Starting phenix.real_space_refine on Sat Mar 7 08:51:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vys_32214/03_2026/7vys_32214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vys_32214/03_2026/7vys_32214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vys_32214/03_2026/7vys_32214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vys_32214/03_2026/7vys_32214.map" model { file = "/net/cci-nas-00/data/ceres_data/7vys_32214/03_2026/7vys_32214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vys_32214/03_2026/7vys_32214.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 293 5.16 5 C 26096 2.51 5 N 6282 2.21 5 O 7406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40113 Number of models: 1 Model: "" Number of chains: 64 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3619 Classifications: {'peptide': 458} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 437} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1022 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 147 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 196 Unusual residues: {'PEE': 2, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "r" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "j" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "k" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "l" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "m" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "s" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "u" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.56 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.56 Time building chain proxies: 8.82, per 1000 atoms: 0.22 Number of scatterers: 40113 At special positions: 0 Unit cell: (182.8, 193.779, 136.689, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 293 16.00 P 36 15.00 O 7406 8.00 N 6282 7.00 C 26096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.04 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied TRANS " TYR r 503 " - " LEU r 458 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8956 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 5 sheets defined 70.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 57 through 61 removed outlier: 4.025A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 removed outlier: 3.637A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 41 through 56 removed outlier: 4.260A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 36 removed outlier: 3.581A pdb=" N SER U 36 " --> pdb=" O PRO U 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 33 through 36' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 83 removed outlier: 3.541A pdb=" N LYS U 82 " --> pdb=" O LEU U 78 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 78 through 83' Processing helix chain 'V' and resid 3 through 12 removed outlier: 4.282A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.210A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.112A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 152 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.743A pdb=" N LEU Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Y' and resid 93 through 98 Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.834A pdb=" N GLN Z 21 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 18 through 22' Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.677A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 50 removed outlier: 3.588A pdb=" N GLU Z 49 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 55 removed outlier: 4.448A pdb=" N GLY Z 55 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 70 through 87 Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 Processing helix chain 'a' and resid 115 through 126 Processing helix chain 'a' and resid 128 through 164 removed outlier: 4.122A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 69 through 74 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'b' and resid 90 through 93 Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 82 through 86 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 128 through 150 Processing helix chain 'd' and resid 28 through 58 removed outlier: 4.853A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 81 through 118 removed outlier: 3.732A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 125 through 144 Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.422A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 95 Processing helix chain 'e' and resid 97 through 108 Processing helix chain 'e' and resid 114 through 133 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 removed outlier: 3.846A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 103 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 removed outlier: 3.935A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 90 Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 Proline residue: i 42 - end of helix removed outlier: 3.577A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 81 Processing helix chain 'i' and resid 91 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.054A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 146 through 149 Processing helix chain 'i' and resid 150 through 170 Processing helix chain 'i' and resid 174 through 193 removed outlier: 3.800A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.573A pdb=" N THR i 201 " --> pdb=" O ASN i 197 " (cutoff:3.500A) Processing helix chain 'i' and resid 226 through 231 Processing helix chain 'i' and resid 232 through 236 Processing helix chain 'i' and resid 237 through 252 removed outlier: 3.737A pdb=" N THR i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.601A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 3.619A pdb=" N THR i 280 " --> pdb=" O ILE i 276 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.758A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 347 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 55 through 73 removed outlier: 3.916A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 Processing helix chain 'j' and resid 83 through 108 removed outlier: 3.532A pdb=" N MET j 87 " --> pdb=" O ASN j 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 21 removed outlier: 3.579A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 52 removed outlier: 3.810A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 57 Processing helix chain 'k' and resid 58 through 86 Processing helix chain 'k' and resid 89 through 93 Processing helix chain 'l' and resid 3 through 14 removed outlier: 3.667A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 22 Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.333A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 83 through 108 Proline residue: l 91 - end of helix removed outlier: 3.829A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 Processing helix chain 'l' and resid 136 through 156 Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.991A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 197 through 205 Processing helix chain 'l' and resid 209 through 224 removed outlier: 4.231A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.694A pdb=" N HIS l 230 " --> pdb=" O PHE l 227 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 removed outlier: 3.517A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) Processing helix chain 'l' and resid 237 through 239 No H-bonds generated for 'chain 'l' and resid 237 through 239' Processing helix chain 'l' and resid 240 through 247 Processing helix chain 'l' and resid 254 through 263 Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 270 through 293 removed outlier: 3.702A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 4.116A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 381 Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.952A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.946A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 470 removed outlier: 5.927A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 488 Processing helix chain 'l' and resid 488 through 507 Processing helix chain 'l' and resid 508 through 510 No H-bonds generated for 'chain 'l' and resid 508 through 510' Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 534 Processing helix chain 'l' and resid 535 through 548 Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.717A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 Processing helix chain 'l' and resid 583 through 601 removed outlier: 3.698A pdb=" N TYR l 587 " --> pdb=" O LEU l 583 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 Processing helix chain 'm' and resid 25 through 46 Processing helix chain 'm' and resid 49 through 75 Processing helix chain 'm' and resid 86 through 110 Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 150 through 174 removed outlier: 4.485A pdb=" N GLY m 174 " --> pdb=" O GLU m 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 12 Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 15 through 23 Proline residue: o 20 - end of helix Processing helix chain 'o' and resid 26 through 52 removed outlier: 3.747A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 62 through 74 Processing helix chain 'o' and resid 76 through 80 Processing helix chain 'o' and resid 83 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 51 removed outlier: 4.439A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 75 Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.804A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.557A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 22 through 39 Processing helix chain 'r' and resid 40 through 43 Processing helix chain 'r' and resid 61 through 81 removed outlier: 4.246A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.612A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.740A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 3.567A pdb=" N TYR r 152 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 4.721A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.026A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 234 Processing helix chain 'r' and resid 236 through 247 removed outlier: 4.103A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 250 No H-bonds generated for 'chain 'r' and resid 248 through 250' Processing helix chain 'r' and resid 253 through 258 Processing helix chain 'r' and resid 258 through 278 removed outlier: 3.699A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 3.634A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.674A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.051A pdb=" N LEU r 351 " --> pdb=" O GLY r 347 " (cutoff:3.500A) Processing helix chain 'r' and resid 352 through 367 Processing helix chain 'r' and resid 372 through 389 Processing helix chain 'r' and resid 391 through 415 removed outlier: 4.165A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA r 404 " --> pdb=" O MET r 400 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 450 Proline residue: r 443 - end of helix removed outlier: 3.553A pdb=" N ASN r 450 " --> pdb=" O LEU r 446 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 455 removed outlier: 3.719A pdb=" N LEU r 455 " --> pdb=" O LYS r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.781A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 Processing helix chain 's' and resid 46 through 57 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 112 Processing helix chain 's' and resid 112 through 124 removed outlier: 4.301A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN s 124 " --> pdb=" O GLY s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 5.305A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.854A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 177 Processing helix chain 's' and resid 178 through 193 Processing helix chain 's' and resid 203 through 208 Processing helix chain 's' and resid 209 through 213 removed outlier: 3.564A pdb=" N ASN s 212 " --> pdb=" O SER s 209 " (cutoff:3.500A) Processing helix chain 's' and resid 216 through 243 removed outlier: 3.708A pdb=" N PHE s 220 " --> pdb=" O ALA s 216 " (cutoff:3.500A) Processing helix chain 's' and resid 251 through 277 removed outlier: 4.268A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 292 removed outlier: 3.619A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 292 through 311 removed outlier: 3.725A pdb=" N LEU s 296 " --> pdb=" O SER s 292 " (cutoff:3.500A) Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 14 Processing helix chain 'u' and resid 21 through 28 Processing helix chain 'u' and resid 28 through 36 Processing helix chain 'u' and resid 36 through 51 Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 92 removed outlier: 3.895A pdb=" N ALA u 79 " --> pdb=" O LYS u 75 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLU u 80 " --> pdb=" O ARG u 76 " (cutoff:3.500A) Proline residue: u 81 - end of helix removed outlier: 3.983A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 116 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 12 through 16 removed outlier: 3.587A pdb=" N LYS v 15 " --> pdb=" O ASP v 12 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 50 Processing helix chain 'v' and resid 59 through 73 Processing helix chain 'v' and resid 81 through 124 Processing helix chain 'w' and resid 39 through 45 Processing helix chain 'w' and resid 49 through 53 removed outlier: 3.609A pdb=" N LEU w 53 " --> pdb=" O THR w 50 " (cutoff:3.500A) Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 94 through 98 Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 166 through 176 removed outlier: 3.734A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN w 176 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 195 removed outlier: 3.565A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (cutoff:3.500A) Processing helix chain 'w' and resid 196 through 198 No H-bonds generated for 'chain 'w' and resid 196 through 198' Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.636A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 removed outlier: 3.819A pdb=" N LYS w 228 " --> pdb=" O HIS w 225 " (cutoff:3.500A) Processing helix chain 'w' and resid 230 through 253 removed outlier: 3.636A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.808A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS w 252 " --> pdb=" O GLU w 248 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 264 removed outlier: 3.911A pdb=" N GLU w 264 " --> pdb=" O ARG w 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 261 through 264' Processing helix chain 'w' and resid 265 through 274 Processing helix chain 'w' and resid 282 through 286 Processing helix chain 'w' and resid 287 through 299 removed outlier: 3.535A pdb=" N GLN w 299 " --> pdb=" O ARG w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 306 Processing helix chain 'w' and resid 307 through 310 removed outlier: 3.851A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 307 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 340 through 348 removed outlier: 4.235A pdb=" N ASN w 344 " --> pdb=" O PRO w 341 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU w 345 " --> pdb=" O GLY w 342 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP w 346 " --> pdb=" O TYR w 343 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY w 348 " --> pdb=" O GLU w 345 " (cutoff:3.500A) Processing helix chain 'w' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.566A pdb=" N LEU U 57 " --> pdb=" O VAL u 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 97 through 98 removed outlier: 5.720A pdb=" N GLU a 97 " --> pdb=" O TYR d 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 5.385A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'w' and resid 84 through 86 removed outlier: 6.552A pdb=" N ILE w 60 " --> pdb=" O LEU w 159 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR w 61 " --> pdb=" O VAL w 205 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL w 207 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP w 63 " --> pdb=" O VAL w 207 " (cutoff:3.500A) 2323 hydrogen bonds defined for protein. 6741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5981 1.31 - 1.44: 11013 1.44 - 1.58: 23057 1.58 - 1.71: 118 1.71 - 1.84: 529 Bond restraints: 40698 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C13 UQ s 402 " pdb=" C14 UQ s 402 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C23 UQ s 402 " pdb=" C24 UQ s 402 " ideal model delta sigma weight residual 1.335 1.543 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C8 UQ s 402 " pdb=" C9 UQ s 402 " ideal model delta sigma weight residual 1.334 1.542 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 40693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 54284 3.49 - 6.98: 483 6.98 - 10.47: 103 10.47 - 13.97: 23 13.97 - 17.46: 12 Bond angle restraints: 54905 Sorted by residual: angle pdb=" C PRO h 94 " pdb=" N PRO h 95 " pdb=" CA PRO h 95 " ideal model delta sigma weight residual 119.66 130.06 -10.40 7.20e-01 1.93e+00 2.09e+02 angle pdb=" N TYR h 92 " pdb=" CA TYR h 92 " pdb=" C TYR h 92 " ideal model delta sigma weight residual 111.28 119.37 -8.09 1.09e+00 8.42e-01 5.51e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.62 -9.29 1.32e+00 5.72e-01 4.94e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.55 -9.22 1.32e+00 5.72e-01 4.87e+01 angle pdb=" C11 CDL l 703 " pdb=" CA5 CDL l 703 " pdb=" OA6 CDL l 703 " ideal model delta sigma weight residual 111.33 120.42 -9.09 1.32e+00 5.72e-01 4.73e+01 ... (remaining 54900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 23496 35.72 - 71.45: 1259 71.45 - 107.17: 89 107.17 - 142.89: 18 142.89 - 178.61: 23 Dihedral angle restraints: 24885 sinusoidal: 11021 harmonic: 13864 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 92.85 -152.84 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" CA ARG c 114 " pdb=" C ARG c 114 " pdb=" N ASN c 115 " pdb=" CA ASN c 115 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA MET b 120 " pdb=" C MET b 120 " pdb=" N LYS b 121 " pdb=" CA LYS b 121 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 24882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5314 0.068 - 0.137: 586 0.137 - 0.205: 22 0.205 - 0.274: 4 0.274 - 0.342: 6 Chirality restraints: 5932 Sorted by residual: chirality pdb=" C6 PLX j 203 " pdb=" C7 PLX j 203 " pdb=" O6 PLX j 203 " pdb=" O7 PLX j 203 " both_signs ideal model delta sigma weight residual False 2.01 2.35 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA TYR h 92 " pdb=" N TYR h 92 " pdb=" C TYR h 92 " pdb=" CB TYR h 92 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C6 PLX a 202 " pdb=" C7 PLX a 202 " pdb=" O6 PLX a 202 " pdb=" O7 PLX a 202 " both_signs ideal model delta sigma weight residual False 2.01 2.33 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 5929 not shown) Planarity restraints: 6679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.444 2.00e-02 2.50e+03 3.90e-01 1.90e+03 pdb=" C18 UQ s 402 " -0.469 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.408 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.012 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.421 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.075 2.00e-02 2.50e+03 2.81e-01 9.89e+02 pdb=" C11 UQ s 402 " 0.082 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.271 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.503 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.183 2.00e-02 2.50e+03 2.17e-01 5.88e+02 pdb=" C13 UQ s 402 " 0.120 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.352 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.041 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.249 2.00e-02 2.50e+03 ... (remaining 6676 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1099 2.71 - 3.26: 38828 3.26 - 3.80: 68291 3.80 - 4.35: 89703 4.35 - 4.90: 143660 Nonbonded interactions: 341581 Sorted by model distance: nonbonded pdb=" O ASP w 285 " pdb=" OD1 ASP w 285 " model vdw 2.160 3.040 nonbonded pdb=" N GLU v 38 " pdb=" OE1 GLU v 38 " model vdw 2.189 3.120 nonbonded pdb=" O HOH i 552 " pdb=" O HOH i 575 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.197 3.040 nonbonded pdb=" NH2 ARG n 47 " pdb=" OE2 GLU n 53 " model vdw 2.199 3.120 ... (remaining 341576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.56 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: 9.320 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: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 34.750 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 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 : 0.008 0.329 40708 Z= 0.467 Angle : 0.881 17.458 54924 Z= 0.437 Chirality : 0.043 0.342 5932 Planarity : 0.009 0.390 6678 Dihedral : 20.516 178.615 15902 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 0.97 % Allowed : 16.95 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 1.73 (0.12), residues: 4666 helix: 2.07 (0.10), residues: 2940 sheet: -0.54 (0.94), residues: 23 loop : -0.48 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG m 173 TYR 0.024 0.001 TYR d 32 PHE 0.032 0.002 PHE i 292 TRP 0.050 0.001 TRP w 353 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00795 (40698) covalent geometry : angle 0.88053 (54905) SS BOND : bond 0.00354 ( 8) SS BOND : angle 2.25562 ( 16) hydrogen bonds : bond 0.12846 ( 2323) hydrogen bonds : angle 5.25413 ( 6741) Misc. bond : bond 0.32874 ( 1) link_TRANS : bond 0.00056 ( 1) link_TRANS : angle 1.28711 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 696 time to evaluate : 1.552 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: X 152 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8465 (mptm) REVERT: d 78 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: d 127 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7973 (tttp) REVERT: f 67 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (mp) REVERT: h 101 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7392 (mttm) REVERT: m 135 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: v 103 GLU cc_start: 0.7725 (tp30) cc_final: 0.7512 (tp30) outliers start: 40 outliers final: 30 residues processed: 727 average time/residue: 0.8782 time to fit residues: 755.8662 Evaluate side-chains 727 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 692 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 152 SER Chi-restraints excluded: chain w residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 27 HIS W 61 GLN Y 49 GLN h 21 GLN ** l 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 66 GLN r 83 HIS r 139 GLN r 192 ASN s 287 HIS u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN w 323 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104231 restraints weight = 41784.374| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.15 r_work: 0.2936 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40708 Z= 0.149 Angle : 0.591 12.325 54924 Z= 0.302 Chirality : 0.042 0.204 5932 Planarity : 0.005 0.054 6678 Dihedral : 19.266 178.435 6733 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.60 % Allowed : 14.86 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 1.91 (0.12), residues: 4666 helix: 2.22 (0.09), residues: 2975 sheet: -0.49 (0.97), residues: 23 loop : -0.46 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.022 0.002 TYR l 587 PHE 0.031 0.002 PHE i 292 TRP 0.024 0.001 TRP w 353 HIS 0.008 0.001 HIS h 98 Details of bonding type rmsd covalent geometry : bond 0.00317 (40698) covalent geometry : angle 0.59035 (54905) SS BOND : bond 0.00524 ( 8) SS BOND : angle 1.37254 ( 16) hydrogen bonds : bond 0.06287 ( 2323) hydrogen bonds : angle 4.30444 ( 6741) Misc. bond : bond 0.00188 ( 1) link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.16515 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 716 time to evaluate : 1.572 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 51 ASP cc_start: 0.8736 (m-30) cc_final: 0.8527 (m-30) REVERT: U 32 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8425 (mp) REVERT: U 79 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: W 51 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8503 (ttm) REVERT: W 85 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: W 123 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8220 (mt-10) REVERT: b 17 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: b 69 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7948 (tt) REVERT: c 36 MET cc_start: 0.7736 (mtm) cc_final: 0.6881 (mmp) REVERT: e 55 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6684 (tt) REVERT: e 78 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8481 (ptpt) REVERT: f 67 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8391 (mp) REVERT: h 101 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7592 (mttm) REVERT: l 21 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8848 (mtt) REVERT: l 383 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7142 (tmt) REVERT: p 28 GLU cc_start: 0.8344 (tt0) cc_final: 0.8031 (tt0) REVERT: r 114 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: r 144 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8488 (t0) REVERT: r 401 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8576 (tmm) REVERT: s 24 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: u 17 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: v 65 GLN cc_start: 0.8271 (mt0) cc_final: 0.7966 (tt0) REVERT: v 70 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8378 (mtpt) REVERT: w 76 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7685 (mm-30) REVERT: w 271 GLU cc_start: 0.7409 (pt0) cc_final: 0.7204 (pt0) REVERT: w 293 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7830 (ttp-110) outliers start: 107 outliers final: 39 residues processed: 770 average time/residue: 0.8906 time to fit residues: 814.1290 Evaluate side-chains 748 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 691 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 163 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 359 optimal weight: 0.9980 chunk 434 optimal weight: 0.0570 chunk 456 optimal weight: 4.9990 chunk 376 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 397 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN g 18 ASN h 21 GLN p 66 GLN r 139 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103938 restraints weight = 41834.239| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.09 r_work: 0.2927 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40708 Z= 0.156 Angle : 0.589 11.011 54924 Z= 0.302 Chirality : 0.042 0.208 5932 Planarity : 0.005 0.048 6678 Dihedral : 18.150 176.289 6680 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.84 % Allowed : 15.13 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 1.94 (0.12), residues: 4666 helix: 2.25 (0.09), residues: 2979 sheet: -0.42 (0.99), residues: 23 loop : -0.47 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 173 TYR 0.024 0.002 TYR l 587 PHE 0.031 0.002 PHE i 292 TRP 0.020 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00344 (40698) covalent geometry : angle 0.58880 (54905) SS BOND : bond 0.00455 ( 8) SS BOND : angle 1.40639 ( 16) hydrogen bonds : bond 0.06401 ( 2323) hydrogen bonds : angle 4.25097 ( 6741) Misc. bond : bond 0.00015 ( 1) link_TRANS : bond 0.00047 ( 1) link_TRANS : angle 0.20239 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 697 time to evaluate : 1.623 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 62 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7825 (mtpp) REVERT: U 79 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: W 51 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8471 (ttm) REVERT: W 85 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: a 72 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8170 (ttm170) REVERT: b 17 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: c 36 MET cc_start: 0.8004 (mtm) cc_final: 0.7163 (mmp) REVERT: e 55 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6624 (tt) REVERT: e 78 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (ptpt) REVERT: e 138 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7354 (mp0) REVERT: f 67 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8384 (mp) REVERT: l 21 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8816 (mtt) REVERT: l 383 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7280 (tmt) REVERT: n 15 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8601 (pp) REVERT: p 135 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7319 (ttp-110) REVERT: r 114 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: r 144 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8546 (t0) REVERT: s 24 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: s 202 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: u 17 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: u 98 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8292 (ptt90) REVERT: v 65 GLN cc_start: 0.8301 (mt0) cc_final: 0.8033 (tt0) REVERT: v 70 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8385 (mtpt) REVERT: w 271 GLU cc_start: 0.7338 (pt0) cc_final: 0.7128 (pt0) REVERT: w 293 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7856 (ttp-110) outliers start: 117 outliers final: 45 residues processed: 760 average time/residue: 0.8695 time to fit residues: 782.5027 Evaluate side-chains 741 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 675 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 62 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 98 ARG Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 123 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 452 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 385 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN e 132 ASN g 18 ASN p 66 GLN r 139 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102539 restraints weight = 41689.474| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.07 r_work: 0.2911 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40708 Z= 0.183 Angle : 0.629 11.603 54924 Z= 0.322 Chirality : 0.044 0.214 5932 Planarity : 0.005 0.050 6678 Dihedral : 17.661 168.842 6680 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 3.23 % Allowed : 15.10 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 1.84 (0.12), residues: 4666 helix: 2.16 (0.09), residues: 2981 sheet: -0.35 (0.99), residues: 23 loop : -0.49 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG m 173 TYR 0.026 0.002 TYR l 587 PHE 0.030 0.002 PHE i 292 TRP 0.028 0.002 TRP w 353 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00418 (40698) covalent geometry : angle 0.62834 (54905) SS BOND : bond 0.00685 ( 8) SS BOND : angle 1.58104 ( 16) hydrogen bonds : bond 0.06988 ( 2323) hydrogen bonds : angle 4.32677 ( 6741) Misc. bond : bond 0.00041 ( 1) link_TRANS : bond 0.00059 ( 1) link_TRANS : angle 0.19579 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 681 time to evaluate : 1.594 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 28 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8644 (mtpt) REVERT: U 79 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: V 51 GLU cc_start: 0.7233 (tt0) cc_final: 0.6985 (tt0) REVERT: W 51 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8396 (ttm) REVERT: W 85 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: a 72 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8205 (ttm170) REVERT: b 17 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: c 36 MET cc_start: 0.8251 (mtm) cc_final: 0.7445 (mmp) REVERT: e 55 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6713 (tt) REVERT: e 78 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8471 (ptpt) REVERT: e 138 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7382 (mp0) REVERT: f 67 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8385 (mp) REVERT: l 383 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7367 (tmt) REVERT: n 15 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8639 (pp) REVERT: p 28 GLU cc_start: 0.8393 (tt0) cc_final: 0.8090 (tt0) REVERT: p 135 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7373 (ttp-110) REVERT: r 114 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: r 144 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8530 (t0) REVERT: s 100 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8916 (mt) REVERT: s 202 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: u 17 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: u 98 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8231 (ptt90) REVERT: v 103 GLU cc_start: 0.8056 (tp30) cc_final: 0.7800 (tp30) REVERT: w 271 GLU cc_start: 0.7354 (pt0) cc_final: 0.7143 (pt0) REVERT: w 293 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7855 (ttp-110) outliers start: 133 outliers final: 59 residues processed: 758 average time/residue: 0.8840 time to fit residues: 793.1800 Evaluate side-chains 751 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 673 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 39 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain u residue 98 ARG Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 272 ASP Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 94 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 229 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN e 132 ASN g 18 ASN i 319 HIS p 66 GLN r 139 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106696 restraints weight = 41888.377| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.07 r_work: 0.2976 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40708 Z= 0.122 Angle : 0.541 10.303 54924 Z= 0.276 Chirality : 0.040 0.197 5932 Planarity : 0.004 0.044 6678 Dihedral : 16.740 162.341 6680 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.31 % Allowed : 16.25 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 2.12 (0.12), residues: 4666 helix: 2.38 (0.09), residues: 2980 sheet: -0.19 (1.03), residues: 23 loop : -0.40 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 173 TYR 0.023 0.001 TYR c 150 PHE 0.033 0.001 PHE i 292 TRP 0.038 0.001 TRP w 353 HIS 0.004 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00248 (40698) covalent geometry : angle 0.54039 (54905) SS BOND : bond 0.00559 ( 8) SS BOND : angle 1.39875 ( 16) hydrogen bonds : bond 0.05445 ( 2323) hydrogen bonds : angle 4.11580 ( 6741) Misc. bond : bond 0.00007 ( 1) link_TRANS : bond 0.00039 ( 1) link_TRANS : angle 0.23321 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 699 time to evaluate : 1.514 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: U 79 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: W 51 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8313 (ttm) REVERT: W 85 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: b 17 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: b 69 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7916 (tt) REVERT: c 36 MET cc_start: 0.8220 (mtm) cc_final: 0.7414 (mmp) REVERT: e 138 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7366 (mp0) REVERT: f 67 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8292 (mp) REVERT: l 383 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7272 (tmt) REVERT: p 28 GLU cc_start: 0.8302 (tt0) cc_final: 0.7982 (tt0) REVERT: r 144 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8490 (t0) REVERT: s 202 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: v 65 GLN cc_start: 0.8301 (mt0) cc_final: 0.8010 (tt0) REVERT: w 271 GLU cc_start: 0.7303 (pt0) cc_final: 0.7074 (pt0) REVERT: w 293 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7796 (ttp-110) outliers start: 95 outliers final: 40 residues processed: 756 average time/residue: 0.8716 time to fit residues: 783.4241 Evaluate side-chains 724 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 674 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 391 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 357 optimal weight: 0.6980 chunk 173 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN e 86 ASN e 132 ASN g 18 ASN p 66 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102422 restraints weight = 41786.037| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.02 r_work: 0.2906 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 40708 Z= 0.198 Angle : 0.641 10.657 54924 Z= 0.329 Chirality : 0.045 0.214 5932 Planarity : 0.005 0.049 6678 Dihedral : 16.746 162.016 6677 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.65 % Allowed : 16.08 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 1.87 (0.12), residues: 4666 helix: 2.17 (0.09), residues: 2981 sheet: -0.23 (1.01), residues: 23 loop : -0.45 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG m 173 TYR 0.028 0.002 TYR l 587 PHE 0.030 0.002 PHE r 122 TRP 0.028 0.002 TRP w 353 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00466 (40698) covalent geometry : angle 0.64036 (54905) SS BOND : bond 0.00569 ( 8) SS BOND : angle 1.67183 ( 16) hydrogen bonds : bond 0.07127 ( 2323) hydrogen bonds : angle 4.32070 ( 6741) Misc. bond : bond 0.00079 ( 1) link_TRANS : bond 0.00085 ( 1) link_TRANS : angle 0.22886 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 676 time to evaluate : 1.550 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 10 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7661 (tppp) REVERT: U 79 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: V 51 GLU cc_start: 0.7245 (tt0) cc_final: 0.6981 (tt0) REVERT: W 51 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8451 (ttm) REVERT: W 85 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: a 72 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8179 (ttm170) REVERT: b 17 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: b 69 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7952 (tt) REVERT: c 36 MET cc_start: 0.8344 (mtm) cc_final: 0.7551 (mmp) REVERT: e 138 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7405 (mp0) REVERT: f 67 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8402 (mp) REVERT: l 383 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7360 (tmt) REVERT: l 562 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8732 (tt) REVERT: p 135 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7395 (ttp-110) REVERT: r 114 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: r 144 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8540 (t0) REVERT: s 202 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: u 17 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: v 15 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7540 (mtmm) REVERT: v 16 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: v 103 GLU cc_start: 0.8048 (tp30) cc_final: 0.7803 (tp30) REVERT: w 271 GLU cc_start: 0.7334 (pt0) cc_final: 0.7105 (pt0) REVERT: w 293 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7875 (ttp-110) outliers start: 109 outliers final: 51 residues processed: 742 average time/residue: 0.8985 time to fit residues: 791.1982 Evaluate side-chains 738 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 670 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 175 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 325 optimal weight: 0.9990 chunk 389 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN e 132 ASN g 18 ASN p 66 GLN r 139 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106043 restraints weight = 41837.865| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.04 r_work: 0.2969 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40708 Z= 0.129 Angle : 0.552 10.402 54924 Z= 0.283 Chirality : 0.041 0.200 5932 Planarity : 0.004 0.046 6678 Dihedral : 16.123 161.450 6677 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 2.26 % Allowed : 16.68 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 2.08 (0.12), residues: 4666 helix: 2.34 (0.09), residues: 2985 sheet: -0.12 (1.03), residues: 23 loop : -0.38 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG m 173 TYR 0.020 0.001 TYR l 587 PHE 0.032 0.001 PHE i 292 TRP 0.030 0.001 TRP w 353 HIS 0.004 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00269 (40698) covalent geometry : angle 0.55172 (54905) SS BOND : bond 0.00411 ( 8) SS BOND : angle 1.49526 ( 16) hydrogen bonds : bond 0.05685 ( 2323) hydrogen bonds : angle 4.14108 ( 6741) Misc. bond : bond 0.00019 ( 1) link_TRANS : bond 0.00055 ( 1) link_TRANS : angle 0.21101 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 680 time to evaluate : 1.601 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: U 10 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7548 (tppp) REVERT: U 79 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: W 51 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8331 (ttm) REVERT: W 85 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: a 72 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8140 (ttm170) REVERT: b 17 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: b 69 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7935 (tt) REVERT: c 36 MET cc_start: 0.8332 (mtm) cc_final: 0.7545 (mmp) REVERT: d 127 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (tttp) REVERT: e 138 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7431 (mp0) REVERT: f 67 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8322 (mp) REVERT: i 88 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6049 (ttmp) REVERT: l 383 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7337 (tmt) REVERT: l 411 MET cc_start: 0.8540 (mmp) cc_final: 0.8332 (mmp) REVERT: p 28 GLU cc_start: 0.8297 (tt0) cc_final: 0.7978 (tt0) REVERT: p 135 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7229 (ttp-110) REVERT: r 144 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8494 (t0) REVERT: s 202 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: u 17 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: u 38 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (ttmp) REVERT: v 15 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7711 (mtmm) REVERT: v 65 GLN cc_start: 0.8280 (mt0) cc_final: 0.8004 (tt0) REVERT: w 271 GLU cc_start: 0.7297 (pt0) cc_final: 0.7056 (pt0) REVERT: w 293 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7821 (ttp-110) outliers start: 93 outliers final: 48 residues processed: 733 average time/residue: 0.8923 time to fit residues: 772.9733 Evaluate side-chains 739 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 674 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 26 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 439 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 419 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 423 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN e 132 ASN g 18 ASN p 66 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN w 132 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104948 restraints weight = 41833.665| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.03 r_work: 0.2941 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40708 Z= 0.151 Angle : 0.587 10.896 54924 Z= 0.300 Chirality : 0.042 0.205 5932 Planarity : 0.005 0.050 6678 Dihedral : 15.953 163.056 6677 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.38 % Allowed : 16.66 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 2.04 (0.12), residues: 4666 helix: 2.29 (0.09), residues: 2982 sheet: -0.13 (1.03), residues: 23 loop : -0.38 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG m 173 TYR 0.024 0.002 TYR l 587 PHE 0.031 0.002 PHE i 292 TRP 0.035 0.001 TRP w 353 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00335 (40698) covalent geometry : angle 0.58631 (54905) SS BOND : bond 0.00449 ( 8) SS BOND : angle 1.79048 ( 16) hydrogen bonds : bond 0.06214 ( 2323) hydrogen bonds : angle 4.18788 ( 6741) Misc. bond : bond 0.00044 ( 1) link_TRANS : bond 0.00041 ( 1) link_TRANS : angle 0.20417 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 679 time to evaluate : 1.581 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: U 10 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7628 (tppp) REVERT: U 79 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: W 51 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8315 (ttm) REVERT: W 85 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: a 72 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8163 (ttm170) REVERT: b 17 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: b 69 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7907 (tt) REVERT: c 36 MET cc_start: 0.8356 (mtm) cc_final: 0.7563 (mmp) REVERT: d 35 LYS cc_start: 0.8585 (tptt) cc_final: 0.8184 (tptt) REVERT: d 127 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8191 (tttp) REVERT: e 138 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7488 (mp0) REVERT: f 67 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8340 (mp) REVERT: i 88 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6169 (ttmp) REVERT: l 383 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7353 (tmt) REVERT: l 411 MET cc_start: 0.8569 (mmp) cc_final: 0.8366 (mmp) REVERT: p 28 GLU cc_start: 0.8343 (tt0) cc_final: 0.8029 (tt0) REVERT: p 135 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7363 (ttp-110) REVERT: r 114 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: r 144 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8509 (t0) REVERT: s 202 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: u 17 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: u 38 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8006 (ttmp) REVERT: v 15 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7698 (mtmm) REVERT: v 65 GLN cc_start: 0.8280 (mt0) cc_final: 0.8004 (tt0) REVERT: v 103 GLU cc_start: 0.8018 (tp30) cc_final: 0.7817 (tp30) REVERT: w 271 GLU cc_start: 0.7315 (pt0) cc_final: 0.7072 (pt0) REVERT: w 293 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7808 (ttp-110) outliers start: 98 outliers final: 54 residues processed: 734 average time/residue: 0.8500 time to fit residues: 736.6878 Evaluate side-chains 741 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 669 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 290 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 378 optimal weight: 0.9980 chunk 419 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 397 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 129 GLN Y 49 GLN d 54 GLN e 132 ASN g 18 ASN p 66 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106356 restraints weight = 41988.866| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.07 r_work: 0.2958 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40708 Z= 0.129 Angle : 0.554 11.091 54924 Z= 0.282 Chirality : 0.040 0.198 5932 Planarity : 0.004 0.048 6678 Dihedral : 15.519 163.467 6677 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.02 % Allowed : 17.14 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 2.15 (0.12), residues: 4666 helix: 2.38 (0.09), residues: 2982 sheet: 0.81 (1.23), residues: 18 loop : -0.33 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG m 173 TYR 0.022 0.001 TYR d 32 PHE 0.032 0.001 PHE i 292 TRP 0.038 0.001 TRP w 353 HIS 0.004 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00274 (40698) covalent geometry : angle 0.55355 (54905) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.61534 ( 16) hydrogen bonds : bond 0.05586 ( 2323) hydrogen bonds : angle 4.10729 ( 6741) Misc. bond : bond 0.00025 ( 1) link_TRANS : bond 0.00051 ( 1) link_TRANS : angle 0.19803 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 681 time to evaluate : 1.545 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: U 10 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7574 (tppp) REVERT: U 79 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: W 51 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8277 (ttm) REVERT: W 85 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: a 72 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8164 (ttm170) REVERT: b 17 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: b 69 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7886 (tt) REVERT: c 36 MET cc_start: 0.8374 (mtm) cc_final: 0.7584 (mmp) REVERT: d 35 LYS cc_start: 0.8596 (tptt) cc_final: 0.8194 (tptt) REVERT: d 127 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8199 (tttp) REVERT: e 138 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7489 (mp0) REVERT: f 67 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8301 (mp) REVERT: i 88 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6034 (ttmp) REVERT: l 383 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7341 (tmt) REVERT: p 28 GLU cc_start: 0.8315 (tt0) cc_final: 0.8005 (tt0) REVERT: p 135 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7317 (ttp-110) REVERT: r 144 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8503 (t0) REVERT: s 202 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: s 206 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8416 (mt-10) REVERT: u 38 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7936 (ttmp) REVERT: v 15 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7685 (mtmm) REVERT: v 65 GLN cc_start: 0.8289 (mt0) cc_final: 0.8020 (tt0) REVERT: w 115 GLU cc_start: 0.8243 (mp0) cc_final: 0.8026 (mp0) REVERT: w 271 GLU cc_start: 0.7281 (pt0) cc_final: 0.7032 (pt0) REVERT: w 293 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7803 (ttp-110) outliers start: 83 outliers final: 51 residues processed: 729 average time/residue: 0.8859 time to fit residues: 766.8225 Evaluate side-chains 732 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 665 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 229 optimal weight: 0.3980 chunk 355 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN d 54 GLN g 18 ASN i 221 HIS l 23 ASN p 66 GLN s 99 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106259 restraints weight = 41769.743| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.02 r_work: 0.2964 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40708 Z= 0.136 Angle : 0.567 11.450 54924 Z= 0.289 Chirality : 0.041 0.200 5932 Planarity : 0.005 0.051 6678 Dihedral : 15.265 164.662 6675 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.97 % Allowed : 17.29 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 2.14 (0.12), residues: 4666 helix: 2.36 (0.09), residues: 2982 sheet: 0.83 (1.23), residues: 18 loop : -0.33 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG m 173 TYR 0.027 0.001 TYR c 150 PHE 0.032 0.002 PHE i 292 TRP 0.039 0.001 TRP w 353 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00293 (40698) covalent geometry : angle 0.56610 (54905) SS BOND : bond 0.00408 ( 8) SS BOND : angle 1.67629 ( 16) hydrogen bonds : bond 0.05788 ( 2323) hydrogen bonds : angle 4.12584 ( 6741) Misc. bond : bond 0.00042 ( 1) link_TRANS : bond 0.00038 ( 1) link_TRANS : angle 0.20394 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 671 time to evaluate : 1.632 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: U 10 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7641 (tppp) REVERT: U 79 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: W 51 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8272 (ttm) REVERT: W 85 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: W 98 MET cc_start: 0.7490 (mmm) cc_final: 0.6625 (mmt) REVERT: a 72 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8147 (ttm170) REVERT: b 17 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: b 69 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (tt) REVERT: c 36 MET cc_start: 0.8357 (mtm) cc_final: 0.7578 (mmp) REVERT: d 35 LYS cc_start: 0.8588 (tptt) cc_final: 0.8196 (tptt) REVERT: d 127 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8199 (tttp) REVERT: e 138 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7507 (mp0) REVERT: f 67 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8309 (mp) REVERT: h 24 GLU cc_start: 0.7643 (tp30) cc_final: 0.7402 (tp30) REVERT: i 88 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6108 (ttmp) REVERT: l 383 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7318 (tmt) REVERT: l 411 MET cc_start: 0.8519 (mmp) cc_final: 0.8306 (mmp) REVERT: m 1 MET cc_start: 0.2198 (tpp) cc_final: 0.1922 (tpt) REVERT: p 28 GLU cc_start: 0.8320 (tt0) cc_final: 0.8004 (tt0) REVERT: p 135 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7322 (ttp-110) REVERT: r 144 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8519 (t0) REVERT: s 202 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: s 206 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8399 (mt-10) REVERT: u 17 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: u 38 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7937 (ttmp) REVERT: v 15 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7696 (mtmm) REVERT: v 65 GLN cc_start: 0.8280 (mt0) cc_final: 0.8014 (tt0) REVERT: w 115 GLU cc_start: 0.8219 (mp0) cc_final: 0.8002 (mp0) REVERT: w 271 GLU cc_start: 0.7299 (pt0) cc_final: 0.7020 (pt0) REVERT: w 293 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7791 (ttp-110) outliers start: 81 outliers final: 52 residues processed: 720 average time/residue: 0.9041 time to fit residues: 768.3774 Evaluate side-chains 738 residues out of total 4157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 669 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 51 ARG Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 165 SER Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 249 MET Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 344 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 49 GLN c 127 ASN d 54 GLN e 132 ASN g 18 ASN l 23 ASN p 66 GLN u 65 GLN u 77 HIS v 47 ASN v 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104771 restraints weight = 42017.294| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.03 r_work: 0.2938 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40708 Z= 0.154 Angle : 0.595 11.352 54924 Z= 0.304 Chirality : 0.042 0.206 5932 Planarity : 0.005 0.054 6678 Dihedral : 15.192 166.681 6675 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 1.89 % Allowed : 17.41 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 are not related in a simple way. whole: 2.03 (0.12), residues: 4666 helix: 2.28 (0.09), residues: 2981 sheet: 0.81 (1.22), residues: 18 loop : -0.37 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG m 173 TYR 0.025 0.002 TYR l 587 PHE 0.030 0.002 PHE i 292 TRP 0.042 0.001 TRP w 353 HIS 0.005 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00339 (40698) covalent geometry : angle 0.59452 (54905) SS BOND : bond 0.00443 ( 8) SS BOND : angle 1.85571 ( 16) hydrogen bonds : bond 0.06308 ( 2323) hydrogen bonds : angle 4.20160 ( 6741) Misc. bond : bond 0.00147 ( 1) link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.20223 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22547.50 seconds wall clock time: 382 minutes 54.40 seconds (22974.40 seconds total)