Starting phenix.real_space_refine on Mon Aug 25 17:21:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y19_38828/08_2025/8y19_38828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y19_38828/08_2025/8y19_38828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y19_38828/08_2025/8y19_38828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y19_38828/08_2025/8y19_38828.map" model { file = "/net/cci-nas-00/data/ceres_data/8y19_38828/08_2025/8y19_38828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y19_38828/08_2025/8y19_38828.cif" } resolution = 2.3 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= -0.002 sd= 0.146 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 171 5.16 5 C 18729 2.51 5 N 4734 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "B" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "C" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9425 Classifications: {'peptide': 1208} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1155} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 8.47, per 1000 atoms: 0.29 Number of scatterers: 29541 At special positions: 0 Unit cell: (151.093, 160.876, 167.398, 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 171 16.00 O 5907 8.00 N 4734 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.04 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.93 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.04 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.04 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.04 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.93 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.04 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.04 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.04 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.93 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.02 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.04 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " 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 ALPHA1-3 " MAN D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " MAN N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG I 2 " - " MAN I 3 " " NAG N 2 " - " MAN N 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN I 3 " - " MAN I 4 " " MAN N 3 " - " MAN N 4 " 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-ASN " NAG A2001 " - " ASN A 19 " " NAG A2002 " - " ASN A 29 " " NAG A2003 " - " ASN A 58 " " NAG A2004 " - " ASN A 114 " " NAG A2005 " - " ASN A 171 " " NAG A2006 " - " ASN A 192 " " NAG A2007 " - " ASN A 251 " " NAG A2008 " - " ASN A 433 " " NAG A2009 " - " ASN A 454 " " NAG A2010 " - " ASN A 684 " " NAG A2011 " - " ASN A 703 " " NAG A2012 " - " ASN A 725 " " NAG A2013 " - " ASN A 771 " " NAG A2014 " - " ASN A 776 " " NAG A2015 " - " ASN A 793 " " NAG A2016 " - " ASN A 924 " " NAG A2017 " - " ASN A1211 " " NAG B2001 " - " ASN B 19 " " NAG B2002 " - " ASN B 29 " " NAG B2003 " - " ASN B 58 " " NAG B2004 " - " ASN B 114 " " NAG B2005 " - " ASN B 171 " " NAG B2006 " - " ASN B 192 " " NAG B2007 " - " ASN B 251 " " NAG B2008 " - " ASN B 433 " " NAG B2009 " - " ASN B 454 " " NAG B2010 " - " ASN B 684 " " NAG B2011 " - " ASN B 703 " " NAG B2012 " - " ASN B 725 " " NAG B2013 " - " ASN B 771 " " NAG B2014 " - " ASN B 776 " " NAG B2015 " - " ASN B 793 " " NAG B2016 " - " ASN B 924 " " NAG B2017 " - " ASN B1211 " " NAG C2001 " - " ASN C 19 " " NAG C2002 " - " ASN C 29 " " NAG C2003 " - " ASN C 58 " " NAG C2004 " - " ASN C 114 " " NAG C2005 " - " ASN C 171 " " NAG C2006 " - " ASN C 192 " " NAG C2007 " - " ASN C 251 " " NAG C2008 " - " ASN C 433 " " NAG C2009 " - " ASN C 454 " " NAG C2010 " - " ASN C 684 " " NAG C2011 " - " ASN C 703 " " NAG C2012 " - " ASN C 725 " " NAG C2013 " - " ASN C 771 " " NAG C2014 " - " ASN C 776 " " NAG C2015 " - " ASN C 793 " " NAG C2016 " - " ASN C 924 " " NAG C2017 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 335 " " NAG G 1 " - " ASN A 355 " " NAG H 1 " - " ASN A 664 " " NAG I 1 " - " ASN B 132 " " NAG J 1 " - " ASN B 188 " " NAG K 1 " - " ASN B 335 " " NAG L 1 " - " ASN B 355 " " NAG M 1 " - " ASN B 664 " " NAG N 1 " - " ASN C 132 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 335 " " NAG Q 1 " - " ASN C 355 " " NAG R 1 " - " ASN C 664 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 476.8 nanoseconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 69 sheets defined 24.1% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.605A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.799A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.581A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.892A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.669A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.971A pdb=" N SER A 484 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 485 " --> pdb=" O VAL A 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 481 through 485' Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.566A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 831 removed outlier: 3.976A pdb=" N GLU A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 863 removed outlier: 3.782A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.652A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.583A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.821A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.828A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.605A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.801A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.582A pdb=" N LEU B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.892A pdb=" N ARG B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.668A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.971A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 485 " --> pdb=" O VAL B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 485' Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.566A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 831 removed outlier: 3.977A pdb=" N GLU B 831 " --> pdb=" O ASP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 863 removed outlier: 3.782A pdb=" N ASN B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 909 Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.652A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.583A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.822A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1057 through 1063 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.828A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.605A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.800A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.582A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.892A pdb=" N ARG C 398 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.669A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.972A pdb=" N SER C 484 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 485 " --> pdb=" O VAL C 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 485' Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.567A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 819 Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.978A pdb=" N GLU C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 863 removed outlier: 3.781A pdb=" N ASN C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 923 removed outlier: 3.651A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.584A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1017 Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.822A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.828A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 8.123A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.890A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.110A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA C 315 " --> pdb=" O CYS C 619 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.992A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.490A pdb=" N LEU A 146 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A 188 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 148 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 186 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 150 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.026A pdb=" N ALA A 315 " --> pdb=" O CYS A 619 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.602A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.581A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.581A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB6, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.359A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AB8, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.562A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.595A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.326A pdb=" N SER A 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.865A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN A1136 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A1142 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A1134 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A1144 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A1132 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A1146 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.294A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC5, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC6, first strand: chain 'A' and resid 1202 through 1205 Processing sheet with id=AC7, first strand: chain 'A' and resid 1175 through 1180 removed outlier: 4.645A pdb=" N GLY A1188 " --> pdb=" O TYR A1193 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 removed outlier: 8.124A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 59 through 68 removed outlier: 3.891A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.992A pdb=" N THR B 241 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP B 174 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.489A pdb=" N LEU B 146 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 188 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 148 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS B 186 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 150 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AD5, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AD7, first strand: chain 'B' and resid 315 through 319 removed outlier: 4.026A pdb=" N ALA B 315 " --> pdb=" O CYS B 619 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.602A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.581A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.581A pdb=" N PHE B 383 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 597 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE3, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.359A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AE5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.561A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.595A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.303A pdb=" N SER B 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.864A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN B1136 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B1142 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B1134 " --> pdb=" O LEU B1142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B1144 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B1132 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B1146 " --> pdb=" O ILE B1130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.295A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 878 through 879 Processing sheet with id=AF2, first strand: chain 'B' and resid 1202 through 1205 Processing sheet with id=AF3, first strand: chain 'B' and resid 1175 through 1180 removed outlier: 4.646A pdb=" N GLY B1188 " --> pdb=" O TYR B1193 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF5, first strand: chain 'C' and resid 38 through 39 removed outlier: 8.123A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 59 through 68 removed outlier: 3.891A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.993A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TRP C 174 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.490A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 109 through 112 Processing sheet with id=AG1, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AG2, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG3, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.602A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.582A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.582A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG7, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.360A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 504 through 507 Processing sheet with id=AG9, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.561A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.595A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.866A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.293A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH5, first strand: chain 'C' and resid 1202 through 1205 Processing sheet with id=AH6, first strand: chain 'C' and resid 1175 through 1180 removed outlier: 4.644A pdb=" N GLY C1188 " --> pdb=" O TYR C1193 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3006 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: 9.55 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4717 1.32 - 1.45: 8887 1.45 - 1.58: 16423 1.58 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 30225 Sorted by residual: bond pdb=" C VAL A 818 " pdb=" O VAL A 818 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.12e-02 7.97e+03 2.16e+01 bond pdb=" C VAL C 818 " pdb=" O VAL C 818 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.12e-02 7.97e+03 2.16e+01 bond pdb=" C VAL B 818 " pdb=" O VAL B 818 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.12e-02 7.97e+03 2.10e+01 bond pdb=" CA CYS C 819 " pdb=" C CYS C 819 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.29e-02 6.01e+03 1.89e+01 bond pdb=" CA CYS A 819 " pdb=" C CYS A 819 " ideal model delta sigma weight residual 1.521 1.466 0.056 1.29e-02 6.01e+03 1.87e+01 ... (remaining 30220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 40411 2.57 - 5.14: 665 5.14 - 7.71: 62 7.71 - 10.29: 13 10.29 - 12.86: 6 Bond angle restraints: 41157 Sorted by residual: angle pdb=" N ASN C 821 " pdb=" CA ASN C 821 " pdb=" C ASN C 821 " ideal model delta sigma weight residual 111.36 123.62 -12.26 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N ASN A 821 " pdb=" CA ASN A 821 " pdb=" C ASN A 821 " ideal model delta sigma weight residual 111.36 123.62 -12.26 1.09e+00 8.42e-01 1.26e+02 angle pdb=" N ASN B 821 " pdb=" CA ASN B 821 " pdb=" C ASN B 821 " ideal model delta sigma weight residual 111.36 123.60 -12.24 1.09e+00 8.42e-01 1.26e+02 angle pdb=" N TYR B 822 " pdb=" CA TYR B 822 " pdb=" C TYR B 822 " ideal model delta sigma weight residual 110.10 122.96 -12.86 1.49e+00 4.50e-01 7.45e+01 angle pdb=" N TYR C 822 " pdb=" CA TYR C 822 " pdb=" C TYR C 822 " ideal model delta sigma weight residual 110.10 122.92 -12.82 1.49e+00 4.50e-01 7.40e+01 ... (remaining 41152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.77: 17916 20.77 - 41.55: 960 41.55 - 62.32: 285 62.32 - 83.10: 36 83.10 - 103.87: 30 Dihedral angle restraints: 19227 sinusoidal: 8589 harmonic: 10638 Sorted by residual: dihedral pdb=" CA SER A 929 " pdb=" C SER A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER B 929 " pdb=" C SER B 929 " pdb=" N GLU B 930 " pdb=" CA GLU B 930 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA SER C 929 " pdb=" C SER C 929 " pdb=" N GLU C 930 " pdb=" CA GLU C 930 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 19224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4318 0.089 - 0.179: 556 0.179 - 0.268: 22 0.268 - 0.358: 6 0.358 - 0.447: 6 Chirality restraints: 4908 Sorted by residual: chirality pdb=" CA TYR B 822 " pdb=" N TYR B 822 " pdb=" C TYR B 822 " pdb=" CB TYR B 822 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA TYR A 822 " pdb=" N TYR A 822 " pdb=" C TYR A 822 " pdb=" CB TYR A 822 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA TYR C 822 " pdb=" N TYR C 822 " pdb=" C TYR C 822 " pdb=" CB TYR C 822 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 4905 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B 93 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 92 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO C 93 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 93 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.057 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7542 2.80 - 3.33: 23409 3.33 - 3.85: 48665 3.85 - 4.38: 56808 4.38 - 4.90: 97695 Nonbonded interactions: 234119 Sorted by model distance: nonbonded pdb=" OD1 ASP C 523 " pdb=" OG SER C 526 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP B 523 " pdb=" OG SER B 526 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP A 523 " pdb=" OG SER A 526 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU B 768 " pdb=" OH TYR C 958 " model vdw 2.337 3.040 nonbonded pdb=" OG SER A 405 " pdb=" O SER A 406 " model vdw 2.346 3.040 ... (remaining 234114 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 6.150 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.280 Find NCS groups from input model: 0.990 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: 0.010 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.899 30390 Z= 0.546 Angle : 0.879 22.646 41580 Z= 0.485 Chirality : 0.058 0.447 4908 Planarity : 0.007 0.103 5172 Dihedral : 14.345 103.873 12183 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.19 % Allowed : 5.45 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.12), residues: 3618 helix: -1.30 (0.15), residues: 786 sheet: -0.22 (0.17), residues: 864 loop : -1.78 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 986 TYR 0.020 0.002 TYR C 822 PHE 0.025 0.002 PHE A 968 TRP 0.016 0.002 TRP A 174 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00643 (30225) covalent geometry : angle 0.82576 (41157) SS BOND : bond 0.18359 ( 72) SS BOND : angle 3.52069 ( 144) hydrogen bonds : bond 0.14774 ( 1068) hydrogen bonds : angle 6.22736 ( 3006) link_ALPHA1-3 : bond 0.00323 ( 6) link_ALPHA1-3 : angle 1.48304 ( 18) link_ALPHA1-4 : bond 0.00787 ( 3) link_ALPHA1-4 : angle 3.83840 ( 9) link_ALPHA1-6 : bond 0.00291 ( 3) link_ALPHA1-6 : angle 1.59331 ( 9) link_BETA1-4 : bond 0.00487 ( 15) link_BETA1-4 : angle 1.92519 ( 45) link_NAG-ASN : bond 0.00400 ( 66) link_NAG-ASN : angle 3.08451 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 490 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8368 (t0) cc_final: 0.8028 (t0) REVERT: A 43 SER cc_start: 0.7974 (t) cc_final: 0.7424 (p) REVERT: A 69 LYS cc_start: 0.7389 (tttm) cc_final: 0.7185 (ttpm) REVERT: A 120 GLU cc_start: 0.6563 (tp30) cc_final: 0.6328 (tp30) REVERT: A 162 VAL cc_start: 0.7905 (t) cc_final: 0.7542 (m) REVERT: A 187 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6480 (ttmm) REVERT: A 213 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5169 (p90) REVERT: A 345 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 351 ASN cc_start: 0.7651 (m-40) cc_final: 0.7388 (t0) REVERT: A 418 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8131 (pt) REVERT: A 500 LYS cc_start: 0.7379 (mtmt) cc_final: 0.7121 (mttt) REVERT: A 613 GLU cc_start: 0.7233 (tp30) cc_final: 0.6880 (tp30) REVERT: A 630 GLN cc_start: 0.8039 (mt0) cc_final: 0.7724 (mt0) REVERT: A 634 LYS cc_start: 0.7925 (tttp) cc_final: 0.7580 (tttp) REVERT: A 655 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 738 MET cc_start: 0.7380 (mmm) cc_final: 0.6912 (mmm) REVERT: A 788 ILE cc_start: 0.7796 (tt) cc_final: 0.7553 (pt) REVERT: A 835 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6587 (t80) REVERT: A 862 MET cc_start: 0.7420 (mmm) cc_final: 0.6980 (mmm) REVERT: A 863 GLN cc_start: 0.6594 (tp40) cc_final: 0.6333 (tp40) REVERT: A 879 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7625 (p) REVERT: A 1050 LYS cc_start: 0.8016 (mttm) cc_final: 0.7795 (mttm) REVERT: A 1060 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6719 (mm-30) REVERT: A 1068 PRO cc_start: 0.7343 (Cg_exo) cc_final: 0.7031 (Cg_endo) REVERT: A 1071 GLN cc_start: 0.6943 (mt0) cc_final: 0.6509 (mp10) REVERT: A 1076 ARG cc_start: 0.7024 (mtp180) cc_final: 0.6560 (mtm180) REVERT: A 1105 ARG cc_start: 0.6136 (ttt90) cc_final: 0.5886 (tpp80) REVERT: A 1173 LYS cc_start: 0.7584 (mtpt) cc_final: 0.6651 (pptt) REVERT: B 27 ASP cc_start: 0.6709 (p0) cc_final: 0.6439 (t0) REVERT: B 39 VAL cc_start: 0.7617 (t) cc_final: 0.7407 (p) REVERT: B 43 SER cc_start: 0.8224 (t) cc_final: 0.7902 (p) REVERT: B 52 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 69 LYS cc_start: 0.7226 (tttm) cc_final: 0.6779 (tttp) REVERT: B 118 TYR cc_start: 0.7351 (m-80) cc_final: 0.6925 (m-80) REVERT: B 155 MET cc_start: 0.8079 (mmm) cc_final: 0.7633 (mmm) REVERT: B 205 GLU cc_start: 0.6942 (tt0) cc_final: 0.6707 (tt0) REVERT: B 218 MET cc_start: 0.8017 (mtm) cc_final: 0.7697 (mtm) REVERT: B 241 THR cc_start: 0.8144 (m) cc_final: 0.7455 (p) REVERT: B 356 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7461 (mm) REVERT: B 369 SER cc_start: 0.8034 (t) cc_final: 0.7559 (p) REVERT: B 399 ASP cc_start: 0.7413 (m-30) cc_final: 0.7198 (m-30) REVERT: B 402 GLN cc_start: 0.7585 (mm110) cc_final: 0.7359 (mm-40) REVERT: B 528 TYR cc_start: 0.7244 (m-80) cc_final: 0.7023 (m-10) REVERT: B 634 LYS cc_start: 0.7409 (tttp) cc_final: 0.7161 (tttp) REVERT: B 655 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 659 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7481 (ttpt) REVERT: B 712 TYR cc_start: 0.8248 (p90) cc_final: 0.7892 (p90) REVERT: B 731 VAL cc_start: 0.7866 (p) cc_final: 0.7635 (m) REVERT: B 780 GLU cc_start: 0.7583 (pm20) cc_final: 0.7291 (pm20) REVERT: B 835 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6472 (t80) REVERT: B 863 GLN cc_start: 0.6793 (tp40) cc_final: 0.6340 (tm130) REVERT: B 865 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7640 (t) REVERT: B 879 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8056 (p) REVERT: B 891 LEU cc_start: 0.7905 (tt) cc_final: 0.7677 (tt) REVERT: B 912 LYS cc_start: 0.7897 (tttt) cc_final: 0.7696 (tptt) REVERT: B 967 MET cc_start: 0.7956 (mtp) cc_final: 0.7527 (mtp) REVERT: B 994 MET cc_start: 0.8067 (tpp) cc_final: 0.7665 (tpp) REVERT: B 1010 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7645 (tttt) REVERT: B 1024 SER cc_start: 0.8013 (m) cc_final: 0.7725 (t) REVERT: B 1038 GLN cc_start: 0.7015 (mm110) cc_final: 0.6357 (mt0) REVERT: B 1066 ASP cc_start: 0.6230 (OUTLIER) cc_final: 0.5893 (p0) REVERT: B 1076 ARG cc_start: 0.6696 (mtp180) cc_final: 0.6471 (mtp85) REVERT: B 1091 GLN cc_start: 0.6850 (tt0) cc_final: 0.6400 (tt0) REVERT: B 1095 ASP cc_start: 0.6594 (m-30) cc_final: 0.6302 (m-30) REVERT: B 1199 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.7066 (p0) REVERT: C 88 LEU cc_start: 0.7756 (mt) cc_final: 0.7183 (pp) REVERT: C 120 GLU cc_start: 0.6548 (tp30) cc_final: 0.6289 (mm-30) REVERT: C 145 ILE cc_start: 0.7593 (mt) cc_final: 0.7155 (mp) REVERT: C 162 VAL cc_start: 0.7961 (t) cc_final: 0.7511 (m) REVERT: C 176 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7670 (mm) REVERT: C 187 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7074 (mmmt) REVERT: C 205 GLU cc_start: 0.6353 (tt0) cc_final: 0.6076 (tt0) REVERT: C 206 ARG cc_start: 0.7390 (mtp85) cc_final: 0.6675 (mtp85) REVERT: C 213 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.5892 (p90) REVERT: C 218 MET cc_start: 0.7747 (mtm) cc_final: 0.7514 (mtm) REVERT: C 273 HIS cc_start: 0.7658 (m-70) cc_final: 0.7452 (m170) REVERT: C 356 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (mp) REVERT: C 402 GLN cc_start: 0.7062 (mm110) cc_final: 0.6784 (mm-40) REVERT: C 415 LYS cc_start: 0.7402 (tttt) cc_final: 0.6962 (ttmm) REVERT: C 503 HIS cc_start: 0.7818 (t70) cc_final: 0.7522 (t70) REVERT: C 511 TYR cc_start: 0.2434 (OUTLIER) cc_final: 0.1582 (m-80) REVERT: C 528 TYR cc_start: 0.7260 (m-80) cc_final: 0.6989 (m-10) REVERT: C 584 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6947 (t0) REVERT: C 630 GLN cc_start: 0.7276 (mt0) cc_final: 0.6533 (mp10) REVERT: C 659 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6895 (tttt) REVERT: C 788 ILE cc_start: 0.7869 (tt) cc_final: 0.7373 (pp) REVERT: C 844 ASN cc_start: 0.7110 (m-40) cc_final: 0.6765 (m-40) REVERT: C 851 ASP cc_start: 0.6514 (m-30) cc_final: 0.6286 (m-30) REVERT: C 879 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8157 (m) REVERT: C 885 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7667 (tptp) REVERT: C 993 THR cc_start: 0.7839 (p) cc_final: 0.7604 (t) REVERT: C 1003 LEU cc_start: 0.7225 (mt) cc_final: 0.7016 (tt) REVERT: C 1013 LEU cc_start: 0.7933 (tp) cc_final: 0.7639 (tm) REVERT: C 1030 GLN cc_start: 0.6708 (mt0) cc_final: 0.6413 (tp40) REVERT: C 1069 GLU cc_start: 0.6929 (tp30) cc_final: 0.6688 (mp0) REVERT: C 1071 GLN cc_start: 0.6775 (mt0) cc_final: 0.6416 (mm-40) REVERT: C 1076 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6584 (mtm-85) REVERT: C 1091 GLN cc_start: 0.6893 (tt0) cc_final: 0.6077 (mt0) REVERT: C 1095 ASP cc_start: 0.6238 (m-30) cc_final: 0.5978 (m-30) REVERT: C 1096 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7395 (tp) REVERT: C 1105 ARG cc_start: 0.6150 (ttt90) cc_final: 0.5928 (tpp80) REVERT: C 1118 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 1149 LYS cc_start: 0.7704 (tttt) cc_final: 0.7485 (tttm) REVERT: C 1181 ASN cc_start: 0.6573 (m-40) cc_final: 0.6368 (m-40) REVERT: C 1219 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.4607 (p90) outliers start: 201 outliers final: 38 residues processed: 634 average time/residue: 0.5674 time to fit residues: 435.6848 Evaluate side-chains 375 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1199 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1118 SER Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 630 GLN A 854 GLN A 876 HIS A1091 GLN A1174 GLN A1201 ASN B 204 GLN B 331 ASN B 353 ASN B 876 HIS B 894 GLN B 998 ASN B1001 GLN B1091 GLN C 26 ASN C 204 GLN C 351 ASN C 531 ASN C 630 GLN C 876 HIS C 894 GLN C1001 GLN C1091 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108353 restraints weight = 31364.267| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.91 r_work: 0.3114 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 30390 Z= 0.142 Angle : 0.672 20.122 41580 Z= 0.344 Chirality : 0.049 0.819 4908 Planarity : 0.006 0.086 5172 Dihedral : 10.073 97.598 5949 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.00 % Allowed : 9.70 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: -0.94 (0.13), residues: 3618 helix: 0.73 (0.19), residues: 801 sheet: -0.15 (0.16), residues: 867 loop : -1.46 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 693 TYR 0.023 0.002 TYR B 212 PHE 0.021 0.002 PHE C 968 TRP 0.016 0.002 TRP C 174 HIS 0.008 0.001 HIS C 799 Details of bonding type rmsd covalent geometry : bond 0.00317 (30225) covalent geometry : angle 0.62707 (41157) SS BOND : bond 0.00406 ( 72) SS BOND : angle 1.36901 ( 144) hydrogen bonds : bond 0.05729 ( 1068) hydrogen bonds : angle 5.24216 ( 3006) link_ALPHA1-3 : bond 0.00399 ( 6) link_ALPHA1-3 : angle 1.92218 ( 18) link_ALPHA1-4 : bond 0.01084 ( 3) link_ALPHA1-4 : angle 3.71635 ( 9) link_ALPHA1-6 : bond 0.00715 ( 3) link_ALPHA1-6 : angle 1.35676 ( 9) link_BETA1-4 : bond 0.00248 ( 15) link_BETA1-4 : angle 1.36379 ( 45) link_NAG-ASN : bond 0.00497 ( 66) link_NAG-ASN : angle 3.22031 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 341 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8603 (t0) cc_final: 0.8365 (t0) REVERT: A 114 ASN cc_start: 0.5176 (m-40) cc_final: 0.4822 (m-40) REVERT: A 120 GLU cc_start: 0.7978 (tp30) cc_final: 0.7699 (tp30) REVERT: A 187 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8445 (tppt) REVERT: A 213 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7528 (p90) REVERT: A 272 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 568 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7553 (p) REVERT: A 570 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7679 (p0) REVERT: A 613 GLU cc_start: 0.8109 (tp30) cc_final: 0.7835 (tp30) REVERT: A 630 GLN cc_start: 0.8815 (mt0) cc_final: 0.8580 (mt0) REVERT: A 835 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6726 (t80) REVERT: A 862 MET cc_start: 0.8544 (mmm) cc_final: 0.8284 (mmm) REVERT: A 1060 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8045 (mm-30) REVERT: A 1068 PRO cc_start: 0.7744 (Cg_exo) cc_final: 0.7468 (Cg_endo) REVERT: A 1076 ARG cc_start: 0.8497 (mtp180) cc_final: 0.8263 (mtm180) REVERT: B 40 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7851 (t) REVERT: B 118 TYR cc_start: 0.7833 (m-80) cc_final: 0.7592 (m-80) REVERT: B 155 MET cc_start: 0.9066 (mmm) cc_final: 0.8697 (mmm) REVERT: B 206 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8870 (mtt90) REVERT: B 241 THR cc_start: 0.8474 (m) cc_final: 0.7832 (p) REVERT: B 356 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 528 TYR cc_start: 0.7378 (m-80) cc_final: 0.6834 (m-10) REVERT: B 771 ASN cc_start: 0.6714 (t0) cc_final: 0.6177 (p0) REVERT: B 835 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7319 (t80) REVERT: B 865 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8299 (t) REVERT: B 872 ASN cc_start: 0.8109 (t0) cc_final: 0.7892 (t0) REVERT: B 891 LEU cc_start: 0.8195 (tt) cc_final: 0.7936 (tt) REVERT: B 994 MET cc_start: 0.8824 (tpp) cc_final: 0.8533 (tpt) REVERT: B 1038 GLN cc_start: 0.8181 (mm110) cc_final: 0.7867 (mt0) REVERT: B 1076 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8096 (mtp85) REVERT: B 1091 GLN cc_start: 0.8524 (tt0) cc_final: 0.8130 (tt0) REVERT: C 88 LEU cc_start: 0.8661 (mt) cc_final: 0.8196 (pp) REVERT: C 162 VAL cc_start: 0.8292 (t) cc_final: 0.7694 (m) REVERT: C 164 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7177 (mptt) REVERT: C 176 ILE cc_start: 0.8668 (tp) cc_final: 0.8368 (mm) REVERT: C 187 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8138 (mmtp) REVERT: C 206 ARG cc_start: 0.8981 (mtp85) cc_final: 0.8609 (mtp85) REVERT: C 213 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7916 (p90) REVERT: C 356 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8804 (mp) REVERT: C 500 LYS cc_start: 0.8553 (mtpm) cc_final: 0.8123 (ptpp) REVERT: C 511 TYR cc_start: 0.3345 (OUTLIER) cc_final: 0.2462 (m-80) REVERT: C 528 TYR cc_start: 0.7518 (m-80) cc_final: 0.6953 (m-10) REVERT: C 584 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7651 (t0) REVERT: C 630 GLN cc_start: 0.8535 (mt0) cc_final: 0.8163 (mp10) REVERT: C 659 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8796 (tttt) REVERT: C 844 ASN cc_start: 0.8844 (m-40) cc_final: 0.8559 (m-40) REVERT: C 885 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8357 (tptp) REVERT: C 1091 GLN cc_start: 0.8600 (tt0) cc_final: 0.8069 (mt0) REVERT: C 1096 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8741 (tp) outliers start: 130 outliers final: 59 residues processed: 444 average time/residue: 0.4623 time to fit residues: 251.9148 Evaluate side-chains 350 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 271 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1030 GLN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1200 LYS Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 885 LYS Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 341 optimal weight: 0.5980 chunk 301 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 854 GLN A 998 ASN A1091 GLN A1174 GLN A1201 ASN B1001 GLN B1059 GLN C 351 ASN C 838 ASN ** C 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106486 restraints weight = 31309.479| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.89 r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30390 Z= 0.161 Angle : 0.675 13.020 41580 Z= 0.350 Chirality : 0.047 0.409 4908 Planarity : 0.005 0.077 5172 Dihedral : 9.446 103.945 5919 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.41 % Allowed : 11.03 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.13), residues: 3618 helix: 1.32 (0.20), residues: 801 sheet: -0.08 (0.16), residues: 861 loop : -1.33 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 693 TYR 0.021 0.002 TYR B 212 PHE 0.019 0.002 PHE B 968 TRP 0.014 0.002 TRP B 174 HIS 0.007 0.001 HIS C 799 Details of bonding type rmsd covalent geometry : bond 0.00367 (30225) covalent geometry : angle 0.64064 (41157) SS BOND : bond 0.00557 ( 72) SS BOND : angle 1.47502 ( 144) hydrogen bonds : bond 0.05912 ( 1068) hydrogen bonds : angle 5.20904 ( 3006) link_ALPHA1-3 : bond 0.00479 ( 6) link_ALPHA1-3 : angle 1.83605 ( 18) link_ALPHA1-4 : bond 0.01667 ( 3) link_ALPHA1-4 : angle 3.72530 ( 9) link_ALPHA1-6 : bond 0.00642 ( 3) link_ALPHA1-6 : angle 1.47576 ( 9) link_BETA1-4 : bond 0.00206 ( 15) link_BETA1-4 : angle 1.47884 ( 45) link_NAG-ASN : bond 0.00464 ( 66) link_NAG-ASN : angle 2.70292 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 283 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.4981 (m-40) cc_final: 0.4683 (m-40) REVERT: A 120 GLU cc_start: 0.7980 (tp30) cc_final: 0.7712 (tp30) REVERT: A 187 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8470 (tppt) REVERT: A 213 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7594 (p90) REVERT: A 570 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7725 (p0) REVERT: A 613 GLU cc_start: 0.8149 (tp30) cc_final: 0.7845 (tp30) REVERT: A 630 GLN cc_start: 0.8766 (mt0) cc_final: 0.8536 (mt0) REVERT: A 835 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6697 (t80) REVERT: A 1060 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8062 (mm-30) REVERT: A 1068 PRO cc_start: 0.7777 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: A 1076 ARG cc_start: 0.8454 (mtp180) cc_final: 0.8230 (mtm180) REVERT: B 40 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8171 (t) REVERT: B 69 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8659 (tttp) REVERT: B 118 TYR cc_start: 0.7895 (m-80) cc_final: 0.7521 (m-80) REVERT: B 206 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8866 (mtt90) REVERT: B 311 VAL cc_start: 0.8329 (t) cc_final: 0.8030 (m) REVERT: B 356 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8453 (mm) REVERT: B 528 TYR cc_start: 0.7339 (m-80) cc_final: 0.6840 (m-10) REVERT: B 835 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7284 (t80) REVERT: B 865 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 872 ASN cc_start: 0.8075 (t0) cc_final: 0.7817 (t0) REVERT: B 891 LEU cc_start: 0.8182 (tt) cc_final: 0.7963 (tt) REVERT: B 994 MET cc_start: 0.8867 (tpp) cc_final: 0.8554 (tpt) REVERT: B 1038 GLN cc_start: 0.8183 (mm110) cc_final: 0.7901 (mt0) REVERT: B 1071 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: B 1076 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8189 (mtp85) REVERT: C 88 LEU cc_start: 0.8689 (mt) cc_final: 0.8153 (pt) REVERT: C 162 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.7900 (m) REVERT: C 164 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7031 (mptt) REVERT: C 176 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8342 (mm) REVERT: C 187 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8102 (mmtp) REVERT: C 206 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8502 (mtp85) REVERT: C 213 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.7763 (p90) REVERT: C 356 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8790 (mp) REVERT: C 402 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8335 (mm-40) REVERT: C 415 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8481 (ttmm) REVERT: C 500 LYS cc_start: 0.8546 (mtpm) cc_final: 0.8140 (ptpp) REVERT: C 511 TYR cc_start: 0.3337 (OUTLIER) cc_final: 0.2451 (m-80) REVERT: C 528 TYR cc_start: 0.7579 (m-80) cc_final: 0.6890 (m-10) REVERT: C 584 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7691 (t0) REVERT: C 630 GLN cc_start: 0.8576 (mt0) cc_final: 0.8196 (mp10) REVERT: C 659 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8773 (tttt) REVERT: C 844 ASN cc_start: 0.8806 (m-40) cc_final: 0.8555 (m-40) REVERT: C 1091 GLN cc_start: 0.8676 (tt0) cc_final: 0.8214 (mp10) outliers start: 143 outliers final: 74 residues processed: 391 average time/residue: 0.4462 time to fit residues: 215.7671 Evaluate side-chains 366 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 270 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1030 GLN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1205 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain C residue 1075 ASP Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 258 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 233 optimal weight: 0.1980 chunk 187 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 840 ASN A1079 ASN A1091 GLN A1135 GLN A1174 GLN B 384 ASN B 562 HIS B 984 GLN B 998 ASN B1001 GLN B1045 GLN B1174 GLN C 26 ASN C 351 ASN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104894 restraints weight = 31021.652| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.89 r_work: 0.3060 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30390 Z= 0.215 Angle : 0.761 15.614 41580 Z= 0.392 Chirality : 0.050 0.415 4908 Planarity : 0.006 0.076 5172 Dihedral : 9.441 100.189 5914 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 4.71 % Allowed : 11.28 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.13), residues: 3618 helix: 1.27 (0.19), residues: 801 sheet: -0.12 (0.17), residues: 837 loop : -1.34 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 693 TYR 0.024 0.002 TYR B 212 PHE 0.021 0.003 PHE A 764 TRP 0.016 0.002 TRP C 444 HIS 0.008 0.001 HIS C 799 Details of bonding type rmsd covalent geometry : bond 0.00509 (30225) covalent geometry : angle 0.71139 (41157) SS BOND : bond 0.00672 ( 72) SS BOND : angle 1.73989 ( 144) hydrogen bonds : bond 0.06694 ( 1068) hydrogen bonds : angle 5.37497 ( 3006) link_ALPHA1-3 : bond 0.00336 ( 6) link_ALPHA1-3 : angle 1.94956 ( 18) link_ALPHA1-4 : bond 0.01317 ( 3) link_ALPHA1-4 : angle 3.70663 ( 9) link_ALPHA1-6 : bond 0.00614 ( 3) link_ALPHA1-6 : angle 1.52958 ( 9) link_BETA1-4 : bond 0.00241 ( 15) link_BETA1-4 : angle 1.66819 ( 45) link_NAG-ASN : bond 0.00486 ( 66) link_NAG-ASN : angle 3.51945 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 269 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.5037 (m-40) cc_final: 0.4739 (m-40) REVERT: A 120 GLU cc_start: 0.7975 (tp30) cc_final: 0.7688 (tp30) REVERT: A 187 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: A 273 HIS cc_start: 0.8291 (m-70) cc_final: 0.8032 (m-70) REVERT: A 375 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8625 (tttt) REVERT: A 570 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7714 (p0) REVERT: A 613 GLU cc_start: 0.8215 (tp30) cc_final: 0.7917 (tp30) REVERT: A 630 GLN cc_start: 0.8820 (mt0) cc_final: 0.8588 (mt0) REVERT: A 735 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7705 (p0) REVERT: A 835 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6889 (t80) REVERT: A 1071 GLN cc_start: 0.8009 (mt0) cc_final: 0.7712 (tt0) REVERT: B 69 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8673 (tttp) REVERT: B 118 TYR cc_start: 0.7941 (m-80) cc_final: 0.7554 (m-80) REVERT: B 180 GLU cc_start: 0.7102 (tp30) cc_final: 0.6873 (mp0) REVERT: B 206 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8876 (mtt90) REVERT: B 213 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.7361 (p90) REVERT: B 311 VAL cc_start: 0.8384 (t) cc_final: 0.8169 (m) REVERT: B 356 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 363 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8550 (t) REVERT: B 528 TYR cc_start: 0.7336 (m-80) cc_final: 0.6911 (m-10) REVERT: B 768 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: B 835 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7352 (t80) REVERT: B 865 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 872 ASN cc_start: 0.8196 (t0) cc_final: 0.7893 (t0) REVERT: B 891 LEU cc_start: 0.8180 (tt) cc_final: 0.7919 (tt) REVERT: B 994 MET cc_start: 0.8920 (tpp) cc_final: 0.8587 (tpt) REVERT: B 1038 GLN cc_start: 0.8201 (mm110) cc_final: 0.7898 (mt0) REVERT: B 1071 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: B 1076 ARG cc_start: 0.8607 (mtp180) cc_final: 0.8296 (mtp85) REVERT: B 1108 GLU cc_start: 0.8806 (tt0) cc_final: 0.8560 (tt0) REVERT: C 162 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8195 (m) REVERT: C 164 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7047 (mptt) REVERT: C 176 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8406 (mm) REVERT: C 187 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8058 (mmtp) REVERT: C 206 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8568 (mtp85) REVERT: C 213 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.7811 (p90) REVERT: C 241 THR cc_start: 0.8939 (m) cc_final: 0.8262 (p) REVERT: C 249 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.5759 (p) REVERT: C 356 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8721 (mp) REVERT: C 399 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: C 402 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8375 (mm-40) REVERT: C 415 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8527 (ttmm) REVERT: C 500 LYS cc_start: 0.8555 (mtpm) cc_final: 0.8088 (mtpt) REVERT: C 511 TYR cc_start: 0.3027 (OUTLIER) cc_final: 0.2497 (m-80) REVERT: C 528 TYR cc_start: 0.7767 (m-80) cc_final: 0.6974 (m-80) REVERT: C 584 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7721 (t0) REVERT: C 630 GLN cc_start: 0.8650 (mt0) cc_final: 0.8268 (mp10) REVERT: C 659 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8880 (tttt) REVERT: C 844 ASN cc_start: 0.8876 (m-40) cc_final: 0.8651 (m-40) REVERT: C 1071 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: C 1091 GLN cc_start: 0.8644 (tt0) cc_final: 0.8194 (mp10) outliers start: 153 outliers final: 82 residues processed: 385 average time/residue: 0.4810 time to fit residues: 229.8787 Evaluate side-chains 369 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 259 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1030 GLN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain B residue 1205 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 96 optimal weight: 6.9990 chunk 310 optimal weight: 0.7980 chunk 302 optimal weight: 4.9990 chunk 332 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 343 optimal weight: 0.4980 chunk 354 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A1091 GLN A1174 GLN B 874 ASN B1174 GLN C 26 ASN C 351 ASN C 863 GLN C1001 GLN C1122 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107973 restraints weight = 31358.296| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.92 r_work: 0.3107 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30390 Z= 0.119 Angle : 0.631 16.756 41580 Z= 0.321 Chirality : 0.045 0.400 4908 Planarity : 0.005 0.072 5172 Dihedral : 8.697 98.618 5912 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.97 % Allowed : 12.20 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.14), residues: 3618 helix: 1.65 (0.20), residues: 804 sheet: 0.01 (0.17), residues: 858 loop : -1.16 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 693 TYR 0.017 0.001 TYR B 212 PHE 0.017 0.001 PHE A 968 TRP 0.014 0.001 TRP B 174 HIS 0.006 0.001 HIS C 799 Details of bonding type rmsd covalent geometry : bond 0.00260 (30225) covalent geometry : angle 0.58018 (41157) SS BOND : bond 0.00376 ( 72) SS BOND : angle 1.38718 ( 144) hydrogen bonds : bond 0.04980 ( 1068) hydrogen bonds : angle 5.05235 ( 3006) link_ALPHA1-3 : bond 0.00460 ( 6) link_ALPHA1-3 : angle 1.95013 ( 18) link_ALPHA1-4 : bond 0.01364 ( 3) link_ALPHA1-4 : angle 3.46999 ( 9) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 1.56313 ( 9) link_BETA1-4 : bond 0.00213 ( 15) link_BETA1-4 : angle 1.41649 ( 45) link_NAG-ASN : bond 0.00414 ( 66) link_NAG-ASN : angle 3.28638 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 275 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.4969 (m-40) cc_final: 0.4681 (m-40) REVERT: A 120 GLU cc_start: 0.7917 (tp30) cc_final: 0.7653 (tp30) REVERT: A 187 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8464 (tppt) REVERT: A 213 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.7567 (p90) REVERT: A 568 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7609 (p) REVERT: A 570 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7673 (p0) REVERT: A 613 GLU cc_start: 0.8179 (tp30) cc_final: 0.7882 (mp0) REVERT: A 630 GLN cc_start: 0.8713 (mt0) cc_final: 0.8451 (mt0) REVERT: A 835 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 891 LEU cc_start: 0.8248 (tt) cc_final: 0.8024 (tt) REVERT: B 40 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8131 (t) REVERT: B 69 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8635 (tttp) REVERT: B 118 TYR cc_start: 0.7905 (m-80) cc_final: 0.7491 (m-80) REVERT: B 206 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8862 (mtt90) REVERT: B 311 VAL cc_start: 0.8274 (t) cc_final: 0.8061 (m) REVERT: B 528 TYR cc_start: 0.7327 (m-80) cc_final: 0.6914 (m-10) REVERT: B 768 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: B 835 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7332 (t80) REVERT: B 872 ASN cc_start: 0.8088 (t0) cc_final: 0.7874 (t0) REVERT: B 891 LEU cc_start: 0.8225 (tt) cc_final: 0.7902 (tt) REVERT: B 994 MET cc_start: 0.8919 (tpp) cc_final: 0.8648 (tpt) REVERT: B 1038 GLN cc_start: 0.8219 (mm110) cc_final: 0.7909 (mt0) REVERT: B 1071 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: B 1076 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8127 (mtp85) REVERT: C 162 VAL cc_start: 0.8461 (t) cc_final: 0.8129 (m) REVERT: C 176 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8342 (mm) REVERT: C 187 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8103 (mmtp) REVERT: C 206 ARG cc_start: 0.8948 (mtp85) cc_final: 0.8532 (mtp85) REVERT: C 213 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.7825 (p90) REVERT: C 249 THR cc_start: 0.6313 (OUTLIER) cc_final: 0.5772 (p) REVERT: C 356 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8820 (mp) REVERT: C 415 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8489 (ttmm) REVERT: C 500 LYS cc_start: 0.8645 (mtpm) cc_final: 0.8297 (ptpp) REVERT: C 511 TYR cc_start: 0.3053 (OUTLIER) cc_final: 0.2256 (m-80) REVERT: C 528 TYR cc_start: 0.7666 (m-80) cc_final: 0.6871 (m-10) REVERT: C 573 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8665 (mp) REVERT: C 584 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7702 (t0) REVERT: C 630 GLN cc_start: 0.8558 (mt0) cc_final: 0.8147 (mp10) REVERT: C 659 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8760 (tttt) REVERT: C 844 ASN cc_start: 0.8805 (m-40) cc_final: 0.8558 (m-40) REVERT: C 1069 GLU cc_start: 0.8178 (mp0) cc_final: 0.7750 (tp30) REVERT: C 1071 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7789 (mm-40) REVERT: C 1091 GLN cc_start: 0.8627 (tt0) cc_final: 0.8162 (mp10) outliers start: 129 outliers final: 63 residues processed: 375 average time/residue: 0.4459 time to fit residues: 206.8442 Evaluate side-chains 344 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 259 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 1002 LYS Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1030 GLN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1124 CYS Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 511 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 659 LYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 964 VAL Chi-restraints excluded: chain C residue 1003 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1089 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1124 CYS Chi-restraints excluded: chain C residue 1219 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9362 > 50: distance: 71 - 75: 28.186 distance: 75 - 76: 10.772 distance: 76 - 77: 23.063 distance: 76 - 79: 30.359 distance: 77 - 78: 11.539 distance: 77 - 86: 11.557 distance: 79 - 80: 10.098 distance: 80 - 81: 10.117 distance: 80 - 82: 6.775 distance: 81 - 83: 4.863 distance: 82 - 84: 5.467 distance: 83 - 85: 5.840 distance: 84 - 85: 6.409 distance: 86 - 87: 32.652 distance: 87 - 88: 21.691 distance: 87 - 90: 11.335 distance: 88 - 89: 34.773 distance: 88 - 95: 31.689 distance: 90 - 91: 20.499 distance: 91 - 92: 6.089 distance: 92 - 93: 8.732 distance: 95 - 96: 22.799 distance: 96 - 97: 10.303 distance: 96 - 99: 26.490 distance: 97 - 98: 14.262 distance: 97 - 102: 17.860 distance: 99 - 100: 29.848 distance: 99 - 101: 23.736 distance: 102 - 103: 18.782 distance: 103 - 104: 17.843 distance: 103 - 106: 18.507 distance: 104 - 105: 15.509 distance: 104 - 109: 44.274 distance: 106 - 107: 14.878 distance: 106 - 108: 14.314 distance: 109 - 110: 12.437 distance: 110 - 111: 6.399 distance: 110 - 113: 27.018 distance: 111 - 112: 24.308 distance: 111 - 117: 25.190 distance: 113 - 114: 12.643 distance: 114 - 115: 3.225 distance: 114 - 116: 3.021 distance: 117 - 118: 34.824 distance: 118 - 119: 28.113 distance: 118 - 121: 28.535 distance: 119 - 120: 17.710 distance: 119 - 124: 25.534 distance: 121 - 122: 10.387 distance: 121 - 123: 16.673 distance: 124 - 125: 8.708 distance: 125 - 126: 40.831 distance: 125 - 128: 51.060 distance: 126 - 127: 46.699 distance: 126 - 130: 52.583 distance: 128 - 129: 14.275 distance: 130 - 131: 48.190 distance: 130 - 136: 47.053 distance: 131 - 132: 54.508 distance: 131 - 134: 55.815 distance: 132 - 133: 14.368 distance: 132 - 137: 3.670 distance: 135 - 136: 53.775 distance: 137 - 138: 25.616 distance: 138 - 139: 15.041 distance: 139 - 140: 7.176 distance: 139 - 141: 8.489 distance: 141 - 142: 8.696 distance: 141 - 166: 7.667 distance: 142 - 143: 5.659 distance: 142 - 145: 16.443 distance: 143 - 144: 9.179 distance: 143 - 149: 6.736 distance: 144 - 163: 12.387 distance: 145 - 146: 15.678 distance: 146 - 147: 7.795 distance: 146 - 148: 4.164