Starting phenix.real_space_refine on Sat Mar 7 09:29:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6l_22077/03_2026/6x6l_22077.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6l_22077/03_2026/6x6l_22077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x6l_22077/03_2026/6x6l_22077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6l_22077/03_2026/6x6l_22077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x6l_22077/03_2026/6x6l_22077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6l_22077/03_2026/6x6l_22077.map" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 25619 2.51 5 N 6868 2.21 5 O 8024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 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: 40613 Number of models: 1 Model: "" Number of chains: 34 Chain: "AX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "BX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "CX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "DX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "EX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "FX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "GX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "HX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "IX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "JX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "KX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "LX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "MX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "NX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "OX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "PX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "QX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "AY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "BY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "CY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "DY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "EY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "FY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "GY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "HY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "IY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "JY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "KY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "LY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "MY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "NY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "OY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "PY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "QY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Time building chain proxies: 8.71, per 1000 atoms: 0.21 Number of scatterers: 40613 At special positions: 0 Unit cell: (202, 201, 98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 8024 8.00 N 6868 7.00 C 25619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYSAY1481 " - pdb=" SG CYSAY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSBY1481 " - pdb=" SG CYSBY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSCY1481 " - pdb=" SG CYSCY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSDY1481 " - pdb=" SG CYSDY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSEY1481 " - pdb=" SG CYSEY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSFY1481 " - pdb=" SG CYSFY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSGY1481 " - pdb=" SG CYSGY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSHY1481 " - pdb=" SG CYSHY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSIY1481 " - pdb=" SG CYSIY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSJY1481 " - pdb=" SG CYSJY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSKY1481 " - pdb=" SG CYSKY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSLY1481 " - pdb=" SG CYSLY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSMY1481 " - pdb=" SG CYSMY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSNY1481 " - pdb=" SG CYSNY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSOY1481 " - pdb=" SG CYSOY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSPY1481 " - pdb=" SG CYSPY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSQY1481 " - pdb=" SG CYSQY1497 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.6 seconds 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9860 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 68 sheets defined 43.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'AX' and resid 82 through 84 No H-bonds generated for 'chain 'AX' and resid 82 through 84' Processing helix chain 'AX' and resid 111 through 129 Processing helix chain 'AX' and resid 272 through 277 Processing helix chain 'AX' and resid 312 through 324 Processing helix chain 'BX' and resid 82 through 84 No H-bonds generated for 'chain 'BX' and resid 82 through 84' Processing helix chain 'BX' and resid 111 through 129 Processing helix chain 'BX' and resid 272 through 277 Processing helix chain 'BX' and resid 312 through 324 Processing helix chain 'CX' and resid 82 through 84 No H-bonds generated for 'chain 'CX' and resid 82 through 84' Processing helix chain 'CX' and resid 111 through 130 Processing helix chain 'CX' and resid 272 through 277 Processing helix chain 'CX' and resid 312 through 324 Processing helix chain 'DX' and resid 82 through 84 No H-bonds generated for 'chain 'DX' and resid 82 through 84' Processing helix chain 'DX' and resid 111 through 129 Processing helix chain 'DX' and resid 272 through 277 Processing helix chain 'DX' and resid 312 through 324 Processing helix chain 'EX' and resid 82 through 84 No H-bonds generated for 'chain 'EX' and resid 82 through 84' Processing helix chain 'EX' and resid 111 through 129 Processing helix chain 'EX' and resid 272 through 277 Processing helix chain 'EX' and resid 312 through 324 Processing helix chain 'FX' and resid 82 through 84 No H-bonds generated for 'chain 'FX' and resid 82 through 84' Processing helix chain 'FX' and resid 111 through 130 Processing helix chain 'FX' and resid 272 through 277 Processing helix chain 'FX' and resid 312 through 324 Processing helix chain 'GX' and resid 82 through 84 No H-bonds generated for 'chain 'GX' and resid 82 through 84' Processing helix chain 'GX' and resid 111 through 130 Processing helix chain 'GX' and resid 272 through 277 Processing helix chain 'GX' and resid 312 through 324 Processing helix chain 'HX' and resid 82 through 84 No H-bonds generated for 'chain 'HX' and resid 82 through 84' Processing helix chain 'HX' and resid 111 through 129 Processing helix chain 'HX' and resid 272 through 277 Processing helix chain 'HX' and resid 312 through 324 Processing helix chain 'IX' and resid 82 through 84 No H-bonds generated for 'chain 'IX' and resid 82 through 84' Processing helix chain 'IX' and resid 110 through 129 removed outlier: 4.687A pdb=" N ASNIX 114 " --> pdb=" O LYSIX 110 " (cutoff:3.500A) Processing helix chain 'IX' and resid 272 through 277 Processing helix chain 'IX' and resid 312 through 324 Processing helix chain 'JX' and resid 82 through 84 No H-bonds generated for 'chain 'JX' and resid 82 through 84' Processing helix chain 'JX' and resid 111 through 129 Processing helix chain 'JX' and resid 272 through 277 Processing helix chain 'JX' and resid 312 through 324 Processing helix chain 'KX' and resid 82 through 84 No H-bonds generated for 'chain 'KX' and resid 82 through 84' Processing helix chain 'KX' and resid 111 through 129 Processing helix chain 'KX' and resid 272 through 277 Processing helix chain 'KX' and resid 312 through 324 Processing helix chain 'LX' and resid 82 through 84 No H-bonds generated for 'chain 'LX' and resid 82 through 84' Processing helix chain 'LX' and resid 111 through 129 Processing helix chain 'LX' and resid 272 through 277 Processing helix chain 'LX' and resid 312 through 324 Processing helix chain 'MX' and resid 82 through 84 No H-bonds generated for 'chain 'MX' and resid 82 through 84' Processing helix chain 'MX' and resid 111 through 129 Processing helix chain 'MX' and resid 272 through 277 Processing helix chain 'MX' and resid 312 through 324 Processing helix chain 'NX' and resid 82 through 84 No H-bonds generated for 'chain 'NX' and resid 82 through 84' Processing helix chain 'NX' and resid 111 through 129 Processing helix chain 'NX' and resid 272 through 277 Processing helix chain 'NX' and resid 312 through 324 Processing helix chain 'OX' and resid 82 through 84 No H-bonds generated for 'chain 'OX' and resid 82 through 84' Processing helix chain 'OX' and resid 111 through 129 Processing helix chain 'OX' and resid 272 through 277 Processing helix chain 'OX' and resid 312 through 324 Processing helix chain 'PX' and resid 82 through 84 No H-bonds generated for 'chain 'PX' and resid 82 through 84' Processing helix chain 'PX' and resid 110 through 129 removed outlier: 4.685A pdb=" N ASNPX 114 " --> pdb=" O LYSPX 110 " (cutoff:3.500A) Processing helix chain 'PX' and resid 272 through 277 Processing helix chain 'PX' and resid 312 through 324 Processing helix chain 'QX' and resid 82 through 84 No H-bonds generated for 'chain 'QX' and resid 82 through 84' Processing helix chain 'QX' and resid 111 through 129 Processing helix chain 'QX' and resid 272 through 277 Processing helix chain 'QX' and resid 312 through 324 Processing helix chain 'AY' and resid 1472 through 1484 Processing helix chain 'AY' and resid 1490 through 1498 Processing helix chain 'AY' and resid 1502 through 1530 removed outlier: 4.558A pdb=" N LYSAY1530 " --> pdb=" O LEUAY1526 " (cutoff:3.500A) Processing helix chain 'AY' and resid 1531 through 1538 Processing helix chain 'AY' and resid 1562 through 1566 removed outlier: 3.508A pdb=" N ILEAY1566 " --> pdb=" O ALAAY1563 " (cutoff:3.500A) Processing helix chain 'AY' and resid 1579 through 1603 Processing helix chain 'BY' and resid 1472 through 1484 Processing helix chain 'BY' and resid 1490 through 1498 Processing helix chain 'BY' and resid 1502 through 1529 Processing helix chain 'BY' and resid 1531 through 1538 Processing helix chain 'BY' and resid 1562 through 1566 Processing helix chain 'BY' and resid 1579 through 1603 Processing helix chain 'CY' and resid 1472 through 1484 Processing helix chain 'CY' and resid 1490 through 1498 Processing helix chain 'CY' and resid 1502 through 1529 Processing helix chain 'CY' and resid 1531 through 1538 Processing helix chain 'CY' and resid 1562 through 1566 Processing helix chain 'CY' and resid 1579 through 1603 Processing helix chain 'DY' and resid 1472 through 1484 Processing helix chain 'DY' and resid 1490 through 1498 Processing helix chain 'DY' and resid 1502 through 1530 removed outlier: 4.531A pdb=" N LYSDY1530 " --> pdb=" O LEUDY1526 " (cutoff:3.500A) Processing helix chain 'DY' and resid 1531 through 1538 Processing helix chain 'DY' and resid 1562 through 1566 Processing helix chain 'DY' and resid 1579 through 1603 Processing helix chain 'EY' and resid 1472 through 1484 Processing helix chain 'EY' and resid 1490 through 1498 Processing helix chain 'EY' and resid 1502 through 1529 Processing helix chain 'EY' and resid 1531 through 1538 Processing helix chain 'EY' and resid 1562 through 1566 removed outlier: 3.503A pdb=" N ILEEY1566 " --> pdb=" O ALAEY1563 " (cutoff:3.500A) Processing helix chain 'EY' and resid 1579 through 1603 Processing helix chain 'FY' and resid 1472 through 1484 Processing helix chain 'FY' and resid 1490 through 1498 Processing helix chain 'FY' and resid 1502 through 1529 Processing helix chain 'FY' and resid 1531 through 1538 Processing helix chain 'FY' and resid 1562 through 1566 Processing helix chain 'FY' and resid 1579 through 1603 Processing helix chain 'GY' and resid 1472 through 1484 Processing helix chain 'GY' and resid 1490 through 1498 Processing helix chain 'GY' and resid 1502 through 1529 Processing helix chain 'GY' and resid 1531 through 1538 Processing helix chain 'GY' and resid 1562 through 1566 Processing helix chain 'GY' and resid 1579 through 1603 Processing helix chain 'HY' and resid 1472 through 1484 Processing helix chain 'HY' and resid 1490 through 1498 Processing helix chain 'HY' and resid 1502 through 1530 removed outlier: 4.546A pdb=" N LYSHY1530 " --> pdb=" O LEUHY1526 " (cutoff:3.500A) Processing helix chain 'HY' and resid 1531 through 1538 Processing helix chain 'HY' and resid 1562 through 1566 Processing helix chain 'HY' and resid 1579 through 1603 Processing helix chain 'IY' and resid 1472 through 1484 Processing helix chain 'IY' and resid 1490 through 1498 Processing helix chain 'IY' and resid 1502 through 1529 Processing helix chain 'IY' and resid 1531 through 1538 Processing helix chain 'IY' and resid 1562 through 1566 Processing helix chain 'IY' and resid 1579 through 1603 Processing helix chain 'JY' and resid 1472 through 1484 Processing helix chain 'JY' and resid 1490 through 1498 Processing helix chain 'JY' and resid 1502 through 1529 Processing helix chain 'JY' and resid 1531 through 1538 Processing helix chain 'JY' and resid 1562 through 1566 Processing helix chain 'JY' and resid 1579 through 1603 Processing helix chain 'KY' and resid 1472 through 1484 Processing helix chain 'KY' and resid 1490 through 1498 Processing helix chain 'KY' and resid 1502 through 1529 Processing helix chain 'KY' and resid 1531 through 1538 Processing helix chain 'KY' and resid 1562 through 1566 Processing helix chain 'KY' and resid 1579 through 1603 Processing helix chain 'LY' and resid 1472 through 1484 Processing helix chain 'LY' and resid 1490 through 1498 Processing helix chain 'LY' and resid 1502 through 1530 removed outlier: 4.596A pdb=" N LYSLY1530 " --> pdb=" O LEULY1526 " (cutoff:3.500A) Processing helix chain 'LY' and resid 1531 through 1538 Processing helix chain 'LY' and resid 1562 through 1566 Processing helix chain 'LY' and resid 1579 through 1603 Processing helix chain 'MY' and resid 1472 through 1484 Processing helix chain 'MY' and resid 1490 through 1498 Processing helix chain 'MY' and resid 1502 through 1530 removed outlier: 4.571A pdb=" N LYSMY1530 " --> pdb=" O LEUMY1526 " (cutoff:3.500A) Processing helix chain 'MY' and resid 1531 through 1538 Processing helix chain 'MY' and resid 1562 through 1566 Processing helix chain 'MY' and resid 1579 through 1603 Processing helix chain 'NY' and resid 1472 through 1484 Processing helix chain 'NY' and resid 1490 through 1498 Processing helix chain 'NY' and resid 1502 through 1529 Processing helix chain 'NY' and resid 1531 through 1538 Processing helix chain 'NY' and resid 1562 through 1566 Processing helix chain 'NY' and resid 1579 through 1603 Processing helix chain 'OY' and resid 1472 through 1484 Processing helix chain 'OY' and resid 1490 through 1498 Processing helix chain 'OY' and resid 1502 through 1529 Processing helix chain 'OY' and resid 1531 through 1538 Processing helix chain 'OY' and resid 1562 through 1566 Processing helix chain 'OY' and resid 1579 through 1603 Processing helix chain 'PY' and resid 1472 through 1484 Processing helix chain 'PY' and resid 1490 through 1498 Processing helix chain 'PY' and resid 1502 through 1530 removed outlier: 4.590A pdb=" N LYSPY1530 " --> pdb=" O LEUPY1526 " (cutoff:3.500A) Processing helix chain 'PY' and resid 1531 through 1538 Processing helix chain 'PY' and resid 1562 through 1566 Processing helix chain 'PY' and resid 1579 through 1603 Processing helix chain 'QY' and resid 1472 through 1484 Processing helix chain 'QY' and resid 1490 through 1498 Processing helix chain 'QY' and resid 1502 through 1529 Processing helix chain 'QY' and resid 1531 through 1538 Processing helix chain 'QY' and resid 1562 through 1566 Processing helix chain 'QY' and resid 1579 through 1603 Processing sheet with id=AA1, first strand: chain 'AX' and resid 41 through 47 removed outlier: 7.754A pdb=" N VALAX 42 " --> pdb=" O THRAX 307 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LYSAX 309 " --> pdb=" O VALAX 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYSAX 44 " --> pdb=" O LYSAX 309 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLUAX 311 " --> pdb=" O LYSAX 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILEAX 46 " --> pdb=" O GLUAX 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AX' and resid 55 through 59 removed outlier: 6.392A pdb=" N ILEAX 55 " --> pdb=" O ILEAX 292 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARGAX 294 " --> pdb=" O ILEAX 55 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILEAX 57 " --> pdb=" O ARGAX 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AX' and resid 102 through 104 Processing sheet with id=AA4, first strand: chain 'AX' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'BX' and resid 41 through 47 removed outlier: 7.695A pdb=" N VALBX 42 " --> pdb=" O THRBX 307 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYSBX 309 " --> pdb=" O VALBX 42 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYSBX 44 " --> pdb=" O LYSBX 309 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLUBX 311 " --> pdb=" O LYSBX 44 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILEBX 46 " --> pdb=" O GLUBX 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BX' and resid 55 through 59 removed outlier: 6.399A pdb=" N ILEBX 55 " --> pdb=" O ILEBX 292 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARGBX 294 " --> pdb=" O ILEBX 55 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILEBX 57 " --> pdb=" O ARGBX 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'BX' and resid 102 through 104 Processing sheet with id=AA8, first strand: chain 'BX' and resid 106 through 108 Processing sheet with id=AA9, first strand: chain 'CX' and resid 41 through 47 removed outlier: 7.720A pdb=" N VALCX 42 " --> pdb=" O THRCX 307 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYSCX 309 " --> pdb=" O VALCX 42 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYSCX 44 " --> pdb=" O LYSCX 309 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLUCX 311 " --> pdb=" O LYSCX 44 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILECX 46 " --> pdb=" O GLUCX 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'CX' and resid 55 through 59 removed outlier: 6.336A pdb=" N ILECX 55 " --> pdb=" O ILECX 292 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARGCX 294 " --> pdb=" O ILECX 55 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILECX 57 " --> pdb=" O ARGCX 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'CX' and resid 102 through 104 Processing sheet with id=AB3, first strand: chain 'CX' and resid 106 through 108 Processing sheet with id=AB4, first strand: chain 'DX' and resid 41 through 47 removed outlier: 7.728A pdb=" N VALDX 42 " --> pdb=" O THRDX 307 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LYSDX 309 " --> pdb=" O VALDX 42 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYSDX 44 " --> pdb=" O LYSDX 309 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLUDX 311 " --> pdb=" O LYSDX 44 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILEDX 46 " --> pdb=" O GLUDX 311 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'DX' and resid 55 through 59 removed outlier: 6.343A pdb=" N ILEDX 55 " --> pdb=" O ILEDX 292 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARGDX 294 " --> pdb=" O ILEDX 55 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILEDX 57 " --> pdb=" O ARGDX 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'DX' and resid 102 through 104 Processing sheet with id=AB7, first strand: chain 'DX' and resid 106 through 108 Processing sheet with id=AB8, first strand: chain 'EX' and resid 41 through 47 removed outlier: 7.728A pdb=" N VALEX 42 " --> pdb=" O THREX 307 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYSEX 309 " --> pdb=" O VALEX 42 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYSEX 44 " --> pdb=" O LYSEX 309 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLUEX 311 " --> pdb=" O LYSEX 44 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILEEX 46 " --> pdb=" O GLUEX 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'EX' and resid 55 through 59 removed outlier: 6.329A pdb=" N ILEEX 55 " --> pdb=" O ILEEX 292 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARGEX 294 " --> pdb=" O ILEEX 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILEEX 57 " --> pdb=" O ARGEX 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'EX' and resid 102 through 104 Processing sheet with id=AC2, first strand: chain 'EX' and resid 106 through 108 Processing sheet with id=AC3, first strand: chain 'FX' and resid 41 through 47 removed outlier: 7.712A pdb=" N VALFX 42 " --> pdb=" O THRFX 307 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LYSFX 309 " --> pdb=" O VALFX 42 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYSFX 44 " --> pdb=" O LYSFX 309 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLUFX 311 " --> pdb=" O LYSFX 44 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILEFX 46 " --> pdb=" O GLUFX 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'FX' and resid 55 through 59 Processing sheet with id=AC5, first strand: chain 'FX' and resid 102 through 104 Processing sheet with id=AC6, first strand: chain 'FX' and resid 106 through 108 Processing sheet with id=AC7, first strand: chain 'GX' and resid 41 through 47 removed outlier: 7.673A pdb=" N VALGX 42 " --> pdb=" O THRGX 307 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LYSGX 309 " --> pdb=" O VALGX 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYSGX 44 " --> pdb=" O LYSGX 309 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLUGX 311 " --> pdb=" O LYSGX 44 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILEGX 46 " --> pdb=" O GLUGX 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'GX' and resid 55 through 59 removed outlier: 6.393A pdb=" N ILEGX 55 " --> pdb=" O ILEGX 292 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARGGX 294 " --> pdb=" O ILEGX 55 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILEGX 57 " --> pdb=" O ARGGX 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'GX' and resid 102 through 104 Processing sheet with id=AD1, first strand: chain 'GX' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'HX' and resid 41 through 47 removed outlier: 7.749A pdb=" N VALHX 42 " --> pdb=" O THRHX 307 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LYSHX 309 " --> pdb=" O VALHX 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYSHX 44 " --> pdb=" O LYSHX 309 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLUHX 311 " --> pdb=" O LYSHX 44 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILEHX 46 " --> pdb=" O GLUHX 311 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'HX' and resid 55 through 59 removed outlier: 6.385A pdb=" N ILEHX 55 " --> pdb=" O ILEHX 292 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARGHX 294 " --> pdb=" O ILEHX 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILEHX 57 " --> pdb=" O ARGHX 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'HX' and resid 102 through 104 Processing sheet with id=AD5, first strand: chain 'HX' and resid 106 through 108 Processing sheet with id=AD6, first strand: chain 'IX' and resid 41 through 47 removed outlier: 7.697A pdb=" N VALIX 42 " --> pdb=" O THRIX 307 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYSIX 309 " --> pdb=" O VALIX 42 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYSIX 44 " --> pdb=" O LYSIX 309 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLUIX 311 " --> pdb=" O LYSIX 44 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILEIX 46 " --> pdb=" O GLUIX 311 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'IX' and resid 55 through 59 removed outlier: 6.414A pdb=" N ILEIX 55 " --> pdb=" O ILEIX 292 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARGIX 294 " --> pdb=" O ILEIX 55 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILEIX 57 " --> pdb=" O ARGIX 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'IX' and resid 102 through 104 Processing sheet with id=AD9, first strand: chain 'IX' and resid 106 through 108 Processing sheet with id=AE1, first strand: chain 'JX' and resid 41 through 47 removed outlier: 7.712A pdb=" N VALJX 42 " --> pdb=" O THRJX 307 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYSJX 309 " --> pdb=" O VALJX 42 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYSJX 44 " --> pdb=" O LYSJX 309 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLUJX 311 " --> pdb=" O LYSJX 44 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILEJX 46 " --> pdb=" O GLUJX 311 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'JX' and resid 55 through 59 removed outlier: 6.327A pdb=" N ILEJX 55 " --> pdb=" O ILEJX 292 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARGJX 294 " --> pdb=" O ILEJX 55 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILEJX 57 " --> pdb=" O ARGJX 294 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'JX' and resid 102 through 104 Processing sheet with id=AE4, first strand: chain 'JX' and resid 106 through 108 Processing sheet with id=AE5, first strand: chain 'KX' and resid 41 through 47 removed outlier: 7.713A pdb=" N VALKX 42 " --> pdb=" O THRKX 307 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYSKX 309 " --> pdb=" O VALKX 42 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYSKX 44 " --> pdb=" O LYSKX 309 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLUKX 311 " --> pdb=" O LYSKX 44 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILEKX 46 " --> pdb=" O GLUKX 311 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KX' and resid 55 through 59 removed outlier: 6.403A pdb=" N ILEKX 55 " --> pdb=" O ILEKX 292 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARGKX 294 " --> pdb=" O ILEKX 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILEKX 57 " --> pdb=" O ARGKX 294 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'KX' and resid 102 through 104 Processing sheet with id=AE8, first strand: chain 'KX' and resid 106 through 108 Processing sheet with id=AE9, first strand: chain 'LX' and resid 41 through 47 removed outlier: 7.678A pdb=" N VALLX 42 " --> pdb=" O THRLX 307 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LYSLX 309 " --> pdb=" O VALLX 42 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYSLX 44 " --> pdb=" O LYSLX 309 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLULX 311 " --> pdb=" O LYSLX 44 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILELX 46 " --> pdb=" O GLULX 311 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LX' and resid 55 through 59 removed outlier: 6.365A pdb=" N ILELX 55 " --> pdb=" O ILELX 292 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARGLX 294 " --> pdb=" O ILELX 55 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILELX 57 " --> pdb=" O ARGLX 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LX' and resid 102 through 104 Processing sheet with id=AF3, first strand: chain 'LX' and resid 106 through 108 Processing sheet with id=AF4, first strand: chain 'MX' and resid 41 through 47 removed outlier: 7.697A pdb=" N VALMX 42 " --> pdb=" O THRMX 307 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LYSMX 309 " --> pdb=" O VALMX 42 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYSMX 44 " --> pdb=" O LYSMX 309 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLUMX 311 " --> pdb=" O LYSMX 44 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILEMX 46 " --> pdb=" O GLUMX 311 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'MX' and resid 55 through 59 removed outlier: 6.377A pdb=" N ILEMX 55 " --> pdb=" O ILEMX 292 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARGMX 294 " --> pdb=" O ILEMX 55 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILEMX 57 " --> pdb=" O ARGMX 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'MX' and resid 102 through 104 Processing sheet with id=AF7, first strand: chain 'MX' and resid 106 through 108 Processing sheet with id=AF8, first strand: chain 'NX' and resid 41 through 47 removed outlier: 7.741A pdb=" N VALNX 42 " --> pdb=" O THRNX 307 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LYSNX 309 " --> pdb=" O VALNX 42 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYSNX 44 " --> pdb=" O LYSNX 309 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLUNX 311 " --> pdb=" O LYSNX 44 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILENX 46 " --> pdb=" O GLUNX 311 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'NX' and resid 55 through 59 removed outlier: 6.384A pdb=" N ILENX 55 " --> pdb=" O ILENX 292 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARGNX 294 " --> pdb=" O ILENX 55 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILENX 57 " --> pdb=" O ARGNX 294 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'NX' and resid 102 through 104 Processing sheet with id=AG2, first strand: chain 'NX' and resid 106 through 108 Processing sheet with id=AG3, first strand: chain 'OX' and resid 41 through 47 removed outlier: 7.685A pdb=" N VALOX 42 " --> pdb=" O THROX 307 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LYSOX 309 " --> pdb=" O VALOX 42 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYSOX 44 " --> pdb=" O LYSOX 309 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLUOX 311 " --> pdb=" O LYSOX 44 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILEOX 46 " --> pdb=" O GLUOX 311 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'OX' and resid 55 through 59 removed outlier: 6.357A pdb=" N ILEOX 55 " --> pdb=" O ILEOX 292 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARGOX 294 " --> pdb=" O ILEOX 55 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILEOX 57 " --> pdb=" O ARGOX 294 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'OX' and resid 102 through 104 Processing sheet with id=AG6, first strand: chain 'OX' and resid 106 through 108 Processing sheet with id=AG7, first strand: chain 'PX' and resid 41 through 47 removed outlier: 7.739A pdb=" N VALPX 42 " --> pdb=" O THRPX 307 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LYSPX 309 " --> pdb=" O VALPX 42 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYSPX 44 " --> pdb=" O LYSPX 309 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLUPX 311 " --> pdb=" O LYSPX 44 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILEPX 46 " --> pdb=" O GLUPX 311 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'PX' and resid 55 through 59 removed outlier: 6.331A pdb=" N ILEPX 55 " --> pdb=" O ILEPX 292 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARGPX 294 " --> pdb=" O ILEPX 55 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILEPX 57 " --> pdb=" O ARGPX 294 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'PX' and resid 102 through 104 Processing sheet with id=AH1, first strand: chain 'PX' and resid 106 through 108 Processing sheet with id=AH2, first strand: chain 'QX' and resid 41 through 47 removed outlier: 7.738A pdb=" N VALQX 42 " --> pdb=" O THRQX 307 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYSQX 309 " --> pdb=" O VALQX 42 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYSQX 44 " --> pdb=" O LYSQX 309 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLUQX 311 " --> pdb=" O LYSQX 44 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILEQX 46 " --> pdb=" O GLUQX 311 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'QX' and resid 55 through 59 removed outlier: 6.344A pdb=" N ILEQX 55 " --> pdb=" O ILEQX 292 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARGQX 294 " --> pdb=" O ILEQX 55 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILEQX 57 " --> pdb=" O ARGQX 294 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'QX' and resid 102 through 104 Processing sheet with id=AH5, first strand: chain 'QX' and resid 106 through 108 2029 hydrogen bonds defined for protein. 5784 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: 8.58 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12880 1.34 - 1.45: 5041 1.45 - 1.57: 23151 1.57 - 1.68: 0 1.68 - 1.80: 170 Bond restraints: 41242 Sorted by residual: bond pdb=" C VALKX 89 " pdb=" N PROKX 90 " ideal model delta sigma weight residual 1.335 1.316 0.019 8.70e-03 1.32e+04 4.74e+00 bond pdb=" C VALNX 89 " pdb=" N PRONX 90 " ideal model delta sigma weight residual 1.335 1.317 0.018 8.70e-03 1.32e+04 4.33e+00 bond pdb=" C VALGX 89 " pdb=" N PROGX 90 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 4.00e+00 bond pdb=" C VALJX 89 " pdb=" N PROJX 90 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.99e+00 bond pdb=" C VALMX 89 " pdb=" N PROMX 90 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.93e+00 ... (remaining 41237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 54866 2.61 - 5.21: 803 5.21 - 7.82: 35 7.82 - 10.43: 3 10.43 - 13.03: 2 Bond angle restraints: 55709 Sorted by residual: angle pdb=" CA GLUAX 268 " pdb=" CB GLUAX 268 " pdb=" CG GLUAX 268 " ideal model delta sigma weight residual 114.10 122.57 -8.47 2.00e+00 2.50e-01 1.79e+01 angle pdb=" C METGY1545 " pdb=" N ASPGY1546 " pdb=" CA ASPGY1546 " ideal model delta sigma weight residual 122.07 128.12 -6.05 1.43e+00 4.89e-01 1.79e+01 angle pdb=" CA GLULX 268 " pdb=" CB GLULX 268 " pdb=" CG GLULX 268 " ideal model delta sigma weight residual 114.10 122.00 -7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA GLUNX 268 " pdb=" CB GLUNX 268 " pdb=" CG GLUNX 268 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLUFX 268 " pdb=" CB GLUFX 268 " pdb=" CG GLUFX 268 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 ... (remaining 55704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 21932 18.17 - 36.34: 2706 36.34 - 54.51: 768 54.51 - 72.69: 163 72.69 - 90.86: 67 Dihedral angle restraints: 25636 sinusoidal: 10574 harmonic: 15062 Sorted by residual: dihedral pdb=" CB CYSNY1481 " pdb=" SG CYSNY1481 " pdb=" SG CYSNY1497 " pdb=" CB CYSNY1497 " ideal model delta sinusoidal sigma weight residual -86.00 -172.66 86.66 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYSQY1481 " pdb=" SG CYSQY1481 " pdb=" SG CYSQY1497 " pdb=" CB CYSQY1497 " ideal model delta sinusoidal sigma weight residual -86.00 -172.63 86.63 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYSAY1481 " pdb=" SG CYSAY1481 " pdb=" SG CYSAY1497 " pdb=" CB CYSAY1497 " ideal model delta sinusoidal sigma weight residual -86.00 -172.55 86.55 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 25633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5666 0.080 - 0.159: 642 0.159 - 0.239: 52 0.239 - 0.318: 14 0.318 - 0.398: 1 Chirality restraints: 6375 Sorted by residual: chirality pdb=" CB ILEFX 78 " pdb=" CA ILEFX 78 " pdb=" CG1 ILEFX 78 " pdb=" CG2 ILEFX 78 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB ILEGY1576 " pdb=" CA ILEGY1576 " pdb=" CG1 ILEGY1576 " pdb=" CG2 ILEGY1576 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB THRPY1555 " pdb=" CA THRPY1555 " pdb=" OG1 THRPY1555 " pdb=" CG2 THRPY1555 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 6372 not shown) Planarity restraints: 7191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASPFY1552 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C ASPFY1552 " -0.038 2.00e-02 2.50e+03 pdb=" O ASPFY1552 " 0.015 2.00e-02 2.50e+03 pdb=" N ILEFY1553 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALJX 66 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C VALJX 66 " -0.037 2.00e-02 2.50e+03 pdb=" O VALJX 66 " 0.014 2.00e-02 2.50e+03 pdb=" N ILEJX 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALFX 66 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C VALFX 66 " -0.036 2.00e-02 2.50e+03 pdb=" O VALFX 66 " 0.014 2.00e-02 2.50e+03 pdb=" N ILEFX 67 " 0.012 2.00e-02 2.50e+03 ... (remaining 7188 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 10778 2.79 - 3.32: 38303 3.32 - 3.85: 74084 3.85 - 4.37: 83372 4.37 - 4.90: 145496 Nonbonded interactions: 352033 Sorted by model distance: nonbonded pdb=" OG1 THRPX 65 " pdb=" O TYRPX 305 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THRJX 65 " pdb=" O TYRJX 305 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THRQX 65 " pdb=" O TYRQX 305 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THRCX 65 " pdb=" O TYRCX 305 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THRMX 65 " pdb=" O TYRMX 305 " model vdw 2.275 3.040 ... (remaining 352028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'AX' selection = chain 'BX' selection = chain 'CX' selection = chain 'DX' selection = chain 'EX' selection = chain 'FX' selection = chain 'GX' selection = chain 'HX' selection = chain 'IX' selection = chain 'JX' selection = chain 'KX' selection = chain 'LX' selection = chain 'MX' selection = chain 'NX' selection = chain 'OX' selection = chain 'PX' selection = chain 'QX' } ncs_group { reference = chain 'AY' selection = chain 'BY' selection = chain 'CY' selection = chain 'DY' selection = chain 'EY' selection = chain 'FY' selection = chain 'GY' selection = chain 'HY' selection = chain 'IY' selection = chain 'JY' selection = chain 'KY' selection = chain 'LY' selection = chain 'MY' selection = chain 'NY' selection = chain 'OY' selection = chain 'PY' selection = chain 'QY' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.220 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.007 0.052 41259 Z= 0.304 Angle : 0.784 13.033 55743 Z= 0.449 Chirality : 0.053 0.398 6375 Planarity : 0.006 0.049 7191 Dihedral : 17.967 90.858 15725 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 10.29 % Allowed : 22.38 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.79 (0.09), residues: 4981 helix: -2.16 (0.08), residues: 2074 sheet: -2.81 (0.15), residues: 680 loop : -2.66 (0.10), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGBX 283 TYR 0.011 0.002 TYREX 122 PHE 0.018 0.003 PHECY1547 TRP 0.010 0.002 TRPAX 58 HIS 0.005 0.001 HISNX 94 Details of bonding type rmsd covalent geometry : bond 0.00691 (41242) covalent geometry : angle 0.78175 (55709) SS BOND : bond 0.00172 ( 17) SS BOND : angle 2.34271 ( 34) hydrogen bonds : bond 0.13388 ( 2029) hydrogen bonds : angle 6.41183 ( 5784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 467 poor density : 1234 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 83 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (m-40) REVERT: BX 49 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8563 (pp) REVERT: BX 130 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6510 (tppt) REVERT: CX 77 TYR cc_start: 0.8624 (t80) cc_final: 0.8105 (t80) REVERT: CX 273 ASP cc_start: 0.8157 (t70) cc_final: 0.7685 (t0) REVERT: DX 91 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8311 (t0) REVERT: DX 114 ASN cc_start: 0.8100 (t0) cc_final: 0.7880 (m-40) REVERT: DX 130 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.5867 (tppt) REVERT: EX 91 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8139 (t0) REVERT: HX 130 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6020 (tppt) REVERT: HX 273 ASP cc_start: 0.8152 (t70) cc_final: 0.7937 (t0) REVERT: IX 77 TYR cc_start: 0.8517 (t80) cc_final: 0.7880 (t80) REVERT: IX 273 ASP cc_start: 0.8085 (t70) cc_final: 0.7600 (t0) REVERT: KX 273 ASP cc_start: 0.8222 (t70) cc_final: 0.7803 (t0) REVERT: LX 91 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8397 (t0) REVERT: OX 77 TYR cc_start: 0.8522 (t80) cc_final: 0.8297 (t80) REVERT: OX 91 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8284 (t0) REVERT: OX 130 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5853 (tppt) REVERT: OX 273 ASP cc_start: 0.8128 (t70) cc_final: 0.7677 (t0) REVERT: OX 324 GLU cc_start: 0.7322 (mp0) cc_final: 0.7120 (mp0) REVERT: PX 91 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8401 (t0) REVERT: AY 1480 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8021 (mm-30) REVERT: AY 1549 ASN cc_start: 0.7466 (m110) cc_final: 0.6437 (m110) REVERT: AY 1596 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7473 (mt-10) REVERT: BY 1528 ASN cc_start: 0.8475 (t0) cc_final: 0.8148 (t0) REVERT: BY 1549 ASN cc_start: 0.7689 (m110) cc_final: 0.7465 (m110) REVERT: BY 1570 ASN cc_start: 0.8300 (p0) cc_final: 0.7981 (p0) REVERT: CY 1480 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8019 (tp30) REVERT: CY 1528 ASN cc_start: 0.8361 (t0) cc_final: 0.8113 (t0) REVERT: CY 1549 ASN cc_start: 0.7383 (m110) cc_final: 0.6062 (m-40) REVERT: CY 1570 ASN cc_start: 0.8323 (p0) cc_final: 0.8104 (p0) REVERT: CY 1601 LYS cc_start: 0.8146 (tmmt) cc_final: 0.7826 (tmmm) REVERT: DY 1480 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7876 (mm-30) REVERT: DY 1570 ASN cc_start: 0.8183 (p0) cc_final: 0.7895 (p0) REVERT: EY 1480 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7919 (mm-30) REVERT: EY 1528 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7677 (t0) REVERT: EY 1596 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7551 (mt-10) REVERT: FY 1480 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7825 (mm-30) REVERT: FY 1518 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: FY 1528 ASN cc_start: 0.8322 (t0) cc_final: 0.7947 (t0) REVERT: FY 1549 ASN cc_start: 0.7547 (m110) cc_final: 0.6304 (m-40) REVERT: FY 1570 ASN cc_start: 0.8069 (p0) cc_final: 0.7841 (p0) REVERT: FY 1596 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7396 (mt-10) REVERT: GY 1480 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7605 (mm-30) REVERT: GY 1517 ASP cc_start: 0.7604 (p0) cc_final: 0.6886 (p0) REVERT: GY 1518 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: GY 1570 ASN cc_start: 0.8365 (p0) cc_final: 0.8107 (p0) REVERT: GY 1596 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7462 (mt-10) REVERT: HY 1480 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7707 (mm-30) REVERT: HY 1549 ASN cc_start: 0.7481 (m110) cc_final: 0.6627 (m110) REVERT: HY 1570 ASN cc_start: 0.8202 (p0) cc_final: 0.7961 (p0) REVERT: IY 1480 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7836 (mm-30) REVERT: IY 1596 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7389 (mt-10) REVERT: JY 1480 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7804 (mm-30) REVERT: JY 1570 ASN cc_start: 0.8204 (p0) cc_final: 0.7935 (p0) REVERT: KY 1480 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7592 (mm-30) REVERT: LY 1480 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7882 (mm-30) REVERT: LY 1499 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7844 (mt-10) REVERT: LY 1513 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8197 (tttp) REVERT: LY 1528 ASN cc_start: 0.8440 (t0) cc_final: 0.8172 (t0) REVERT: LY 1570 ASN cc_start: 0.8323 (p0) cc_final: 0.8068 (p0) REVERT: LY 1596 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7187 (mm-30) REVERT: MY 1480 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7654 (mm-30) REVERT: MY 1517 ASP cc_start: 0.7687 (p0) cc_final: 0.7217 (p0) REVERT: MY 1518 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: MY 1549 ASN cc_start: 0.7926 (m-40) cc_final: 0.6814 (m-40) REVERT: MY 1570 ASN cc_start: 0.8196 (p0) cc_final: 0.7958 (p0) REVERT: MY 1596 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7536 (mt-10) REVERT: NY 1480 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7868 (mm-30) REVERT: NY 1549 ASN cc_start: 0.7461 (m110) cc_final: 0.7240 (m110) REVERT: NY 1570 ASN cc_start: 0.8179 (p0) cc_final: 0.7919 (p0) REVERT: NY 1596 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7229 (mm-30) REVERT: OY 1480 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7792 (mm-30) REVERT: OY 1517 ASP cc_start: 0.8152 (p0) cc_final: 0.7923 (p0) REVERT: OY 1528 ASN cc_start: 0.8303 (t0) cc_final: 0.7971 (t0) REVERT: OY 1596 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7213 (mm-30) REVERT: PY 1549 ASN cc_start: 0.7376 (m110) cc_final: 0.7071 (m-40) REVERT: PY 1570 ASN cc_start: 0.8294 (p0) cc_final: 0.7945 (p0) REVERT: QY 1480 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7783 (mm-30) REVERT: QY 1499 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7874 (mt-10) REVERT: QY 1549 ASN cc_start: 0.7502 (m110) cc_final: 0.6798 (m-40) REVERT: QY 1570 ASN cc_start: 0.8352 (p0) cc_final: 0.8132 (p0) outliers start: 467 outliers final: 255 residues processed: 1617 average time/residue: 0.7257 time to fit residues: 1420.5265 Evaluate side-chains 1116 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 845 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 56 THR Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 87 SER Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 130 LYS Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 56 THR Chi-restraints excluded: chain CX residue 83 ASN Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 49 LEU Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 87 SER Chi-restraints excluded: chain DX residue 91 ASN Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 130 LYS Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain DX residue 319 SER Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 56 THR Chi-restraints excluded: chain EX residue 87 SER Chi-restraints excluded: chain EX residue 91 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 319 SER Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 56 THR Chi-restraints excluded: chain FX residue 87 SER Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 274 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 49 LEU Chi-restraints excluded: chain GX residue 56 THR Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 319 SER Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 56 THR Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 130 LYS Chi-restraints excluded: chain HX residue 270 SER Chi-restraints excluded: chain HX residue 274 SER Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 317 GLU Chi-restraints excluded: chain HX residue 319 SER Chi-restraints excluded: chain HX residue 321 VAL Chi-restraints excluded: chain IX residue 39 VAL Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 56 THR Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 87 SER Chi-restraints excluded: chain IX residue 91 ASN Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 303 SER Chi-restraints excluded: chain IX residue 319 SER Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 87 SER Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 319 SER Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 49 LEU Chi-restraints excluded: chain KX residue 56 THR Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 272 SER Chi-restraints excluded: chain KX residue 274 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 56 THR Chi-restraints excluded: chain LX residue 62 ASP Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 91 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 274 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 319 SER Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 56 THR Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 87 SER Chi-restraints excluded: chain MX residue 91 ASN Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 56 THR Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 319 SER Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 49 LEU Chi-restraints excluded: chain OX residue 56 THR Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 87 SER Chi-restraints excluded: chain OX residue 89 VAL Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 130 LYS Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 319 SER Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 62 ASP Chi-restraints excluded: chain PX residue 87 SER Chi-restraints excluded: chain PX residue 91 ASN Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 274 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 319 SER Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 40 LYS Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 56 THR Chi-restraints excluded: chain QX residue 87 SER Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 91 ASN Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 319 SER Chi-restraints excluded: chain AY residue 1470 SER Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1504 SER Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1526 LEU Chi-restraints excluded: chain AY residue 1562 ASP Chi-restraints excluded: chain BY residue 1479 SER Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1518 GLU Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1526 LEU Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1502 SER Chi-restraints excluded: chain CY residue 1526 LEU Chi-restraints excluded: chain CY residue 1561 VAL Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1555 THR Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1526 LEU Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1479 SER Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1518 GLU Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1526 LEU Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1479 SER Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1502 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1526 LEU Chi-restraints excluded: chain GY residue 1561 VAL Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain GY residue 1564 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1504 SER Chi-restraints excluded: chain HY residue 1524 SER Chi-restraints excluded: chain HY residue 1526 LEU Chi-restraints excluded: chain HY residue 1561 VAL Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain HY residue 1564 ASP Chi-restraints excluded: chain HY residue 1585 GLU Chi-restraints excluded: chain IY residue 1479 SER Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1561 VAL Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1504 SER Chi-restraints excluded: chain JY residue 1526 LEU Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain JY residue 1603 LEU Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1479 SER Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1504 SER Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1526 LEU Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1479 SER Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1513 LYS Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1479 SER Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1526 LEU Chi-restraints excluded: chain NY residue 1561 VAL Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1470 SER Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1524 SER Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1470 SER Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain PY residue 1502 SER Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1526 LEU Chi-restraints excluded: chain PY residue 1561 VAL Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1479 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1518 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1526 LEU Chi-restraints excluded: chain QY residue 1561 VAL Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.0670 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 2.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** AX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN CX 91 ASN ** CX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 83 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DX 297 GLN EX 83 ASN FX 83 ASN GX 83 ASN IX 83 ASN JX 83 ASN JX 91 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 297 GLN KX 83 ASN KX 93 ASN LX 83 ASN MX 83 ASN NX 83 ASN OX 83 ASN ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** QX 83 ASN AY1476 HIS AY1484 ASN AY1549 ASN BY1476 HIS BY1583 GLN CY1476 HIS CY1484 ASN CY1549 ASN DY1476 HIS DY1484 ASN DY1528 ASN DY1549 ASN EY1476 HIS EY1583 GLN FY1476 HIS FY1549 ASN GY1476 HIS GY1583 GLN HY1476 HIS HY1484 ASN HY1549 ASN IY1476 HIS IY1583 GLN JY1476 HIS KY1476 HIS KY1484 ASN KY1515 GLN KY1549 ASN LY1476 HIS LY1484 ASN MY1476 HIS MY1484 ASN NY1476 HIS NY1528 ASN NY1549 ASN OY1476 HIS OY1549 ASN PY1476 HIS PY1515 GLN PY1528 ASN PY1549 ASN QY1476 HIS QY1549 ASN QY1583 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.106712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091705 restraints weight = 84630.952| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.48 r_work: 0.3229 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41259 Z= 0.160 Angle : 0.595 9.933 55743 Z= 0.320 Chirality : 0.044 0.254 6375 Planarity : 0.005 0.041 7191 Dihedral : 9.783 161.010 5793 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 8.92 % Allowed : 25.23 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.10), residues: 4981 helix: 0.05 (0.10), residues: 2074 sheet: -2.48 (0.17), residues: 714 loop : -2.24 (0.11), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGIX 283 TYR 0.022 0.001 TYRAX 77 PHE 0.010 0.001 PHEEX 96 TRP 0.005 0.001 TRPPX 58 HIS 0.008 0.001 HISJX 94 Details of bonding type rmsd covalent geometry : bond 0.00355 (41242) covalent geometry : angle 0.59498 (55709) SS BOND : bond 0.00058 ( 17) SS BOND : angle 0.49024 ( 34) hydrogen bonds : bond 0.04044 ( 2029) hydrogen bonds : angle 4.98202 ( 5784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 405 poor density : 1017 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 91 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8233 (t0) REVERT: AX 120 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7645 (ttp-110) REVERT: AX 273 ASP cc_start: 0.8610 (t0) cc_final: 0.8388 (t0) REVERT: AX 286 LYS cc_start: 0.9016 (mttt) cc_final: 0.8800 (mtmt) REVERT: AX 324 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: BX 49 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8587 (pp) REVERT: BX 83 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8286 (m-40) REVERT: CX 89 VAL cc_start: 0.9268 (p) cc_final: 0.9062 (m) REVERT: CX 91 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (m-40) REVERT: CX 120 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7589 (tmm160) REVERT: CX 273 ASP cc_start: 0.8517 (t70) cc_final: 0.8173 (t0) REVERT: CX 324 GLU cc_start: 0.7352 (mp0) cc_final: 0.7126 (mp0) REVERT: DX 94 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.7029 (p90) REVERT: EX 83 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8460 (m110) REVERT: EX 91 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8320 (t0) REVERT: FX 83 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8560 (m110) REVERT: FX 89 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9090 (m) REVERT: FX 130 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6122 (mmtm) REVERT: FX 273 ASP cc_start: 0.8524 (t0) cc_final: 0.7533 (t0) REVERT: FX 289 TYR cc_start: 0.8837 (m-80) cc_final: 0.8609 (m-80) REVERT: FX 294 ARG cc_start: 0.7831 (mtp85) cc_final: 0.6991 (mtp85) REVERT: GX 83 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8495 (m110) REVERT: IX 62 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: JX 130 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.5953 (mmtm) REVERT: JX 263 GLU cc_start: 0.7603 (tt0) cc_final: 0.7384 (tt0) REVERT: JX 324 GLU cc_start: 0.7505 (mp0) cc_final: 0.7303 (mp0) REVERT: KX 83 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8529 (m110) REVERT: KX 87 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8629 (p) REVERT: KX 120 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7718 (ttp-110) REVERT: LX 130 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6059 (mmtm) REVERT: MX 118 MET cc_start: 0.7965 (ttm) cc_final: 0.7733 (ttm) REVERT: MX 130 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6148 (mmtm) REVERT: MX 263 GLU cc_start: 0.7492 (tt0) cc_final: 0.7214 (tp30) REVERT: MX 273 ASP cc_start: 0.8527 (t0) cc_final: 0.8191 (t0) REVERT: NX 87 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8694 (p) REVERT: OX 69 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9019 (mt) REVERT: OX 273 ASP cc_start: 0.8527 (t70) cc_final: 0.8035 (t0) REVERT: PX 42 VAL cc_start: 0.8604 (p) cc_final: 0.8393 (m) REVERT: PX 91 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8304 (t0) REVERT: PX 130 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6011 (mmtm) REVERT: PX 268 GLU cc_start: 0.8153 (pm20) cc_final: 0.7932 (tm-30) REVERT: PX 324 GLU cc_start: 0.7422 (mp0) cc_final: 0.6990 (mp0) REVERT: QX 130 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6020 (mmtm) REVERT: QX 263 GLU cc_start: 0.7487 (tt0) cc_final: 0.7250 (tp30) REVERT: QX 273 ASP cc_start: 0.8574 (t70) cc_final: 0.8333 (t0) REVERT: AY 1480 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8016 (mm-30) REVERT: AY 1492 GLU cc_start: 0.8576 (tp30) cc_final: 0.8354 (tp30) REVERT: AY 1499 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8218 (mt-10) REVERT: AY 1549 ASN cc_start: 0.7118 (m-40) cc_final: 0.6868 (m-40) REVERT: AY 1596 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7293 (mt-10) REVERT: BY 1480 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8074 (mm-30) REVERT: BY 1549 ASN cc_start: 0.7676 (m110) cc_final: 0.7422 (m110) REVERT: CY 1503 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8633 (t70) REVERT: CY 1601 LYS cc_start: 0.8224 (tmmt) cc_final: 0.7885 (tmmm) REVERT: DY 1505 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8795 (mt-10) REVERT: EY 1480 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8028 (mm-30) REVERT: EY 1528 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.7799 (t0) REVERT: EY 1583 GLN cc_start: 0.8629 (tt0) cc_final: 0.8420 (tt0) REVERT: FY 1480 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7959 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8469 (t70) REVERT: FY 1528 ASN cc_start: 0.8448 (t0) cc_final: 0.8170 (t0) REVERT: GY 1480 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7939 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8315 (t70) REVERT: GY 1517 ASP cc_start: 0.7965 (p0) cc_final: 0.7304 (p0) REVERT: GY 1518 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: HY 1479 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (p) REVERT: HY 1480 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7908 (mm-30) REVERT: HY 1499 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7944 (mt-10) REVERT: HY 1503 ASP cc_start: 0.8945 (m-30) cc_final: 0.8598 (t70) REVERT: HY 1523 TYR cc_start: 0.9289 (t80) cc_final: 0.9062 (t80) REVERT: IY 1480 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8053 (mm-30) REVERT: IY 1498 LEU cc_start: 0.8102 (mt) cc_final: 0.7887 (mt) REVERT: IY 1503 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8546 (t70) REVERT: IY 1549 ASN cc_start: 0.8005 (m-40) cc_final: 0.6798 (m-40) REVERT: IY 1596 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7323 (mt-10) REVERT: JY 1480 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8078 (mm-30) REVERT: JY 1503 ASP cc_start: 0.8896 (m-30) cc_final: 0.8481 (t70) REVERT: JY 1580 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8395 (mp) REVERT: KY 1480 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7942 (mm-30) REVERT: KY 1503 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8430 (t70) REVERT: KY 1549 ASN cc_start: 0.7153 (m-40) cc_final: 0.6579 (m110) REVERT: LY 1503 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8501 (t70) REVERT: LY 1528 ASN cc_start: 0.8505 (t0) cc_final: 0.7933 (t0) REVERT: MY 1514 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7902 (ttp80) REVERT: MY 1517 ASP cc_start: 0.8057 (p0) cc_final: 0.7540 (p0) REVERT: MY 1518 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: MY 1523 TYR cc_start: 0.9212 (t80) cc_final: 0.8926 (t80) REVERT: MY 1549 ASN cc_start: 0.7258 (m-40) cc_final: 0.6601 (m-40) REVERT: NY 1480 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7948 (mm-30) REVERT: NY 1528 ASN cc_start: 0.8481 (t0) cc_final: 0.8095 (t0) REVERT: NY 1596 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7187 (mm-30) REVERT: OY 1503 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8308 (t70) REVERT: OY 1528 ASN cc_start: 0.8392 (t0) cc_final: 0.8089 (t0) REVERT: QY 1484 ASN cc_start: 0.8871 (m110) cc_final: 0.8654 (m110) REVERT: QY 1523 TYR cc_start: 0.9184 (t80) cc_final: 0.8930 (t80) REVERT: QY 1530 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8431 (mttm) outliers start: 405 outliers final: 138 residues processed: 1338 average time/residue: 0.6903 time to fit residues: 1130.0555 Evaluate side-chains 1055 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 878 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 32 LYS Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 91 ASN Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 283 ARG Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 283 ARG Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 83 ASN Chi-restraints excluded: chain CX residue 91 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 274 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 62 ASP Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 91 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 83 ASN Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 270 SER Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 130 LYS Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 41 VAL Chi-restraints excluded: chain KX residue 83 ASN Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 130 LYS Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain MX residue 283 ARG Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 91 ASN Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 130 LYS Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 130 LYS Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1498 LEU Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1518 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain HY residue 1479 SER Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1518 GLU Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1503 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1503 ASP Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1498 LEU Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1518 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1580 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 460 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 297 GLN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 91 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 297 GLN CX 91 ASN ** CX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 297 GLN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 297 GLN FX 83 ASN FX 297 GLN GX 83 ASN ** GX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GX 297 GLN ** HX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HX 297 GLN IX 91 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 297 GLN JX 91 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KX 91 ASN KX 93 ASN ** KX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 83 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 297 GLN ** MX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 297 GLN NX 91 ASN NX 297 GLN OX 83 ASN OX 91 ASN OX 93 ASN OX 297 GLN ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PX 297 GLN QX 83 ASN QX 91 ASN ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1515 GLN BY1549 ASN BY1583 GLN CY1484 ASN DY1484 ASN GY1583 GLN IY1528 ASN IY1583 GLN JY1583 GLN LY1484 ASN MY1484 ASN PY1515 GLN PY1583 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088750 restraints weight = 85491.703| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.41 r_work: 0.3179 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 41259 Z= 0.238 Angle : 0.627 10.284 55743 Z= 0.337 Chirality : 0.045 0.213 6375 Planarity : 0.004 0.053 7191 Dihedral : 7.578 77.225 5529 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 9.47 % Allowed : 25.95 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.11), residues: 4981 helix: 0.74 (0.11), residues: 2091 sheet: -2.38 (0.17), residues: 714 loop : -1.99 (0.11), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGHY1514 TYR 0.015 0.001 TYRFX 77 PHE 0.023 0.002 PHEHX 96 TRP 0.009 0.001 TRPPX 58 HIS 0.010 0.002 HISJX 94 Details of bonding type rmsd covalent geometry : bond 0.00539 (41242) covalent geometry : angle 0.62758 (55709) SS BOND : bond 0.00101 ( 17) SS BOND : angle 0.18928 ( 34) hydrogen bonds : bond 0.04209 ( 2029) hydrogen bonds : angle 4.84592 ( 5784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 430 poor density : 925 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 120 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7794 (ttp-110) REVERT: AX 268 GLU cc_start: 0.8231 (pm20) cc_final: 0.7981 (pm20) REVERT: AX 286 LYS cc_start: 0.9012 (mttt) cc_final: 0.8803 (mtmt) REVERT: AX 324 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: BX 49 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8619 (pp) REVERT: BX 83 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8362 (m-40) REVERT: CX 120 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7716 (tmm160) REVERT: CX 265 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8391 (t0) REVERT: CX 273 ASP cc_start: 0.8490 (t70) cc_final: 0.8221 (t0) REVERT: DX 91 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8432 (t0) REVERT: DX 120 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7802 (ttp-110) REVERT: EX 120 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7746 (ttp-110) REVERT: FX 130 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6216 (mmtm) REVERT: FX 263 GLU cc_start: 0.7602 (tt0) cc_final: 0.7363 (tp30) REVERT: GX 83 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8591 (m-40) REVERT: GX 120 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7752 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8383 (ttt-90) REVERT: IX 62 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: JX 263 GLU cc_start: 0.7601 (tt0) cc_final: 0.7388 (tt0) REVERT: KX 103 LYS cc_start: 0.8662 (mppt) cc_final: 0.8451 (mmtt) REVERT: KX 118 MET cc_start: 0.8052 (ttm) cc_final: 0.7756 (ttm) REVERT: KX 120 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7819 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8591 (t0) cc_final: 0.8374 (t0) REVERT: KX 289 TYR cc_start: 0.8863 (m-80) cc_final: 0.8595 (m-80) REVERT: LX 130 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6142 (mmtm) REVERT: MX 49 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8718 (pp) REVERT: MX 273 ASP cc_start: 0.8565 (t0) cc_final: 0.8353 (t0) REVERT: NX 62 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: OX 69 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9087 (mt) REVERT: OX 273 ASP cc_start: 0.8568 (t70) cc_final: 0.8083 (t0) REVERT: OX 324 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: PX 42 VAL cc_start: 0.8664 (p) cc_final: 0.8441 (m) REVERT: PX 324 GLU cc_start: 0.7430 (mp0) cc_final: 0.6999 (mp0) REVERT: QX 294 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7159 (mtp85) REVERT: AY 1480 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8002 (mm-30) REVERT: AY 1585 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: BY 1480 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8031 (mm-30) REVERT: BY 1549 ASN cc_start: 0.7731 (m-40) cc_final: 0.7321 (m110) REVERT: CY 1503 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8588 (t70) REVERT: CY 1517 ASP cc_start: 0.8539 (p0) cc_final: 0.8233 (p0) REVERT: CY 1528 ASN cc_start: 0.8549 (t0) cc_final: 0.8177 (t0) REVERT: CY 1572 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8350 (mm) REVERT: DY 1480 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8075 (mm-30) REVERT: EY 1480 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8073 (mm-30) REVERT: EY 1528 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7958 (t0) REVERT: EY 1549 ASN cc_start: 0.7872 (m-40) cc_final: 0.7377 (m-40) REVERT: FY 1480 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8012 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8494 (t70) REVERT: FY 1528 ASN cc_start: 0.8489 (t0) cc_final: 0.8003 (t0) REVERT: FY 1596 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7299 (mt-10) REVERT: GY 1480 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8003 (mm-30) REVERT: GY 1499 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7899 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8469 (t70) REVERT: GY 1517 ASP cc_start: 0.8012 (p0) cc_final: 0.7350 (p0) REVERT: GY 1518 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: HY 1503 ASP cc_start: 0.8934 (m-30) cc_final: 0.8587 (t70) REVERT: IY 1480 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8176 (mm-30) REVERT: IY 1503 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8497 (t70) REVERT: IY 1585 GLU cc_start: 0.8131 (tp30) cc_final: 0.7927 (tp30) REVERT: IY 1596 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7390 (mt-10) REVERT: JY 1480 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8161 (mm-30) REVERT: JY 1503 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8561 (t70) REVERT: KY 1480 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7987 (mm-30) REVERT: KY 1503 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8463 (t70) REVERT: LY 1499 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8003 (mt-10) REVERT: LY 1503 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8618 (t70) REVERT: LY 1528 ASN cc_start: 0.8528 (t0) cc_final: 0.7875 (t0) REVERT: LY 1572 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8375 (mm) REVERT: LY 1596 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7103 (mm-30) REVERT: MY 1480 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7973 (mm-30) REVERT: MY 1499 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8106 (mt-10) REVERT: MY 1514 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7965 (ttp80) REVERT: MY 1517 ASP cc_start: 0.8038 (p0) cc_final: 0.7577 (p0) REVERT: MY 1518 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: MY 1523 TYR cc_start: 0.9236 (t80) cc_final: 0.8879 (t80) REVERT: MY 1527 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7649 (ttm-80) REVERT: MY 1572 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8338 (mm) REVERT: MY 1596 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7503 (mt-10) REVERT: NY 1480 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8040 (mm-30) REVERT: NY 1528 ASN cc_start: 0.8482 (t0) cc_final: 0.8103 (t0) REVERT: NY 1538 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7962 (mptp) REVERT: NY 1585 GLU cc_start: 0.8040 (tp30) cc_final: 0.7807 (tp30) REVERT: NY 1596 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7149 (mm-30) REVERT: OY 1486 ASP cc_start: 0.7336 (p0) cc_final: 0.7068 (p0) REVERT: OY 1503 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8374 (t70) REVERT: QY 1480 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7978 (mm-30) REVERT: QY 1484 ASN cc_start: 0.8938 (m110) cc_final: 0.8691 (m110) REVERT: QY 1499 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8018 (mt-10) REVERT: QY 1506 ARG cc_start: 0.8896 (mtp-110) cc_final: 0.8645 (mtp-110) REVERT: QY 1572 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8488 (mm) outliers start: 430 outliers final: 204 residues processed: 1263 average time/residue: 0.7046 time to fit residues: 1082.5009 Evaluate side-chains 1011 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 770 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 32 LYS Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 56 THR Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 94 HIS Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 283 ARG Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 274 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 62 ASP Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 91 ASN Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 283 ARG Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 120 ARG Chi-restraints excluded: chain GX residue 266 SER Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 265 ASN Chi-restraints excluded: chain HX residue 270 SER Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 274 SER Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 41 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 322 ILE Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 94 HIS Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 49 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 274 SER Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 62 ASP Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 109 GLU Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 324 GLU Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 322 ILE Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1498 LEU Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain CY residue 1572 ILE Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1518 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1580 ILE Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain EY residue 1572 ILE Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain HY residue 1479 SER Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1518 GLU Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1512 ILE Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1503 ASP Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1503 ASP Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain LY residue 1572 ILE Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain MY residue 1572 ILE Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1503 ASP Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1470 SER Chi-restraints excluded: chain OY residue 1473 GLU Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1555 THR Chi-restraints excluded: chain QY residue 1562 ASP Chi-restraints excluded: chain QY residue 1572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 123 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 335 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 157 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 447 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** CX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN FX 83 ASN GX 83 ASN ** GX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HX 91 ASN IX 91 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 91 ASN JX 265 ASN KX 91 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 83 ASN ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN QX 297 GLN AY1484 ASN CY1484 ASN DY1484 ASN EY1583 GLN GY1583 GLN HY1484 ASN LY1484 ASN MY1484 ASN PY1515 GLN PY1583 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.105763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090995 restraints weight = 85076.901| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.47 r_work: 0.3228 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41259 Z= 0.149 Angle : 0.584 11.621 55743 Z= 0.312 Chirality : 0.043 0.200 6375 Planarity : 0.004 0.057 7191 Dihedral : 7.022 73.621 5514 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 8.13 % Allowed : 27.41 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.11), residues: 4981 helix: 1.13 (0.11), residues: 2074 sheet: -2.22 (0.17), residues: 714 loop : -1.85 (0.11), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGKX 283 TYR 0.015 0.001 TYRFX 77 PHE 0.018 0.001 PHELX 96 TRP 0.009 0.001 TRPPX 58 HIS 0.008 0.001 HISPX 94 Details of bonding type rmsd covalent geometry : bond 0.00335 (41242) covalent geometry : angle 0.58346 (55709) SS BOND : bond 0.00382 ( 17) SS BOND : angle 1.07567 ( 34) hydrogen bonds : bond 0.03741 ( 2029) hydrogen bonds : angle 4.73602 ( 5784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 369 poor density : 975 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 93 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8580 (p0) REVERT: AX 120 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7809 (ttp-110) REVERT: AX 324 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: BX 42 VAL cc_start: 0.8591 (p) cc_final: 0.8383 (m) REVERT: BX 49 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8549 (pp) REVERT: BX 83 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8246 (m-40) REVERT: CX 265 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8388 (t0) REVERT: CX 273 ASP cc_start: 0.8422 (t70) cc_final: 0.8179 (t0) REVERT: DX 120 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7718 (ttp-110) REVERT: DX 324 GLU cc_start: 0.7222 (mp0) cc_final: 0.6879 (mp0) REVERT: EX 83 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8404 (m110) REVERT: EX 120 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7703 (ttp-110) REVERT: FX 89 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9072 (m) REVERT: FX 130 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6271 (mmtm) REVERT: FX 263 GLU cc_start: 0.7661 (tt0) cc_final: 0.7452 (tp30) REVERT: FX 289 TYR cc_start: 0.8837 (m-80) cc_final: 0.8602 (m-80) REVERT: GX 83 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8538 (m-40) REVERT: GX 273 ASP cc_start: 0.8435 (t0) cc_final: 0.8220 (t0) REVERT: GX 277 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8574 (ttt-90) REVERT: HX 49 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8720 (pp) REVERT: HX 277 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8391 (ttt-90) REVERT: HX 324 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7494 (mp0) REVERT: IX 62 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: IX 83 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8795 (t0) REVERT: IX 107 MET cc_start: 0.8887 (ttm) cc_final: 0.8673 (ptm) REVERT: IX 277 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8587 (ttm-80) REVERT: JX 91 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8281 (t0) REVERT: KX 87 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8544 (p) REVERT: KX 118 MET cc_start: 0.8120 (ttm) cc_final: 0.7850 (ttm) REVERT: KX 120 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7775 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8595 (t0) cc_final: 0.8200 (t0) REVERT: KX 289 TYR cc_start: 0.8827 (m-80) cc_final: 0.8588 (m-80) REVERT: LX 49 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8685 (pp) REVERT: LX 89 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9059 (m) REVERT: LX 107 MET cc_start: 0.8762 (ttm) cc_final: 0.8548 (ttm) REVERT: LX 130 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6034 (mmtm) REVERT: MX 263 GLU cc_start: 0.7702 (tt0) cc_final: 0.7475 (tp30) REVERT: MX 273 ASP cc_start: 0.8463 (t0) cc_final: 0.8234 (t0) REVERT: MX 289 TYR cc_start: 0.8844 (m-80) cc_final: 0.8621 (m-80) REVERT: NX 87 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (p) REVERT: OX 69 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9060 (mt) REVERT: OX 273 ASP cc_start: 0.8514 (t70) cc_final: 0.8131 (t0) REVERT: OX 277 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8420 (ttt-90) REVERT: PX 42 VAL cc_start: 0.8520 (p) cc_final: 0.8318 (m) REVERT: PX 83 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8499 (m110) REVERT: PX 263 GLU cc_start: 0.7718 (tt0) cc_final: 0.7517 (tp30) REVERT: PX 273 ASP cc_start: 0.8485 (t0) cc_final: 0.8229 (t0) REVERT: PX 324 GLU cc_start: 0.7495 (mp0) cc_final: 0.7043 (mp0) REVERT: QX 263 GLU cc_start: 0.7627 (tt0) cc_final: 0.7406 (tp30) REVERT: AY 1480 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8016 (mm-30) REVERT: AY 1492 GLU cc_start: 0.8516 (tp30) cc_final: 0.8268 (tp30) REVERT: AY 1523 TYR cc_start: 0.9197 (t80) cc_final: 0.8882 (t80) REVERT: AY 1585 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: AY 1596 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7412 (mt-10) REVERT: BY 1480 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7937 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8591 (t70) REVERT: CY 1517 ASP cc_start: 0.8576 (p0) cc_final: 0.8261 (p0) REVERT: CY 1528 ASN cc_start: 0.8494 (t0) cc_final: 0.8181 (t0) REVERT: EY 1503 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8714 (t70) REVERT: EY 1528 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8017 (t0) REVERT: FY 1480 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8024 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8531 (t70) REVERT: FY 1528 ASN cc_start: 0.8495 (t0) cc_final: 0.8023 (t0) REVERT: GY 1480 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7665 (mm-30) REVERT: GY 1484 ASN cc_start: 0.8722 (m110) cc_final: 0.8333 (m110) REVERT: GY 1499 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7921 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8427 (t70) REVERT: GY 1514 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7892 (ttp80) REVERT: GY 1517 ASP cc_start: 0.8019 (p0) cc_final: 0.7337 (p0) REVERT: GY 1518 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: HY 1503 ASP cc_start: 0.8925 (m-30) cc_final: 0.8577 (t70) REVERT: HY 1527 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7511 (ttm170) REVERT: HY 1528 ASN cc_start: 0.8462 (t0) cc_final: 0.7669 (t0) REVERT: IY 1480 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8112 (mm-30) REVERT: IY 1503 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8503 (t70) REVERT: JY 1480 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8042 (mm-30) REVERT: JY 1503 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8545 (t70) REVERT: KY 1480 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7972 (mm-30) REVERT: KY 1503 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8590 (t70) REVERT: KY 1527 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: LY 1499 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8071 (mt-10) REVERT: LY 1528 ASN cc_start: 0.8467 (t0) cc_final: 0.8155 (t0) REVERT: LY 1585 GLU cc_start: 0.8075 (tp30) cc_final: 0.7859 (tp30) REVERT: MY 1506 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8707 (mtp85) REVERT: MY 1517 ASP cc_start: 0.8089 (p0) cc_final: 0.7565 (p0) REVERT: MY 1518 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: NY 1528 ASN cc_start: 0.8495 (t0) cc_final: 0.8120 (t0) REVERT: NY 1538 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7932 (mptp) REVERT: OY 1503 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8503 (t70) REVERT: PY 1506 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8362 (mtp85) REVERT: PY 1527 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7880 (ttm-80) REVERT: PY 1528 ASN cc_start: 0.8201 (t0) cc_final: 0.7528 (t0) REVERT: QY 1480 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8031 (mm-30) outliers start: 369 outliers final: 162 residues processed: 1268 average time/residue: 0.6914 time to fit residues: 1070.8319 Evaluate side-chains 1016 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 811 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 60 SER Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 266 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 283 ARG Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 274 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 283 ARG Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 49 LEU Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 277 ARG Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 283 ARG Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 95 ILE Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 265 ASN Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 91 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 317 GLU Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 41 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 69 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1561 VAL Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1528 ASN Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1503 ASP Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1506 ARG Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1506 ARG Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 278 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 289 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** CX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 83 ASN DX 91 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** FX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GX 83 ASN ** GX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HX 91 ASN ** HX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 91 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN JX 91 ASN JX 265 ASN KX 91 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 83 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 91 ASN OX 91 ASN ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PX 83 ASN QX 83 ASN ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN CY1484 ASN DY1484 ASN DY1583 GLN EY1583 GLN LY1484 ASN LY1583 GLN MY1484 ASN OY1528 ASN PY1515 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090954 restraints weight = 85119.846| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.47 r_work: 0.3223 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41259 Z= 0.159 Angle : 0.593 10.339 55743 Z= 0.318 Chirality : 0.044 0.218 6375 Planarity : 0.004 0.063 7191 Dihedral : 6.708 72.348 5501 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 8.20 % Allowed : 28.71 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.11), residues: 4981 helix: 1.30 (0.11), residues: 2074 sheet: -1.91 (0.20), residues: 544 loop : -1.79 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGFY1514 TYR 0.015 0.001 TYRBX 77 PHE 0.018 0.001 PHEPX 96 TRP 0.009 0.001 TRPPX 58 HIS 0.009 0.001 HISDX 94 Details of bonding type rmsd covalent geometry : bond 0.00361 (41242) covalent geometry : angle 0.59255 (55709) SS BOND : bond 0.00309 ( 17) SS BOND : angle 1.31876 ( 34) hydrogen bonds : bond 0.03758 ( 2029) hydrogen bonds : angle 4.69010 ( 5784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 372 poor density : 934 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 89 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9100 (m) REVERT: AX 93 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8524 (p0) REVERT: AX 120 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7752 (ttp-110) REVERT: AX 324 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: BX 42 VAL cc_start: 0.8548 (p) cc_final: 0.8342 (m) REVERT: BX 49 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (pp) REVERT: BX 83 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8254 (m-40) REVERT: BX 120 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7807 (ttp80) REVERT: CX 49 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8677 (pp) REVERT: CX 265 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8393 (t0) REVERT: DX 120 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7697 (ttp-110) REVERT: DX 268 GLU cc_start: 0.7996 (pm20) cc_final: 0.7697 (tm-30) REVERT: EX 83 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8420 (m110) REVERT: EX 120 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7753 (ttp-110) REVERT: FX 89 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9054 (m) REVERT: FX 130 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6205 (mmtm) REVERT: FX 289 TYR cc_start: 0.8818 (m-80) cc_final: 0.8593 (m-80) REVERT: GX 83 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: HX 49 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8683 (pp) REVERT: HX 120 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7770 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8337 (ttt-90) REVERT: IX 62 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: IX 83 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (t0) REVERT: IX 103 LYS cc_start: 0.8711 (tppt) cc_final: 0.8322 (mmtt) REVERT: IX 277 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8592 (ttm-80) REVERT: JX 120 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7806 (ttp-110) REVERT: KX 87 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8574 (p) REVERT: KX 103 LYS cc_start: 0.8546 (mppt) cc_final: 0.8305 (mmtt) REVERT: KX 118 MET cc_start: 0.8122 (ttm) cc_final: 0.7869 (ttm) REVERT: KX 120 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7787 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8552 (t0) cc_final: 0.8244 (t0) REVERT: KX 289 TYR cc_start: 0.8813 (m-80) cc_final: 0.8533 (m-80) REVERT: LX 49 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8707 (pp) REVERT: LX 89 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9077 (m) REVERT: MX 277 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8092 (ttm-80) REVERT: NX 87 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8686 (p) REVERT: NX 103 LYS cc_start: 0.8705 (mppt) cc_final: 0.8408 (mmtt) REVERT: NX 316 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7870 (m-70) REVERT: OX 91 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8380 (t0) REVERT: OX 273 ASP cc_start: 0.8490 (t70) cc_final: 0.8028 (t0) REVERT: OX 277 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: PX 263 GLU cc_start: 0.7769 (tt0) cc_final: 0.7514 (tp30) REVERT: PX 273 ASP cc_start: 0.8469 (t0) cc_final: 0.8174 (t0) REVERT: PX 324 GLU cc_start: 0.7445 (mp0) cc_final: 0.6955 (mp0) REVERT: QX 49 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8670 (pp) REVERT: QX 89 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.8994 (m) REVERT: AY 1480 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8071 (mm-30) REVERT: AY 1492 GLU cc_start: 0.8531 (tp30) cc_final: 0.8324 (tp30) REVERT: AY 1585 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: AY 1596 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7380 (mt-10) REVERT: BY 1480 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7964 (mm-30) REVERT: BY 1523 TYR cc_start: 0.9190 (t80) cc_final: 0.8908 (t80) REVERT: CY 1503 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (t70) REVERT: CY 1517 ASP cc_start: 0.8637 (p0) cc_final: 0.8322 (p0) REVERT: CY 1528 ASN cc_start: 0.8505 (t0) cc_final: 0.8193 (t0) REVERT: DY 1473 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8750 (tp30) REVERT: DY 1499 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7962 (mt-10) REVERT: DY 1505 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8903 (mt-10) REVERT: DY 1523 TYR cc_start: 0.9214 (t80) cc_final: 0.9001 (t80) REVERT: EY 1503 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8702 (t70) REVERT: EY 1528 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8039 (t0) REVERT: FY 1480 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8063 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (t70) REVERT: FY 1528 ASN cc_start: 0.8483 (t0) cc_final: 0.8036 (t0) REVERT: GY 1480 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7883 (mm-30) REVERT: GY 1499 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8094 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8284 (t70) REVERT: GY 1517 ASP cc_start: 0.7989 (p0) cc_final: 0.7355 (p0) REVERT: GY 1518 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: GY 1587 GLU cc_start: 0.8820 (tp30) cc_final: 0.8584 (tp30) REVERT: HY 1503 ASP cc_start: 0.8851 (m-30) cc_final: 0.8514 (t70) REVERT: HY 1527 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7645 (ttm170) REVERT: HY 1528 ASN cc_start: 0.8505 (t0) cc_final: 0.7743 (t0) REVERT: IY 1480 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8111 (mm-30) REVERT: IY 1499 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8154 (mt-10) REVERT: IY 1503 ASP cc_start: 0.8814 (m-30) cc_final: 0.8517 (t70) REVERT: IY 1587 GLU cc_start: 0.8874 (tp30) cc_final: 0.8658 (tp30) REVERT: IY 1596 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7331 (mt-10) REVERT: JY 1480 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8007 (mm-30) REVERT: JY 1499 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7953 (mp0) REVERT: JY 1503 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8502 (t70) REVERT: JY 1580 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (mp) REVERT: KY 1480 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7955 (mm-30) REVERT: KY 1503 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8726 (t70) REVERT: KY 1523 TYR cc_start: 0.9265 (t80) cc_final: 0.8980 (t80) REVERT: LY 1528 ASN cc_start: 0.8517 (t0) cc_final: 0.8181 (t0) REVERT: LY 1596 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7033 (mm-30) REVERT: MY 1480 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7970 (mm-30) REVERT: MY 1517 ASP cc_start: 0.8171 (p0) cc_final: 0.7697 (p0) REVERT: MY 1518 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: NY 1528 ASN cc_start: 0.8473 (t0) cc_final: 0.8106 (t0) REVERT: NY 1538 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7854 (mptp) REVERT: OY 1503 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8554 (t70) REVERT: PY 1492 GLU cc_start: 0.8210 (tp30) cc_final: 0.8007 (tp30) REVERT: PY 1506 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8181 (mtp85) REVERT: PY 1523 TYR cc_start: 0.9236 (t80) cc_final: 0.8955 (t80) REVERT: PY 1528 ASN cc_start: 0.8186 (t0) cc_final: 0.7530 (t0) REVERT: PY 1576 ILE cc_start: 0.6749 (tp) cc_final: 0.6501 (tp) REVERT: QY 1480 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7924 (mm-30) REVERT: QY 1505 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: QY 1506 ARG cc_start: 0.8923 (mtp-110) cc_final: 0.8557 (mtp-110) outliers start: 372 outliers final: 170 residues processed: 1233 average time/residue: 0.6857 time to fit residues: 1034.4633 Evaluate side-chains 1015 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 796 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 60 SER Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 283 ARG Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 274 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 283 ARG Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 41 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 94 HIS Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 49 LEU Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 265 ASN Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 120 ARG Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 41 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 283 ARG Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 49 LEU Chi-restraints excluded: chain MX residue 69 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 274 SER Chi-restraints excluded: chain MX residue 277 ARG Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 316 HIS Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 303 SER Chi-restraints excluded: chain AY residue 1479 SER Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1503 ASP Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1469 LEU Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1506 ARG Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1562 ASP Chi-restraints excluded: chain QY residue 1576 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 96 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 305 optimal weight: 0.0270 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** CX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 83 ASN DX 91 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** FX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GX 83 ASN GX 91 ASN ** GX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HX 91 ASN ** HX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 91 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KX 91 ASN KX 93 ASN ** KX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 83 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN PX 83 ASN QX 91 ASN ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN CY1484 ASN DY1484 ASN DY1583 GLN EY1583 GLN HY1484 ASN IY1528 ASN LY1484 ASN LY1583 GLN MY1484 ASN OY1528 ASN PY1515 GLN PY1549 ASN PY1583 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092415 restraints weight = 85094.008| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.49 r_work: 0.3239 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41259 Z= 0.144 Angle : 0.594 10.662 55743 Z= 0.318 Chirality : 0.043 0.210 6375 Planarity : 0.004 0.070 7191 Dihedral : 6.501 69.416 5497 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 7.49 % Allowed : 30.47 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.11), residues: 4981 helix: 1.41 (0.12), residues: 2074 sheet: -1.84 (0.20), residues: 544 loop : -1.72 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGFY1514 TYR 0.013 0.001 TYRBX 77 PHE 0.017 0.001 PHEPX 96 TRP 0.010 0.001 TRPDX 58 HIS 0.006 0.001 HISDX 94 Details of bonding type rmsd covalent geometry : bond 0.00330 (41242) covalent geometry : angle 0.59372 (55709) SS BOND : bond 0.00148 ( 17) SS BOND : angle 0.89699 ( 34) hydrogen bonds : bond 0.03651 ( 2029) hydrogen bonds : angle 4.66744 ( 5784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 340 poor density : 922 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 89 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9095 (m) REVERT: AX 93 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8537 (p0) REVERT: AX 120 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7795 (ttp-110) REVERT: AX 324 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: BX 49 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8512 (pp) REVERT: BX 83 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: BX 120 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7830 (ttp80) REVERT: CX 49 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8658 (pp) REVERT: CX 265 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8391 (t0) REVERT: DX 120 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7663 (ttp-110) REVERT: DX 268 GLU cc_start: 0.8032 (pm20) cc_final: 0.7735 (tm-30) REVERT: DX 324 GLU cc_start: 0.7316 (mp0) cc_final: 0.7046 (mp0) REVERT: EX 83 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8537 (m-40) REVERT: FX 89 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9041 (m) REVERT: FX 130 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6169 (mmtm) REVERT: FX 289 TYR cc_start: 0.8768 (m-80) cc_final: 0.8537 (m-80) REVERT: GX 83 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8610 (m-40) REVERT: GX 91 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8042 (t0) REVERT: GX 277 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8560 (ttt-90) REVERT: HX 49 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8660 (pp) REVERT: HX 120 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7784 (ttp-110) REVERT: HX 273 ASP cc_start: 0.8518 (t0) cc_final: 0.8249 (t0) REVERT: HX 277 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8348 (ttt-90) REVERT: IX 62 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: IX 83 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8708 (t0) REVERT: IX 103 LYS cc_start: 0.8698 (tppt) cc_final: 0.8327 (mmtt) REVERT: IX 107 MET cc_start: 0.8881 (ptm) cc_final: 0.8584 (ptm) REVERT: IX 277 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8561 (ttm-80) REVERT: JX 120 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7787 (ttp-110) REVERT: KX 87 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8606 (p) REVERT: KX 103 LYS cc_start: 0.8524 (mppt) cc_final: 0.8273 (mmtt) REVERT: KX 118 MET cc_start: 0.8065 (ttm) cc_final: 0.7818 (ttm) REVERT: KX 120 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7814 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8515 (t0) cc_final: 0.8229 (t0) REVERT: KX 289 TYR cc_start: 0.8783 (m-80) cc_final: 0.8506 (m-80) REVERT: LX 49 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8676 (pp) REVERT: LX 89 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9067 (m) REVERT: MX 273 ASP cc_start: 0.8388 (t0) cc_final: 0.8163 (t0) REVERT: MX 277 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8180 (ttm-80) REVERT: NX 87 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8685 (p) REVERT: NX 103 LYS cc_start: 0.8656 (mppt) cc_final: 0.8394 (mmtt) REVERT: OX 69 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9009 (mt) REVERT: OX 91 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8303 (t0) REVERT: OX 273 ASP cc_start: 0.8444 (t70) cc_final: 0.7984 (t0) REVERT: OX 277 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8393 (ttt-90) REVERT: PX 273 ASP cc_start: 0.8407 (t0) cc_final: 0.8204 (t0) REVERT: QX 49 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8686 (pp) REVERT: QX 89 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.8964 (m) REVERT: AY 1585 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: BY 1480 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7848 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (t70) REVERT: CY 1517 ASP cc_start: 0.8667 (p0) cc_final: 0.8360 (p0) REVERT: CY 1528 ASN cc_start: 0.8489 (t0) cc_final: 0.8203 (t0) REVERT: DY 1527 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: EY 1503 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8691 (t70) REVERT: EY 1523 TYR cc_start: 0.9217 (t80) cc_final: 0.8999 (t80) REVERT: EY 1528 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8057 (t0) REVERT: FY 1503 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8524 (t70) REVERT: FY 1528 ASN cc_start: 0.8478 (t0) cc_final: 0.8036 (t0) REVERT: GY 1480 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7778 (mm-30) REVERT: GY 1484 ASN cc_start: 0.8718 (m110) cc_final: 0.8351 (m110) REVERT: GY 1499 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7921 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8270 (t70) REVERT: GY 1517 ASP cc_start: 0.8066 (p0) cc_final: 0.7503 (p0) REVERT: GY 1518 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: GY 1523 TYR cc_start: 0.9295 (t80) cc_final: 0.9093 (t80) REVERT: GY 1545 MET cc_start: 0.8751 (tpp) cc_final: 0.8530 (mmm) REVERT: HY 1503 ASP cc_start: 0.8842 (m-30) cc_final: 0.8492 (t70) REVERT: HY 1523 TYR cc_start: 0.9232 (t80) cc_final: 0.8959 (t80) REVERT: HY 1528 ASN cc_start: 0.8465 (t0) cc_final: 0.7708 (t0) REVERT: HY 1572 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8450 (mm) REVERT: IY 1503 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8504 (t70) REVERT: JY 1480 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8068 (mm-30) REVERT: JY 1499 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8036 (mp0) REVERT: JY 1503 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8472 (t70) REVERT: JY 1580 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8339 (mp) REVERT: KY 1480 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7939 (mm-30) REVERT: LY 1528 ASN cc_start: 0.8537 (t0) cc_final: 0.8202 (t0) REVERT: MY 1480 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7973 (mm-30) REVERT: MY 1517 ASP cc_start: 0.8174 (p0) cc_final: 0.7718 (p0) REVERT: MY 1518 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: MY 1523 TYR cc_start: 0.9079 (t80) cc_final: 0.8876 (t80) REVERT: MY 1596 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7256 (mt-10) REVERT: NY 1473 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8644 (mt-10) REVERT: NY 1480 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7976 (mm-30) REVERT: NY 1528 ASN cc_start: 0.8438 (t0) cc_final: 0.8073 (t0) REVERT: OY 1503 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8574 (t70) REVERT: OY 1523 TYR cc_start: 0.9207 (t80) cc_final: 0.8926 (t80) REVERT: OY 1559 THR cc_start: 0.8751 (m) cc_final: 0.8522 (p) REVERT: PY 1498 LEU cc_start: 0.7008 (mt) cc_final: 0.6574 (mt) REVERT: PY 1499 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: PY 1528 ASN cc_start: 0.8165 (t0) cc_final: 0.7530 (t0) REVERT: PY 1576 ILE cc_start: 0.6727 (tp) cc_final: 0.6483 (tp) REVERT: QY 1480 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7963 (mm-30) REVERT: QY 1506 ARG cc_start: 0.8902 (mtp-110) cc_final: 0.8540 (ttm110) outliers start: 340 outliers final: 152 residues processed: 1178 average time/residue: 0.6704 time to fit residues: 968.8906 Evaluate side-chains 1040 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 840 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 266 SER Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 274 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 283 ARG Chi-restraints excluded: chain FX residue 41 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 94 HIS Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 49 LEU Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 91 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 277 ARG Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 265 ASN Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 317 GLU Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 120 ARG Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 94 HIS Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 69 LEU Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 91 ASN Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 277 ARG Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 264 ASP Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1479 SER Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1572 ILE Chi-restraints excluded: chain IY residue 1473 GLU Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1502 SER Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1469 LEU Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1499 GLU Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1504 SER Chi-restraints excluded: chain PY residue 1512 ILE Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1520 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 20 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 403 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 345 optimal weight: 4.9990 chunk 450 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** AX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** CX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 314 GLN DX 83 ASN DX 91 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FX 314 GLN GX 83 ASN GX 91 ASN HX 91 ASN ** HX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** KX 297 GLN LX 83 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 83 ASN ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 314 GLN ** NX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN OX 93 ASN ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** QX 83 ASN ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN CY1484 ASN DY1484 ASN DY1583 GLN EY1583 GLN LY1484 ASN LY1583 GLN MY1484 ASN OY1528 ASN PY1515 GLN PY1549 ASN PY1583 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085984 restraints weight = 86428.300| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.45 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 41259 Z= 0.360 Angle : 0.727 11.067 55743 Z= 0.391 Chirality : 0.048 0.244 6375 Planarity : 0.005 0.074 7191 Dihedral : 6.987 81.192 5491 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 8.72 % Allowed : 30.36 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.11), residues: 4981 helix: 1.10 (0.11), residues: 2091 sheet: -2.09 (0.19), residues: 544 loop : -1.71 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARGFY1514 TYR 0.037 0.002 TYRCX 122 PHE 0.023 0.003 PHEPX 96 TRP 0.013 0.001 TRPDX 58 HIS 0.009 0.002 HISHX 316 Details of bonding type rmsd covalent geometry : bond 0.00831 (41242) covalent geometry : angle 0.72630 (55709) SS BOND : bond 0.00207 ( 17) SS BOND : angle 1.47110 ( 34) hydrogen bonds : bond 0.04654 ( 2029) hydrogen bonds : angle 4.91240 ( 5784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 396 poor density : 748 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 120 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7574 (ttp-170) REVERT: AX 324 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: BX 49 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8743 (pp) REVERT: BX 83 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8312 (m110) REVERT: BX 120 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7913 (ttp80) REVERT: CX 49 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8811 (pp) REVERT: CX 265 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8329 (t0) REVERT: CX 283 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7640 (ttp80) REVERT: DX 49 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8879 (pp) REVERT: DX 120 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7869 (ttp-110) REVERT: DX 268 GLU cc_start: 0.8163 (pm20) cc_final: 0.7865 (tm-30) REVERT: EX 83 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8491 (m110) REVERT: EX 120 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7648 (ttp-170) REVERT: FX 91 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8325 (t0) REVERT: FX 130 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6178 (mmtm) REVERT: FX 316 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (m-70) REVERT: GX 83 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8543 (m-40) REVERT: GX 277 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8645 (ttt-90) REVERT: GX 316 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8241 (m-70) REVERT: HX 49 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8837 (pp) REVERT: HX 62 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: HX 120 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7889 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8419 (ttt-90) REVERT: IX 62 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: IX 107 MET cc_start: 0.8930 (ptm) cc_final: 0.8612 (ptm) REVERT: IX 277 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8600 (ttt-90) REVERT: JX 120 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7968 (ttp-110) REVERT: JX 316 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8135 (m-70) REVERT: KX 120 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7806 (ttp-110) REVERT: KX 265 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8547 (t0) REVERT: KX 273 ASP cc_start: 0.8521 (t0) cc_final: 0.8320 (t0) REVERT: KX 316 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7991 (m-70) REVERT: LX 107 MET cc_start: 0.8840 (ttm) cc_final: 0.8637 (ptm) REVERT: LX 130 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6007 (mmtm) REVERT: LX 283 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8026 (ttm170) REVERT: MX 83 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8594 (m-40) REVERT: MX 103 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7816 (mppt) REVERT: MX 316 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8343 (m-70) REVERT: NX 103 LYS cc_start: 0.8758 (mppt) cc_final: 0.8486 (mmtt) REVERT: NX 316 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8098 (m-70) REVERT: OX 263 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: OX 277 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8446 (ttt-90) REVERT: QX 316 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.8177 (m-70) REVERT: AY 1585 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: BY 1480 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8020 (mm-30) REVERT: BY 1492 GLU cc_start: 0.8484 (tp30) cc_final: 0.8265 (tp30) REVERT: BY 1499 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8127 (mp0) REVERT: BY 1596 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7158 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8579 (t70) REVERT: CY 1517 ASP cc_start: 0.8638 (p0) cc_final: 0.8328 (p0) REVERT: CY 1528 ASN cc_start: 0.8664 (t0) cc_final: 0.7989 (t0) REVERT: DY 1505 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8882 (mt-10) REVERT: EY 1528 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7978 (t0) REVERT: FY 1503 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8436 (t70) REVERT: FY 1528 ASN cc_start: 0.8597 (t0) cc_final: 0.8032 (t0) REVERT: FY 1596 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7357 (mm-30) REVERT: GY 1480 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8112 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8437 (t70) REVERT: GY 1514 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7774 (ttp80) REVERT: GY 1517 ASP cc_start: 0.8113 (p0) cc_final: 0.7635 (p0) REVERT: GY 1518 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: GY 1523 TYR cc_start: 0.9289 (t80) cc_final: 0.9074 (t80) REVERT: GY 1545 MET cc_start: 0.8861 (tpp) cc_final: 0.8633 (mmm) REVERT: HY 1503 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8629 (t70) REVERT: HY 1528 ASN cc_start: 0.8545 (t0) cc_final: 0.7730 (t0) REVERT: HY 1572 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8572 (mm) REVERT: IY 1503 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8553 (t70) REVERT: JY 1492 GLU cc_start: 0.8456 (tp30) cc_final: 0.8246 (tp30) REVERT: JY 1499 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8105 (mp0) REVERT: JY 1503 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8611 (t70) REVERT: KY 1480 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7936 (mm-30) REVERT: KY 1523 TYR cc_start: 0.9314 (t80) cc_final: 0.9040 (t80) REVERT: KY 1527 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8105 (ttm-80) REVERT: MY 1505 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: MY 1514 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7725 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.8185 (p0) cc_final: 0.7927 (p0) REVERT: MY 1518 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: NY 1528 ASN cc_start: 0.8587 (t0) cc_final: 0.7795 (t0) REVERT: OY 1503 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8538 (t70) REVERT: OY 1528 ASN cc_start: 0.8488 (t0) cc_final: 0.8219 (t0) REVERT: OY 1584 TYR cc_start: 0.8204 (t80) cc_final: 0.7949 (t80) REVERT: PY 1499 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: QY 1480 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8100 (mm-30) REVERT: QY 1505 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8465 (mt-10) REVERT: QY 1528 ASN cc_start: 0.8465 (t0) cc_final: 0.8061 (t0) outliers start: 396 outliers final: 186 residues processed: 1068 average time/residue: 0.6996 time to fit residues: 911.3250 Evaluate side-chains 904 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 664 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 56 THR Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 109 GLU Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 263 GLU Chi-restraints excluded: chain BX residue 266 SER Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 283 ARG Chi-restraints excluded: chain DX residue 49 LEU Chi-restraints excluded: chain DX residue 62 ASP Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 41 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 91 ASN Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 94 HIS Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 283 ARG Chi-restraints excluded: chain FX residue 316 HIS Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 49 LEU Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 120 ARG Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 277 ARG Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 316 HIS Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 62 ASP Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 120 ARG Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 316 HIS Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 265 ASN Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 62 ASP Chi-restraints excluded: chain LX residue 94 HIS Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 283 ARG Chi-restraints excluded: chain MX residue 49 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 103 LYS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain MX residue 316 HIS Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 316 HIS Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 56 THR Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 263 GLU Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 56 THR Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 322 ILE Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 316 HIS Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1561 VAL Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1503 ASP Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain HY residue 1572 ILE Chi-restraints excluded: chain IY residue 1473 GLU Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1502 SER Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1521 LEU Chi-restraints excluded: chain KY residue 1526 LEU Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain LY residue 1568 SER Chi-restraints excluded: chain MY residue 1469 LEU Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1505 GLU Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1555 THR Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1503 ASP Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain PY residue 1499 GLU Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1504 SER Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1530 LYS Chi-restraints excluded: chain QY residue 1562 ASP Chi-restraints excluded: chain QY residue 1576 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 477 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 330 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 297 optimal weight: 0.9980 chunk 486 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 387 optimal weight: 4.9990 chunk 363 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GX 83 ASN HX 91 ASN ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 83 ASN MX 91 ASN OX 91 ASN OX 93 ASN ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** QX 91 ASN AY1484 ASN BY1583 GLN CY1484 ASN DY1484 ASN DY1557 ASN DY1583 GLN HY1484 ASN LY1583 GLN MY1484 ASN PY1549 ASN PY1583 GLN QY1557 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090270 restraints weight = 84619.760| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.47 r_work: 0.3214 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41259 Z= 0.168 Angle : 0.646 10.721 55743 Z= 0.346 Chirality : 0.044 0.227 6375 Planarity : 0.005 0.069 7191 Dihedral : 6.430 76.109 5483 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.41 % Allowed : 32.80 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.11), residues: 4981 helix: 1.34 (0.11), residues: 2074 sheet: -2.00 (0.20), residues: 544 loop : -1.74 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARGFY1514 TYR 0.030 0.001 TYRCX 122 PHE 0.016 0.001 PHEEX 82 TRP 0.009 0.001 TRPPX 58 HIS 0.006 0.001 HISDX 94 Details of bonding type rmsd covalent geometry : bond 0.00386 (41242) covalent geometry : angle 0.64326 (55709) SS BOND : bond 0.00405 ( 17) SS BOND : angle 2.62078 ( 34) hydrogen bonds : bond 0.03863 ( 2029) hydrogen bonds : angle 4.82329 ( 5784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 832 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 93 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8590 (p0) REVERT: AX 120 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7743 (ttp-110) REVERT: AX 324 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: BX 49 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8556 (pp) REVERT: BX 83 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8186 (m-40) REVERT: BX 120 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7868 (ttp80) REVERT: BX 277 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.7775 (ttm-80) REVERT: CX 49 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8665 (pp) REVERT: CX 265 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8293 (t0) REVERT: DX 120 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7788 (ttp-110) REVERT: DX 268 GLU cc_start: 0.7994 (pm20) cc_final: 0.7782 (tm-30) REVERT: DX 277 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8129 (ttt-90) REVERT: DX 316 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7870 (m-70) REVERT: DX 324 GLU cc_start: 0.7373 (mp0) cc_final: 0.6996 (mp0) REVERT: EX 83 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8431 (m110) REVERT: EX 120 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7769 (ttp-110) REVERT: FX 130 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6044 (mmtm) REVERT: FX 289 TYR cc_start: 0.8810 (m-80) cc_final: 0.8568 (m-80) REVERT: FX 316 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7914 (m-70) REVERT: GX 83 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8420 (m-40) REVERT: GX 103 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8195 (tptt) REVERT: HX 49 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8688 (pp) REVERT: HX 62 ASP cc_start: 0.8326 (m-30) cc_final: 0.7964 (m-30) REVERT: HX 91 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8299 (t0) REVERT: HX 120 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7813 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8420 (ttt-90) REVERT: IX 62 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: IX 83 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8835 (t0) REVERT: IX 107 MET cc_start: 0.8863 (ptm) cc_final: 0.8588 (ptm) REVERT: IX 277 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8525 (ttt-90) REVERT: JX 83 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8319 (m110) REVERT: JX 120 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7815 (ttp-110) REVERT: JX 322 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7841 (mp) REVERT: KX 87 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8684 (t) REVERT: KX 118 MET cc_start: 0.8083 (ttm) cc_final: 0.7850 (ttm) REVERT: KX 120 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7798 (ttp-110) REVERT: KX 289 TYR cc_start: 0.8824 (m-80) cc_final: 0.8508 (m-80) REVERT: KX 316 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7782 (m-70) REVERT: LX 130 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.5885 (mmtm) REVERT: MX 83 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8582 (m-40) REVERT: NX 103 LYS cc_start: 0.8719 (mppt) cc_final: 0.8429 (mmtt) REVERT: NX 316 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7908 (m-70) REVERT: OX 91 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8369 (t0) REVERT: OX 277 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8445 (ttt-90) REVERT: QX 89 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8948 (m) REVERT: AY 1585 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: BY 1480 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7928 (mm-30) REVERT: BY 1527 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7759 (ttm-80) REVERT: BY 1549 ASN cc_start: 0.7712 (m-40) cc_final: 0.6611 (m-40) REVERT: CY 1503 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8474 (t70) REVERT: CY 1517 ASP cc_start: 0.8654 (p0) cc_final: 0.8359 (p0) REVERT: CY 1528 ASN cc_start: 0.8601 (t0) cc_final: 0.8170 (t0) REVERT: DY 1505 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8809 (mt-10) REVERT: EY 1503 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8786 (t0) REVERT: EY 1523 TYR cc_start: 0.9210 (t80) cc_final: 0.8979 (t80) REVERT: EY 1528 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7840 (t0) REVERT: FY 1503 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8515 (t70) REVERT: FY 1528 ASN cc_start: 0.8490 (t0) cc_final: 0.8040 (t0) REVERT: GY 1480 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7976 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8325 (t70) REVERT: GY 1514 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7580 (ttp80) REVERT: GY 1517 ASP cc_start: 0.8091 (p0) cc_final: 0.7528 (p0) REVERT: GY 1518 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: GY 1545 MET cc_start: 0.8703 (tpp) cc_final: 0.8487 (mmm) REVERT: HY 1480 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8148 (mm-30) REVERT: HY 1503 ASP cc_start: 0.8835 (m-30) cc_final: 0.8539 (t70) REVERT: HY 1528 ASN cc_start: 0.8464 (t0) cc_final: 0.7718 (t0) REVERT: HY 1572 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8495 (mm) REVERT: HY 1585 GLU cc_start: 0.8341 (tp30) cc_final: 0.8139 (tp30) REVERT: IY 1503 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8506 (t70) REVERT: IY 1514 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7870 (tmm-80) REVERT: IY 1596 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7308 (mt-10) REVERT: JY 1499 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8179 (mp0) REVERT: JY 1503 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8539 (t70) REVERT: KY 1480 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7972 (mm-30) REVERT: KY 1523 TYR cc_start: 0.9249 (t80) cc_final: 0.9030 (t80) REVERT: KY 1527 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8036 (ttm-80) REVERT: MY 1514 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7697 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.8190 (p0) cc_final: 0.7797 (p0) REVERT: MY 1518 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: NY 1528 ASN cc_start: 0.8519 (t0) cc_final: 0.8152 (t0) REVERT: OY 1499 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7983 (mp0) REVERT: OY 1503 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8563 (t70) REVERT: OY 1523 TYR cc_start: 0.9109 (t80) cc_final: 0.8900 (t80) REVERT: OY 1528 ASN cc_start: 0.8388 (t0) cc_final: 0.8130 (t0) REVERT: PY 1498 LEU cc_start: 0.7247 (mt) cc_final: 0.6955 (mt) REVERT: PY 1527 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: PY 1576 ILE cc_start: 0.6942 (tp) cc_final: 0.6737 (tp) REVERT: QY 1505 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: QY 1506 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8453 (ttm110) REVERT: QY 1523 TYR cc_start: 0.9209 (t80) cc_final: 0.8938 (t80) REVERT: QY 1528 ASN cc_start: 0.8390 (t0) cc_final: 0.8036 (t0) REVERT: QY 1548 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.6921 (mmmm) outliers start: 291 outliers final: 149 residues processed: 1059 average time/residue: 0.6812 time to fit residues: 883.0927 Evaluate side-chains 951 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 751 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 270 SER Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 266 SER Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 277 ARG Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 62 ASP Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 316 HIS Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 91 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 316 HIS Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 91 ASN Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 321 VAL Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 120 ARG Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 317 GLU Chi-restraints excluded: chain JX residue 322 ILE Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 69 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 316 HIS Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 283 ARG Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 94 HIS Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1559 THR Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1509 ILE Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1572 ILE Chi-restraints excluded: chain IY residue 1473 GLU Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1502 SER Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1528 ASN Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain LY residue 1568 SER Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1559 THR Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1504 SER Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1585 GLU Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1548 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 229 optimal weight: 1.9990 chunk 457 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 422 optimal weight: 0.0970 chunk 152 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 367 optimal weight: 0.7980 chunk 426 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 487 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN CX 93 ASN DX 83 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** FX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GX 83 ASN HX 91 ASN ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN IX 91 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KX 93 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 83 ASN ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1583 GLN CY1484 ASN DY1484 ASN DY1557 ASN DY1583 GLN EY1583 GLN HY1484 ASN LY1583 GLN MY1484 ASN PY1515 GLN PY1583 GLN QY1557 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.105276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090458 restraints weight = 85202.001| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.47 r_work: 0.3214 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 41259 Z= 0.178 Angle : 0.665 10.926 55743 Z= 0.356 Chirality : 0.044 0.263 6375 Planarity : 0.005 0.079 7191 Dihedral : 6.389 74.756 5482 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.08 % Allowed : 33.71 % Favored : 60.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.11), residues: 4981 helix: 1.35 (0.11), residues: 2074 sheet: -1.95 (0.20), residues: 544 loop : -1.72 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARGFY1514 TYR 0.044 0.001 TYRCX 122 PHE 0.016 0.002 PHEMX 96 TRP 0.013 0.001 TRPDX 58 HIS 0.014 0.001 HISCX 94 Details of bonding type rmsd covalent geometry : bond 0.00416 (41242) covalent geometry : angle 0.66193 (55709) SS BOND : bond 0.00566 ( 17) SS BOND : angle 2.69333 ( 34) hydrogen bonds : bond 0.03970 ( 2029) hydrogen bonds : angle 4.85484 ( 5784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 762 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 120 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7505 (ttp-170) REVERT: BX 49 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8588 (pp) REVERT: BX 83 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: BX 120 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7906 (ttp80) REVERT: BX 277 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.7884 (ttm-80) REVERT: CX 49 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8667 (pp) REVERT: CX 62 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: CX 265 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8299 (t0) REVERT: DX 120 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7777 (ttp-110) REVERT: DX 268 GLU cc_start: 0.8021 (pm20) cc_final: 0.7776 (tm-30) REVERT: DX 277 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8128 (ttt-90) REVERT: EX 83 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (m110) REVERT: EX 120 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7797 (ttp-110) REVERT: FX 91 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8149 (t0) REVERT: FX 130 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6033 (mmtm) REVERT: FX 289 TYR cc_start: 0.8845 (m-80) cc_final: 0.8638 (m-80) REVERT: FX 324 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: GX 83 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8425 (m-40) REVERT: GX 277 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8616 (ttt-90) REVERT: HX 49 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8722 (pp) REVERT: HX 62 ASP cc_start: 0.8243 (m-30) cc_final: 0.7939 (m-30) REVERT: HX 91 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8272 (t0) REVERT: HX 120 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7841 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8438 (ttt-90) REVERT: HX 324 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7503 (mp0) REVERT: IX 62 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: IX 83 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8477 (m-40) REVERT: IX 107 MET cc_start: 0.8904 (ptm) cc_final: 0.8629 (ptm) REVERT: IX 277 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8569 (ttm-80) REVERT: JX 120 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7808 (ttp-110) REVERT: KX 49 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (pp) REVERT: KX 87 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8618 (p) REVERT: KX 289 TYR cc_start: 0.8808 (m-80) cc_final: 0.8510 (m-80) REVERT: KX 316 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7805 (m-70) REVERT: LX 89 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9096 (m) REVERT: LX 107 MET cc_start: 0.8833 (ptm) cc_final: 0.8607 (ptm) REVERT: LX 130 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.5860 (mmtm) REVERT: MX 83 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8465 (m-40) REVERT: NX 103 LYS cc_start: 0.8683 (mppt) cc_final: 0.8411 (mmtt) REVERT: NX 316 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7939 (m-70) REVERT: OX 69 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9032 (mt) REVERT: OX 91 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8353 (t0) REVERT: OX 273 ASP cc_start: 0.8461 (t0) cc_final: 0.7951 (t0) REVERT: OX 277 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8460 (ttt-90) REVERT: PX 263 GLU cc_start: 0.7790 (tt0) cc_final: 0.7541 (tp30) REVERT: PX 324 GLU cc_start: 0.7372 (mp0) cc_final: 0.7044 (mp0) REVERT: QX 107 MET cc_start: 0.8786 (ttm) cc_final: 0.8335 (ttt) REVERT: AY 1585 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: BY 1480 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7944 (mm-30) REVERT: BY 1514 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7955 (tmm-80) REVERT: BY 1523 TYR cc_start: 0.9189 (t80) cc_final: 0.8978 (t80) REVERT: CY 1503 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8471 (t70) REVERT: CY 1517 ASP cc_start: 0.8674 (p0) cc_final: 0.8356 (p0) REVERT: CY 1528 ASN cc_start: 0.8604 (t0) cc_final: 0.8152 (t0) REVERT: DY 1505 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8833 (mt-10) REVERT: DY 1523 TYR cc_start: 0.9212 (t80) cc_final: 0.8970 (t80) REVERT: EY 1503 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8807 (t0) REVERT: EY 1528 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8065 (t0) REVERT: FY 1503 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8521 (t70) REVERT: FY 1528 ASN cc_start: 0.8453 (t0) cc_final: 0.8039 (t0) REVERT: FY 1596 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7191 (mt-10) REVERT: GY 1480 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7933 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (t70) REVERT: GY 1514 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7667 (ttp80) REVERT: GY 1517 ASP cc_start: 0.8102 (p0) cc_final: 0.7582 (p0) REVERT: GY 1518 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: GY 1545 MET cc_start: 0.8764 (tpp) cc_final: 0.8539 (mmm) REVERT: HY 1480 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7964 (mm-30) REVERT: HY 1503 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8574 (t70) REVERT: HY 1528 ASN cc_start: 0.8477 (t0) cc_final: 0.7721 (t0) REVERT: HY 1585 GLU cc_start: 0.8356 (tp30) cc_final: 0.8150 (tp30) REVERT: IY 1503 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8513 (t70) REVERT: JY 1499 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8173 (mp0) REVERT: JY 1503 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8526 (t70) REVERT: KY 1527 ARG cc_start: 0.8263 (ttp80) cc_final: 0.8034 (ttm-80) REVERT: KY 1528 ASN cc_start: 0.8259 (t0) cc_final: 0.7963 (t0) REVERT: MY 1514 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7811 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.8183 (p0) cc_final: 0.7818 (p0) REVERT: MY 1518 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: NY 1528 ASN cc_start: 0.8509 (t0) cc_final: 0.8146 (t0) REVERT: OY 1503 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8597 (t70) REVERT: OY 1522 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9195 (mt) REVERT: OY 1528 ASN cc_start: 0.8408 (t0) cc_final: 0.8146 (t0) REVERT: PY 1506 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8598 (mtp-110) REVERT: PY 1576 ILE cc_start: 0.7005 (tp) cc_final: 0.6798 (tp) REVERT: QY 1506 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8502 (ttm110) REVERT: QY 1528 ASN cc_start: 0.8365 (t0) cc_final: 0.8030 (t0) REVERT: QY 1548 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.6985 (mmmm) outliers start: 276 outliers final: 152 residues processed: 982 average time/residue: 0.6810 time to fit residues: 817.0760 Evaluate side-chains 933 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 731 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 266 SER Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 277 ARG Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 62 ASP Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 49 LEU Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 83 ASN Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 91 ASN Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 324 GLU Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 277 ARG Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 91 ASN Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 265 ASN Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 41 VAL Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 94 HIS Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 120 ARG Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 49 LEU Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 69 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 316 HIS Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 94 HIS Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1559 THR Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1509 ILE Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain HY residue 1473 GLU Chi-restraints excluded: chain HY residue 1503 ASP Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain IY residue 1473 GLU Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1502 SER Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain LY residue 1568 SER Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1559 THR Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1522 ILE Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1504 SER Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1585 GLU Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1548 LYS Chi-restraints excluded: chain QY residue 1562 ASP Chi-restraints excluded: chain QY residue 1576 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 400 optimal weight: 0.9990 chunk 402 optimal weight: 1.9990 chunk 406 optimal weight: 0.7980 chunk 463 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 382 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN CX 93 ASN DX 83 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** FX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GX 83 ASN HX 91 ASN ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 83 ASN ** MX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN OX 93 ASN ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1583 GLN CY1484 ASN DY1484 ASN DY1557 ASN DY1583 GLN IY1583 GLN LY1583 GLN MY1484 ASN PY1515 GLN PY1583 GLN QY1557 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.091949 restraints weight = 84638.229| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.44 r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41259 Z= 0.163 Angle : 0.664 10.959 55743 Z= 0.354 Chirality : 0.044 0.251 6375 Planarity : 0.005 0.053 7191 Dihedral : 6.269 72.913 5479 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.38 % Allowed : 34.83 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.11), residues: 4981 helix: 1.34 (0.11), residues: 2074 sheet: -1.90 (0.20), residues: 544 loop : -1.68 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARGKX 294 TYR 0.040 0.001 TYRCX 122 PHE 0.016 0.001 PHEMX 96 TRP 0.014 0.001 TRPDX 58 HIS 0.013 0.001 HISCX 94 Details of bonding type rmsd covalent geometry : bond 0.00380 (41242) covalent geometry : angle 0.66092 (55709) SS BOND : bond 0.00452 ( 17) SS BOND : angle 2.59391 ( 34) hydrogen bonds : bond 0.03903 ( 2029) hydrogen bonds : angle 4.85488 ( 5784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 785 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 49 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8667 (pp) REVERT: AX 120 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7525 (ttp-170) REVERT: BX 49 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8581 (pp) REVERT: BX 83 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: BX 120 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7903 (ttp80) REVERT: BX 277 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7879 (ttm-80) REVERT: CX 49 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8672 (pp) REVERT: DX 120 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7701 (ttp-110) REVERT: DX 277 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8090 (ttt-90) REVERT: DX 294 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7785 (mtp85) REVERT: EX 83 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8458 (m110) REVERT: EX 120 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7762 (ttp-110) REVERT: FX 130 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6030 (mmtm) REVERT: FX 324 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: GX 83 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8561 (m-40) REVERT: HX 49 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8734 (pp) REVERT: HX 62 ASP cc_start: 0.8272 (m-30) cc_final: 0.7949 (m-30) REVERT: HX 89 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9078 (m) REVERT: HX 91 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8204 (t0) REVERT: HX 120 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7831 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8428 (ttt-90) REVERT: IX 62 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: IX 83 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8411 (m-40) REVERT: IX 107 MET cc_start: 0.8881 (ptm) cc_final: 0.8581 (ptm) REVERT: IX 277 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8529 (ttm-80) REVERT: KX 87 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8598 (p) REVERT: KX 289 TYR cc_start: 0.8815 (m-80) cc_final: 0.8483 (m-80) REVERT: KX 316 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7731 (m-70) REVERT: KX 317 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7753 (pp20) REVERT: LX 89 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.9103 (m) REVERT: LX 130 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.5940 (mmtm) REVERT: MX 83 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: MX 122 TYR cc_start: 0.8364 (t80) cc_final: 0.8141 (t80) REVERT: NX 87 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8646 (p) REVERT: OX 69 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9039 (mt) REVERT: OX 91 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8417 (t0) REVERT: OX 273 ASP cc_start: 0.8387 (t0) cc_final: 0.8157 (t0) REVERT: OX 277 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8445 (ttt-90) REVERT: PX 263 GLU cc_start: 0.7803 (tt0) cc_final: 0.7583 (tp30) REVERT: PX 317 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7682 (pp20) REVERT: PX 324 GLU cc_start: 0.7340 (mp0) cc_final: 0.6992 (mp0) REVERT: AY 1585 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: BY 1480 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7981 (mm-30) REVERT: BY 1492 GLU cc_start: 0.8475 (tp30) cc_final: 0.8259 (tp30) REVERT: BY 1514 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7909 (tmm-80) REVERT: CY 1503 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8525 (t0) REVERT: CY 1517 ASP cc_start: 0.8633 (p0) cc_final: 0.8322 (p0) REVERT: DY 1514 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7806 (tmm-80) REVERT: EY 1528 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8072 (t0) REVERT: FY 1503 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8524 (t70) REVERT: FY 1528 ASN cc_start: 0.8450 (t0) cc_final: 0.7996 (t0) REVERT: GY 1499 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8073 (pm20) REVERT: GY 1503 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8335 (t70) REVERT: GY 1514 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7719 (ttp80) REVERT: GY 1517 ASP cc_start: 0.8140 (p0) cc_final: 0.7654 (p0) REVERT: GY 1518 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: GY 1545 MET cc_start: 0.8744 (tpp) cc_final: 0.8479 (mmm) REVERT: HY 1498 LEU cc_start: 0.7629 (mt) cc_final: 0.7412 (mt) REVERT: HY 1503 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8595 (t70) REVERT: HY 1528 ASN cc_start: 0.8459 (t0) cc_final: 0.7708 (t0) REVERT: HY 1585 GLU cc_start: 0.8353 (tp30) cc_final: 0.8145 (tp30) REVERT: IY 1503 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (t70) REVERT: IY 1596 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7242 (mt-10) REVERT: JY 1495 GLU cc_start: 0.8761 (tp30) cc_final: 0.8361 (mm-30) REVERT: JY 1499 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7978 (mp0) REVERT: JY 1503 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8562 (t70) REVERT: LY 1523 TYR cc_start: 0.9166 (t80) cc_final: 0.8917 (t80) REVERT: LY 1528 ASN cc_start: 0.8452 (t0) cc_final: 0.8111 (t0) REVERT: MY 1514 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7837 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.8203 (p0) cc_final: 0.7804 (p0) REVERT: MY 1518 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: NY 1528 ASN cc_start: 0.8432 (t0) cc_final: 0.8109 (t0) REVERT: OY 1503 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8653 (t70) REVERT: OY 1522 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9179 (mt) REVERT: OY 1528 ASN cc_start: 0.8393 (t0) cc_final: 0.8128 (t0) REVERT: PY 1506 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8630 (mtp-110) REVERT: PY 1576 ILE cc_start: 0.6964 (tp) cc_final: 0.6749 (tp) REVERT: QY 1506 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8476 (ttm110) REVERT: QY 1523 TYR cc_start: 0.9235 (t80) cc_final: 0.8983 (t80) REVERT: QY 1528 ASN cc_start: 0.8369 (t0) cc_final: 0.8053 (t0) REVERT: QY 1548 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.6761 (mmmm) outliers start: 244 outliers final: 153 residues processed: 972 average time/residue: 0.6817 time to fit residues: 810.5835 Evaluate side-chains 934 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 737 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 274 SER Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 266 SER Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 277 ARG Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 49 LEU Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 283 ARG Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain EX residue 83 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 317 GLU Chi-restraints excluded: chain FX residue 83 ASN Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 91 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 324 GLU Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 83 ASN Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 91 ASN Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 265 ASN Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 41 VAL Chi-restraints excluded: chain IX residue 62 ASP Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 94 HIS Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 69 LEU Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 89 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 317 GLU Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 274 SER Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 94 HIS Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 274 SER Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1503 ASP Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1473 GLU Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1509 ILE Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain HY residue 1473 GLU Chi-restraints excluded: chain HY residue 1503 ASP Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain IY residue 1473 GLU Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1502 SER Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain LY residue 1568 SER Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1559 THR Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1522 ILE Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1504 SER Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1585 GLU Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1548 LYS Chi-restraints excluded: chain QY residue 1576 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 267 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 421 optimal weight: 3.9990 chunk 293 optimal weight: 0.4980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 83 ASN ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GX 83 ASN HX 91 ASN ** HX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 83 ASN ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1484 ASN BY1583 GLN CY1484 ASN DY1528 ASN DY1583 GLN LY1484 ASN LY1583 GLN MY1484 ASN PY1484 ASN PY1515 GLN PY1583 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090046 restraints weight = 85848.161| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.46 r_work: 0.3206 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 41259 Z= 0.230 Angle : 0.702 13.603 55743 Z= 0.374 Chirality : 0.045 0.249 6375 Planarity : 0.005 0.059 7191 Dihedral : 6.276 74.004 5477 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.24 % Allowed : 35.18 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.11), residues: 4981 helix: 1.27 (0.11), residues: 2091 sheet: -1.90 (0.19), residues: 544 loop : -1.64 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARGAX 294 TYR 0.043 0.001 TYRCX 122 PHE 0.018 0.002 PHEIX 96 TRP 0.015 0.001 TRPQX 58 HIS 0.010 0.002 HISPX 94 Details of bonding type rmsd covalent geometry : bond 0.00536 (41242) covalent geometry : angle 0.69745 (55709) SS BOND : bond 0.00453 ( 17) SS BOND : angle 3.29749 ( 34) hydrogen bonds : bond 0.04122 ( 2029) hydrogen bonds : angle 4.85055 ( 5784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15795.79 seconds wall clock time: 269 minutes 44.53 seconds (16184.53 seconds total)