_start: 0.7797 (tttt) cc_final: 0.7516 (tmtt) REVERT: C 117 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: C 133 LYS cc_start: 0.1640 (OUTLIER) cc_final: 0.1209 (ptmt) REVERT: C 187 ILE cc_start: 0.8113 (mm) cc_final: 0.7718 (tp) REVERT: C 191 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6703 (p90) REVERT: C 282 PHE cc_start: 0.8151 (m-80) cc_final: 0.7908 (m-80) REVERT: C 446 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8368 (p90) REVERT: C 570 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8746 (mm) REVERT: C 593 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.8359 (m) REVERT: C 812 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7831 (tmmt) REVERT: C 823 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6972 (mm-40) REVERT: C 918 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.1942 (ptt90) REVERT: C 948 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8419 (mp) REVERT: C 991 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: C 1059 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: C 1087 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8288 (mm-30) outliers start: 134 outliers final: 76 residues processed: 358 average time/residue: 0.6612 time to fit residues: 276.3101 Evaluate side-chains 354 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 246 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1226 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 99 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 322 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 232 optimal weight: 40.0000 chunk 302 optimal weight: 6.9990 chunk 340 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 196 HIS A 258 ASN A 839 GLN A1111 ASN B 520 ASN B 911 GLN B 912 GLN B1111 ASN C 809 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113919 restraints weight = 28591.634| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.34 r_work: 0.3193 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29133 Z= 0.162 Angle : 0.674 12.039 39810 Z= 0.350 Chirality : 0.046 0.217 4659 Planarity : 0.005 0.059 5004 Dihedral : 8.992 86.337 5659 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 4.81 % Allowed : 16.83 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3471 helix: 0.86 (0.20), residues: 756 sheet: 0.60 (0.17), residues: 771 loop : -1.15 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.021 0.002 TYR B1138 PHE 0.025 0.002 PHE B 191 TRP 0.010 0.001 TRP B 51 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00366 (29007) covalent geometry : angle 0.64415 (39477) SS BOND : bond 0.00487 ( 45) SS BOND : angle 1.64299 ( 90) hydrogen bonds : bond 0.06177 ( 1025) hydrogen bonds : angle 5.28092 ( 2904) link_BETA1-4 : bond 0.00375 ( 24) link_BETA1-4 : angle 1.63291 ( 72) link_NAG-ASN : bond 0.00459 ( 57) link_NAG-ASN : angle 2.73576 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 250 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: -0.1020 (OUTLIER) cc_final: -0.1260 (tp) REVERT: A 239 TYR cc_start: 0.7821 (m-80) cc_final: 0.7456 (m-80) REVERT: A 278 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6537 (pttp) REVERT: A 282 PHE cc_start: 0.8243 (m-80) cc_final: 0.7947 (m-80) REVERT: A 421 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7456 (pttt) REVERT: A 446 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8104 (p90) REVERT: A 460 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8895 (mtp) REVERT: A 510 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8119 (mm-30) REVERT: A 585 MET cc_start: 0.8566 (mtt) cc_final: 0.8162 (mtt) REVERT: A 634 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7518 (t70) REVERT: A 683 MET cc_start: 0.5790 (ptm) cc_final: 0.5572 (ptt) REVERT: A 818 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 839 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: A 971 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7934 (mp-120) REVERT: A 1059 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7819 (mm-30) REVERT: A 1095 LEU cc_start: 0.8629 (tp) cc_final: 0.8084 (mt) REVERT: B 59 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8071 (mttm) REVERT: B 67 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7454 (p0) REVERT: B 230 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6908 (mt-10) REVERT: B 408 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8598 (tmtm) REVERT: B 446 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.7352 (p90) REVERT: B 510 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8103 (tp30) REVERT: B 570 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8572 (mm) REVERT: B 624 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7746 (ttm110) REVERT: B 712 MET cc_start: 0.9003 (mmm) cc_final: 0.8589 (mpt) REVERT: B 784 THR cc_start: 0.8603 (p) cc_final: 0.8249 (t) REVERT: B 805 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7980 (tp-100) REVERT: B 812 LYS cc_start: 0.8047 (mttm) cc_final: 0.7810 (mttm) REVERT: B 894 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8312 (mmmt) REVERT: B 948 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 992 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7981 (mmmt) REVERT: B 1063 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: B 1208 MET cc_start: 0.8541 (tmm) cc_final: 0.8053 (tmt) REVERT: C 59 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7197 (mmtm) REVERT: C 90 LYS cc_start: 0.7813 (tttt) cc_final: 0.7527 (tmtt) REVERT: C 117 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: C 133 LYS cc_start: 0.1580 (OUTLIER) cc_final: 0.1109 (ptmt) REVERT: C 187 ILE cc_start: 0.8114 (mm) cc_final: 0.7891 (tp) REVERT: C 191 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6714 (p90) REVERT: C 282 PHE cc_start: 0.8135 (m-80) cc_final: 0.7862 (m-80) REVERT: C 446 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8367 (p90) REVERT: C 510 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7907 (mm-30) REVERT: C 570 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8585 (mm) REVERT: C 593 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8334 (m) REVERT: C 793 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: C 812 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7834 (tmmt) REVERT: C 823 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.6973 (mm-40) REVERT: C 918 ARG cc_start: 0.3620 (OUTLIER) cc_final: 0.1790 (ptt90) REVERT: C 948 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 991 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: C 1059 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: C 1061 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (mp0) REVERT: C 1087 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8310 (mm-30) outliers start: 145 outliers final: 82 residues processed: 364 average time/residue: 0.6293 time to fit residues: 268.9551 Evaluate side-chains 361 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 246 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1228 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 196 HIS A 679 HIS A 839 GLN A1111 ASN B 520 ASN B 911 GLN B 912 GLN B 915 GLN B1111 ASN C 809 ASN C 911 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114166 restraints weight = 28727.105| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.33 r_work: 0.3194 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 29133 Z= 0.162 Angle : 0.677 12.084 39810 Z= 0.352 Chirality : 0.046 0.248 4659 Planarity : 0.005 0.060 5004 Dihedral : 8.850 84.507 5653 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 4.58 % Allowed : 17.10 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3471 helix: 1.01 (0.20), residues: 738 sheet: 0.60 (0.17), residues: 771 loop : -1.16 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.021 0.002 TYR B1138 PHE 0.025 0.002 PHE B 191 TRP 0.009 0.001 TRP A 957 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00371 (29007) covalent geometry : angle 0.64512 (39477) SS BOND : bond 0.00544 ( 45) SS BOND : angle 1.90506 ( 90) hydrogen bonds : bond 0.06140 ( 1025) hydrogen bonds : angle 5.28892 ( 2904) link_BETA1-4 : bond 0.00382 ( 24) link_BETA1-4 : angle 1.62560 ( 72) link_NAG-ASN : bond 0.00461 ( 57) link_NAG-ASN : angle 2.75293 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 250 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: A 239 TYR cc_start: 0.7813 (m-80) cc_final: 0.7455 (m-80) REVERT: A 278 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6531 (pttp) REVERT: A 282 PHE cc_start: 0.8235 (m-80) cc_final: 0.7937 (m-80) REVERT: A 389 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6236 (pp30) REVERT: A 421 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7437 (pttt) REVERT: A 446 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8116 (p90) REVERT: A 460 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8893 (mtp) REVERT: A 510 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8109 (mm-30) REVERT: A 585 MET cc_start: 0.8562 (mtt) cc_final: 0.8152 (mtt) REVERT: A 634 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7564 (t70) REVERT: A 683 MET cc_start: 0.5728 (ptm) cc_final: 0.5520 (ptt) REVERT: A 818 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8589 (tp) REVERT: A 862 LEU cc_start: 0.8173 (pp) cc_final: 0.7600 (mp) REVERT: A 971 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7934 (mp-120) REVERT: A 1059 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 1095 LEU cc_start: 0.8554 (tp) cc_final: 0.8059 (mt) REVERT: B 59 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8071 (mttm) REVERT: B 67 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7446 (p0) REVERT: B 148 LYS cc_start: 0.2867 (OUTLIER) cc_final: 0.2555 (ttpt) REVERT: B 230 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: B 408 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8600 (tmtm) REVERT: B 446 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.7351 (p90) REVERT: B 510 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8092 (tp30) REVERT: B 570 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8571 (mm) REVERT: B 624 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7747 (ttm110) REVERT: B 712 MET cc_start: 0.8994 (mmm) cc_final: 0.8579 (mpt) REVERT: B 784 THR cc_start: 0.8609 (p) cc_final: 0.8270 (t) REVERT: B 805 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7980 (tp-100) REVERT: B 812 LYS cc_start: 0.8038 (mttm) cc_final: 0.7821 (mttm) REVERT: B 948 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8590 (mt) REVERT: B 992 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7970 (mmmt) REVERT: B 1063 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: B 1208 MET cc_start: 0.8538 (tmm) cc_final: 0.8050 (tmt) REVERT: C 59 LYS cc_start: 0.7592 (mtmt) cc_final: 0.7192 (mmtm) REVERT: C 90 LYS cc_start: 0.7814 (tttt) cc_final: 0.7532 (tmtt) REVERT: C 117 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: C 133 LYS cc_start: 0.1760 (OUTLIER) cc_final: 0.1196 (ptmt) REVERT: C 187 ILE cc_start: 0.8114 (mm) cc_final: 0.7894 (tp) REVERT: C 191 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6723 (p90) REVERT: C 232 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.6074 (p) REVERT: C 282 PHE cc_start: 0.8135 (m-80) cc_final: 0.7845 (m-80) REVERT: C 446 TYR cc_start: 0.9200 (OUTLIER) cc_final: 0.8365 (p90) REVERT: C 510 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7908 (mm-30) REVERT: C 570 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8590 (mm) REVERT: C 593 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8323 (m) REVERT: C 812 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7833 (tmmt) REVERT: C 823 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6969 (mm-40) REVERT: C 918 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.1689 (ptt90) REVERT: C 948 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 991 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: C 1059 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: C 1061 GLU cc_start: 0.8645 (mp0) cc_final: 0.8378 (mp0) REVERT: C 1087 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8298 (mm-30) outliers start: 138 outliers final: 88 residues processed: 360 average time/residue: 0.6387 time to fit residues: 270.2248 Evaluate side-chains 369 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 248 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 679 HIS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 819 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1224 LEU Chi-restraints excluded: chain C residue 1228 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 296 optimal weight: 0.0980 chunk 192 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 239 optimal weight: 0.1980 chunk 337 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 234 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 196 HIS A 679 HIS A 839 GLN A1111 ASN B 465 GLN B 520 ASN B 911 GLN B 912 GLN B1111 ASN C 334 ASN C 809 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116026 restraints weight = 28823.417| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.34 r_work: 0.3218 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29133 Z= 0.125 Angle : 0.624 12.017 39810 Z= 0.324 Chirality : 0.044 0.207 4659 Planarity : 0.004 0.060 5004 Dihedral : 8.554 89.360 5653 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.58 % Rotamer: Outliers : 3.95 % Allowed : 17.73 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3471 helix: 1.20 (0.20), residues: 735 sheet: 0.68 (0.18), residues: 756 loop : -1.09 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1066 TYR 0.020 0.001 TYR B1138 PHE 0.023 0.001 PHE C 119 TRP 0.011 0.001 TRP B 51 HIS 0.029 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00272 (29007) covalent geometry : angle 0.59430 (39477) SS BOND : bond 0.00481 ( 45) SS BOND : angle 1.59800 ( 90) hydrogen bonds : bond 0.05289 ( 1025) hydrogen bonds : angle 5.12019 ( 2904) link_BETA1-4 : bond 0.00405 ( 24) link_BETA1-4 : angle 1.53068 ( 72) link_NAG-ASN : bond 0.00443 ( 57) link_NAG-ASN : angle 2.61378 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 257 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: A 239 TYR cc_start: 0.7767 (m-80) cc_final: 0.7409 (m-80) REVERT: A 278 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6496 (pttp) REVERT: A 282 PHE cc_start: 0.8213 (m-80) cc_final: 0.7946 (m-80) REVERT: A 421 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7333 (pttt) REVERT: A 441 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8503 (mp) REVERT: A 446 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8146 (p90) REVERT: A 460 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8894 (mtp) REVERT: A 510 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8049 (mm-30) REVERT: A 585 MET cc_start: 0.8554 (mtt) cc_final: 0.8183 (mtt) REVERT: A 634 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7574 (t70) REVERT: A 862 LEU cc_start: 0.8203 (pp) cc_final: 0.7654 (mp) REVERT: A 971 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7927 (mp-120) REVERT: A 1059 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 1095 LEU cc_start: 0.8509 (tp) cc_final: 0.8011 (mt) REVERT: B 59 LYS cc_start: 0.8304 (mtmt) cc_final: 0.8022 (mttm) REVERT: B 67 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 117 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: B 173 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7205 (pp) REVERT: B 229 GLN cc_start: 0.6075 (OUTLIER) cc_final: 0.5824 (pm20) REVERT: B 230 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: B 408 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8568 (tmtm) REVERT: B 446 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7347 (p90) REVERT: B 510 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8022 (tp30) REVERT: B 624 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7465 (tpt170) REVERT: B 627 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.6912 (ttp-170) REVERT: B 712 MET cc_start: 0.8978 (mmm) cc_final: 0.8577 (mpt) REVERT: B 773 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7116 (t) REVERT: B 784 THR cc_start: 0.8562 (p) cc_final: 0.8283 (t) REVERT: B 805 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7968 (tp-100) REVERT: B 812 LYS cc_start: 0.7998 (mttm) cc_final: 0.7764 (mttm) REVERT: B 948 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8585 (mt) REVERT: B 992 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7973 (mmmt) REVERT: B 1063 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: B 1107 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8485 (mm-40) REVERT: B 1208 MET cc_start: 0.8552 (tmm) cc_final: 0.8061 (tmt) REVERT: C 59 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7228 (mmtm) REVERT: C 90 LYS cc_start: 0.7799 (tttt) cc_final: 0.7519 (tmtt) REVERT: C 117 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: C 133 LYS cc_start: 0.1643 (OUTLIER) cc_final: 0.1104 (ptmt) REVERT: C 187 ILE cc_start: 0.8105 (mm) cc_final: 0.7724 (tp) REVERT: C 191 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6671 (p90) REVERT: C 232 THR cc_start: 0.6178 (OUTLIER) cc_final: 0.5956 (p) REVERT: C 237 LYS cc_start: 0.6977 (mttm) cc_final: 0.6765 (mtpp) REVERT: C 282 PHE cc_start: 0.8088 (m-80) cc_final: 0.7786 (m-80) REVERT: C 446 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8498 (p90) REVERT: C 510 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7891 (mm-30) REVERT: C 541 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8393 (p) REVERT: C 570 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 593 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8297 (m) REVERT: C 812 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7781 (tmmt) REVERT: C 918 ARG cc_start: 0.3687 (OUTLIER) cc_final: 0.1689 (ptt90) REVERT: C 948 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8415 (mp) REVERT: C 991 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: C 1059 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: C 1061 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: C 1087 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8267 (mm-30) outliers start: 119 outliers final: 63 residues processed: 356 average time/residue: 0.6576 time to fit residues: 275.0045 Evaluate side-chains 352 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 252 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 911 GLN Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1228 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 115 optimal weight: 0.0570 chunk 103 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 312 optimal weight: 8.9990 chunk 177 optimal weight: 0.0270 chunk 131 optimal weight: 5.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 196 HIS A 280 ASN A 679 HIS A 839 GLN A1111 ASN B 520 ASN B 912 GLN B 915 GLN B1111 ASN C 809 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114873 restraints weight = 28551.874| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.34 r_work: 0.3204 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29133 Z= 0.154 Angle : 0.662 11.905 39810 Z= 0.343 Chirality : 0.046 0.251 4659 Planarity : 0.004 0.061 5004 Dihedral : 8.451 85.799 5643 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 3.69 % Allowed : 18.03 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3471 helix: 1.15 (0.20), residues: 735 sheet: 0.62 (0.18), residues: 768 loop : -1.10 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1071 TYR 0.021 0.002 TYR B1138 PHE 0.025 0.002 PHE B 191 TRP 0.009 0.001 TRP B 51 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00349 (29007) covalent geometry : angle 0.63270 (39477) SS BOND : bond 0.00499 ( 45) SS BOND : angle 1.69868 ( 90) hydrogen bonds : bond 0.05841 ( 1025) hydrogen bonds : angle 5.18027 ( 2904) link_BETA1-4 : bond 0.00379 ( 24) link_BETA1-4 : angle 1.56772 ( 72) link_NAG-ASN : bond 0.00440 ( 57) link_NAG-ASN : angle 2.63650 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 253 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6295 (pp) REVERT: A 239 TYR cc_start: 0.7768 (m-80) cc_final: 0.7408 (m-80) REVERT: A 278 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6505 (pttp) REVERT: A 282 PHE cc_start: 0.8195 (m-80) cc_final: 0.7916 (m-80) REVERT: A 421 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7448 (pttt) REVERT: A 446 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8105 (p90) REVERT: A 460 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8860 (mtp) REVERT: A 510 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8074 (mm-30) REVERT: A 585 MET cc_start: 0.8561 (mtt) cc_final: 0.8180 (mtt) REVERT: A 634 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7581 (t70) REVERT: A 862 LEU cc_start: 0.8200 (pp) cc_final: 0.7691 (mp) REVERT: A 971 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7942 (mp-120) REVERT: A 1059 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 1095 LEU cc_start: 0.8541 (tp) cc_final: 0.8024 (mt) REVERT: B 59 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8060 (mttm) REVERT: B 67 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7423 (p0) REVERT: B 173 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7246 (pp) REVERT: B 229 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5878 (pm20) REVERT: B 230 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: B 408 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8594 (tmtm) REVERT: B 446 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.7354 (p90) REVERT: B 510 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8045 (tp30) REVERT: B 624 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7746 (ttm110) REVERT: B 627 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.6952 (ttp-170) REVERT: B 712 MET cc_start: 0.8991 (mmm) cc_final: 0.8574 (mpt) REVERT: B 773 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7120 (t) REVERT: B 784 THR cc_start: 0.8600 (p) cc_final: 0.8294 (t) REVERT: B 805 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7977 (tp-100) REVERT: B 812 LYS cc_start: 0.8009 (mttm) cc_final: 0.7776 (mttm) REVERT: B 912 GLN cc_start: 0.5771 (OUTLIER) cc_final: 0.3439 (mm-40) REVERT: B 948 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 992 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7983 (mmmt) REVERT: B 1063 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: B 1107 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8478 (mm-40) REVERT: B 1208 MET cc_start: 0.8535 (tmm) cc_final: 0.8058 (tmt) REVERT: C 59 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7235 (mmtm) REVERT: C 90 LYS cc_start: 0.7799 (tttt) cc_final: 0.7528 (tmtt) REVERT: C 117 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: C 133 LYS cc_start: 0.1661 (OUTLIER) cc_final: 0.1124 (ptmt) REVERT: C 187 ILE cc_start: 0.8108 (mm) cc_final: 0.7729 (tp) REVERT: C 191 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6673 (p90) REVERT: C 232 THR cc_start: 0.6219 (OUTLIER) cc_final: 0.5998 (p) REVERT: C 237 LYS cc_start: 0.7016 (mttm) cc_final: 0.6781 (mtpt) REVERT: C 282 PHE cc_start: 0.8105 (m-80) cc_final: 0.7785 (m-80) REVERT: C 446 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8377 (p90) REVERT: C 510 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7908 (mm-30) REVERT: C 541 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8400 (p) REVERT: C 570 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8748 (mm) REVERT: C 593 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8299 (m) REVERT: C 812 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7835 (tmmt) REVERT: C 918 ARG cc_start: 0.3616 (OUTLIER) cc_final: 0.1597 (ptt90) REVERT: C 948 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8415 (mp) REVERT: C 991 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: C 1061 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: C 1087 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8272 (mm-30) outliers start: 111 outliers final: 67 residues processed: 345 average time/residue: 0.6108 time to fit residues: 247.5265 Evaluate side-chains 355 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 253 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 922 CYS Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1065 ASP Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 812 LYS Chi-restraints excluded: chain C residue 918 ARG Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 991 GLN Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1061 GLU Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1107 GLN Chi-restraints excluded: chain C residue 1174 THR Chi-restraints excluded: chain C residue 1228 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 300 optimal weight: 0.0470 chunk 245 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 196 HIS A 679 HIS A 839 GLN A1111 ASN B 520 ASN B 911 GLN B 912 GLN B1111 ASN C 269 GLN C 809 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117657 restraints weight = 28952.450| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.37 r_work: 0.3241 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 29133 Z= 0.111 Angle : 0.599 11.913 39810 Z= 0.309 Chirality : 0.043 0.232 4659 Planarity : 0.004 0.060 5004 Dihedral : 8.076 74.382 5643 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 3.02 % Allowed : 18.69 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3471 helix: 1.34 (0.20), residues: 735 sheet: 0.68 (0.18), residues: 762 loop : -1.02 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1066 TYR 0.020 0.001 TYR B1138 PHE 0.023 0.001 PHE C 119 TRP 0.011 0.001 TRP B 51 HIS 0.004 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00238 (29007) covalent geometry : angle 0.57198 (39477) SS BOND : bond 0.00376 ( 45) SS BOND : angle 1.28455 ( 90) hydrogen bonds : bond 0.04739 ( 1025) hydrogen bonds : angle 5.00518 ( 2904) link_BETA1-4 : bond 0.00444 ( 24) link_BETA1-4 : angle 1.47145 ( 72) link_NAG-ASN : bond 0.00438 ( 57) link_NAG-ASN : angle 2.51121 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13915.80 seconds wall clock time: 236 minutes 29.01 seconds (14189.01 seconds total)