Starting phenix.real_space_refine on Fri Jan 17 15:27:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x19_37988/01_2025/8x19_37988_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x19_37988/01_2025/8x19_37988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x19_37988/01_2025/8x19_37988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x19_37988/01_2025/8x19_37988.map" model { file = "/net/cci-nas-00/data/ceres_data/8x19_37988/01_2025/8x19_37988_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x19_37988/01_2025/8x19_37988_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 312 5.49 5 Mg 1 5.21 5 S 256 5.16 5 Be 1 3.05 5 C 34778 2.51 5 N 10076 2.21 5 O 11277 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 56704 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "I" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7122 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 52, 'TRANS': 811} Chain breaks: 2 Chain: "J" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1350 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 13, 'TRANS': 148} Chain breaks: 1 Chain: "K" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3209 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain breaks: 1 Chain: "M" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3213 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3185 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "O" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3287 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3368 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 422} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3293 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "T" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3146 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 1 Chain: "U" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2802 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1757 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Chain: "W" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1542 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 178} Chain: "X" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "Y" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.84, per 1000 atoms: 0.47 Number of scatterers: 56704 At special positions: 0 Unit cell: (184.092, 189.428, 225.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 256 16.00 P 312 15.00 Mg 1 11.99 F 3 9.00 O 11277 8.00 N 10076 7.00 C 34778 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.79 Conformation dependent library (CDL) restraints added in 5.2 seconds 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11908 Finding SS restraints... Secondary structure from input PDB file: 272 helices and 55 sheets defined 49.4% alpha, 9.9% beta 124 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 16.58 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.523A pdb=" N ARG A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 47 through 74 removed outlier: 3.637A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 91 removed outlier: 3.915A pdb=" N ALA A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.717A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.549A pdb=" N LEU A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 52 through 81 Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 100 through 117 Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.625A pdb=" N LEU C 70 " --> pdb=" O PRO C 66 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 112 removed outlier: 3.678A pdb=" N ALA C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 41 removed outlier: 3.581A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 75 removed outlier: 3.596A pdb=" N TYR D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 removed outlier: 3.743A pdb=" N VAL D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 46 through 73 Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.649A pdb=" N LYS E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 46 removed outlier: 3.785A pdb=" N GLN F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 81 removed outlier: 3.545A pdb=" N GLU F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 97 Processing helix chain 'F' and resid 101 through 120 removed outlier: 3.545A pdb=" N SER F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 removed outlier: 3.537A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 77 removed outlier: 4.061A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.807A pdb=" N MET G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA G 114 " --> pdb=" O CYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.554A pdb=" N GLY H 28 " --> pdb=" O ASN H 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE H 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 25 through 29' Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 50 through 76 removed outlier: 3.905A pdb=" N GLY H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA H 76 " --> pdb=" O TYR H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'I' and resid 94 through 116 removed outlier: 3.841A pdb=" N GLU I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 251 removed outlier: 3.639A pdb=" N ALA I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU I 180 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 635 Processing helix chain 'I' and resid 648 through 664 Processing helix chain 'I' and resid 675 through 677 No H-bonds generated for 'chain 'I' and resid 675 through 677' Processing helix chain 'I' and resid 678 through 690 Processing helix chain 'I' and resid 701 through 708 removed outlier: 3.655A pdb=" N LYS I 706 " --> pdb=" O GLN I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 737 removed outlier: 4.154A pdb=" N ARG I 737 " --> pdb=" O GLN I 733 " (cutoff:3.500A) Processing helix chain 'I' and resid 748 through 752 Processing helix chain 'I' and resid 757 through 764 removed outlier: 3.609A pdb=" N SER I 761 " --> pdb=" O GLN I 757 " (cutoff:3.500A) Processing helix chain 'I' and resid 783 through 793 removed outlier: 3.794A pdb=" N SER I 787 " --> pdb=" O MET I 783 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU I 788 " --> pdb=" O GLU I 784 " (cutoff:3.500A) Processing helix chain 'I' and resid 800 through 814 Proline residue: I 810 - end of helix Processing helix chain 'I' and resid 825 through 834 removed outlier: 3.639A pdb=" N LEU I 833 " --> pdb=" O LEU I 829 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG I 834 " --> pdb=" O HIS I 830 " (cutoff:3.500A) Processing helix chain 'I' and resid 862 through 873 Processing helix chain 'I' and resid 875 through 884 Processing helix chain 'I' and resid 887 through 903 Processing helix chain 'I' and resid 903 through 908 removed outlier: 3.992A pdb=" N PHE I 907 " --> pdb=" O HIS I 903 " (cutoff:3.500A) Processing helix chain 'I' and resid 927 through 932 Processing helix chain 'I' and resid 942 through 946 removed outlier: 4.020A pdb=" N ARG I 945 " --> pdb=" O ASP I 942 " (cutoff:3.500A) Processing helix chain 'I' and resid 956 through 962 Processing helix chain 'I' and resid 962 through 968 removed outlier: 3.759A pdb=" N ARG I 966 " --> pdb=" O THR I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 970 through 978 Processing helix chain 'I' and resid 1886 through 1911 Processing helix chain 'I' and resid 1919 through 1927 Processing helix chain 'I' and resid 1945 through 1949 Processing helix chain 'I' and resid 1952 through 1957 Processing helix chain 'I' and resid 1961 through 1977 removed outlier: 4.381A pdb=" N GLU I1971 " --> pdb=" O ASP I1967 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE I1972 " --> pdb=" O GLN I1968 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG I1975 " --> pdb=" O GLU I1971 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE I1977 " --> pdb=" O ILE I1973 " (cutoff:3.500A) Processing helix chain 'I' and resid 1998 through 2014 removed outlier: 3.523A pdb=" N GLN I2003 " --> pdb=" O LEU I1999 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU I2013 " --> pdb=" O GLN I2009 " (cutoff:3.500A) Processing helix chain 'I' and resid 2018 through 2020 No H-bonds generated for 'chain 'I' and resid 2018 through 2020' Processing helix chain 'I' and resid 2021 through 2028 Processing helix chain 'I' and resid 2042 through 2057 removed outlier: 3.902A pdb=" N ALA I2057 " --> pdb=" O ARG I2053 " (cutoff:3.500A) Processing helix chain 'I' and resid 2070 through 2082 removed outlier: 4.217A pdb=" N VAL I2074 " --> pdb=" O ARG I2070 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR I2080 " --> pdb=" O GLU I2076 " (cutoff:3.500A) Processing helix chain 'I' and resid 2094 through 2107 Processing helix chain 'I' and resid 2141 through 2150 removed outlier: 4.439A pdb=" N ASP I2145 " --> pdb=" O ASN I2141 " (cutoff:3.500A) Processing helix chain 'I' and resid 2172 through 2192 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 170 through 193 removed outlier: 3.597A pdb=" N GLU J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 277 Processing helix chain 'J' and resid 312 through 330 Processing helix chain 'K' and resid 43 through 48 Processing helix chain 'K' and resid 68 through 80 Processing helix chain 'K' and resid 103 through 116 Processing helix chain 'K' and resid 126 through 139 Processing helix chain 'K' and resid 176 through 192 Processing helix chain 'K' and resid 199 through 207 Processing helix chain 'K' and resid 215 through 224 Processing helix chain 'K' and resid 251 through 255 Processing helix chain 'K' and resid 272 through 283 removed outlier: 3.555A pdb=" N ALA K 276 " --> pdb=" O ASN K 272 " (cutoff:3.500A) Proline residue: K 278 - end of helix Processing helix chain 'K' and resid 293 through 303 Processing helix chain 'K' and resid 308 through 315 removed outlier: 4.429A pdb=" N HIS K 312 " --> pdb=" O GLU K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 326 Processing helix chain 'K' and resid 328 through 341 Processing helix chain 'K' and resid 357 through 369 Processing helix chain 'K' and resid 378 through 383 Processing helix chain 'K' and resid 387 through 394 Processing helix chain 'L' and resid 21 through 37 Processing helix chain 'L' and resid 84 through 94 Processing helix chain 'L' and resid 101 through 105 removed outlier: 3.792A pdb=" N CYS L 105 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 148 Processing helix chain 'M' and resid 42 through 59 removed outlier: 3.802A pdb=" N GLU M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU M 55 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 88 Processing helix chain 'M' and resid 99 through 102 Processing helix chain 'M' and resid 107 through 119 Processing helix chain 'M' and resid 175 through 183 removed outlier: 4.091A pdb=" N SER M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN M 181 " --> pdb=" O PHE M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 249 removed outlier: 4.193A pdb=" N ARG M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 removed outlier: 3.645A pdb=" N MET M 260 " --> pdb=" O ILE M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 289 Processing helix chain 'M' and resid 303 through 307 Processing helix chain 'M' and resid 308 through 319 Processing helix chain 'M' and resid 347 through 350 Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 367 through 383 Processing helix chain 'M' and resid 387 through 401 Processing helix chain 'M' and resid 402 through 420 removed outlier: 3.542A pdb=" N SER M 406 " --> pdb=" O THR M 402 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU M 410 " --> pdb=" O SER M 406 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR M 411 " --> pdb=" O VAL M 407 " (cutoff:3.500A) Proline residue: M 412 - end of helix Processing helix chain 'M' and resid 426 through 437 removed outlier: 3.677A pdb=" N VAL M 430 " --> pdb=" O GLU M 426 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU M 432 " --> pdb=" O GLU M 428 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU M 436 " --> pdb=" O GLU M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 448 Processing helix chain 'N' and resid 49 through 66 Processing helix chain 'N' and resid 82 through 95 Processing helix chain 'N' and resid 106 through 109 removed outlier: 3.650A pdb=" N PHE N 109 " --> pdb=" O SER N 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 106 through 109' Processing helix chain 'N' and resid 114 through 126 removed outlier: 3.524A pdb=" N SER N 126 " --> pdb=" O ALA N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 183 Processing helix chain 'N' and resid 184 through 186 No H-bonds generated for 'chain 'N' and resid 184 through 186' Processing helix chain 'N' and resid 244 through 251 Processing helix chain 'N' and resid 257 through 261 removed outlier: 3.992A pdb=" N LEU N 260 " --> pdb=" O PHE N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 284 Processing helix chain 'N' and resid 301 through 304 Processing helix chain 'N' and resid 305 through 316 removed outlier: 3.966A pdb=" N ARG N 314 " --> pdb=" O SER N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 352 Processing helix chain 'N' and resid 363 through 378 Processing helix chain 'N' and resid 383 through 397 Processing helix chain 'N' and resid 398 through 416 removed outlier: 3.588A pdb=" N ALA N 402 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA N 408 " --> pdb=" O GLN N 404 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG N 416 " --> pdb=" O VAL N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 433 Processing helix chain 'N' and resid 435 through 442 Processing helix chain 'O' and resid 42 through 58 Processing helix chain 'O' and resid 77 through 88 Processing helix chain 'O' and resid 99 through 102 removed outlier: 3.558A pdb=" N TYR O 102 " --> pdb=" O SER O 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 102' Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.762A pdb=" N LEU O 112 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG O 117 " --> pdb=" O MET O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 184 Processing helix chain 'O' and resid 208 through 212 removed outlier: 4.159A pdb=" N THR O 211 " --> pdb=" O THR O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 249 Processing helix chain 'O' and resid 256 through 260 Processing helix chain 'O' and resid 271 through 276 Processing helix chain 'O' and resid 277 through 288 Processing helix chain 'O' and resid 303 through 307 removed outlier: 3.580A pdb=" N MET O 306 " --> pdb=" O GLU O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 320 removed outlier: 3.559A pdb=" N HIS O 316 " --> pdb=" O PHE O 312 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'O' and resid 367 through 382 removed outlier: 3.514A pdb=" N GLU O 382 " --> pdb=" O ARG O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 387 through 401 Processing helix chain 'O' and resid 402 through 409 Processing helix chain 'O' and resid 409 through 420 Processing helix chain 'O' and resid 426 through 437 Processing helix chain 'O' and resid 439 through 450 removed outlier: 4.342A pdb=" N LYS O 445 " --> pdb=" O LYS O 441 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE O 446 " --> pdb=" O SER O 442 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN O 450 " --> pdb=" O ILE O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 454 removed outlier: 3.702A pdb=" N TYR O 454 " --> pdb=" O GLN O 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 451 through 454' Processing helix chain 'P' and resid 42 through 46 removed outlier: 4.137A pdb=" N GLY P 45 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET P 46 " --> pdb=" O SER P 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 42 through 46' Processing helix chain 'P' and resid 49 through 66 Processing helix chain 'P' and resid 82 through 95 Processing helix chain 'P' and resid 106 through 109 removed outlier: 3.826A pdb=" N PHE P 109 " --> pdb=" O SER P 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 106 through 109' Processing helix chain 'P' and resid 114 through 125 Processing helix chain 'P' and resid 175 through 185 removed outlier: 3.543A pdb=" N ASP P 185 " --> pdb=" O SER P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 253 removed outlier: 4.067A pdb=" N ARG P 253 " --> pdb=" O VAL P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 262 Processing helix chain 'P' and resid 272 through 286 Processing helix chain 'P' and resid 300 through 304 Processing helix chain 'P' and resid 305 through 317 removed outlier: 4.003A pdb=" N ARG P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU P 317 " --> pdb=" O ASN P 313 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 346 Processing helix chain 'P' and resid 349 through 352 Processing helix chain 'P' and resid 363 through 378 Processing helix chain 'P' and resid 383 through 397 Processing helix chain 'P' and resid 398 through 416 removed outlier: 3.607A pdb=" N ILE P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR P 407 " --> pdb=" O ILE P 403 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA P 408 " --> pdb=" O GLN P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 422 through 433 Processing helix chain 'P' and resid 436 through 443 Processing helix chain 'Q' and resid 35 through 39 removed outlier: 3.948A pdb=" N GLY Q 38 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 58 removed outlier: 3.501A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 88 removed outlier: 3.846A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 119 Processing helix chain 'Q' and resid 173 through 183 removed outlier: 3.844A pdb=" N PHE Q 177 " --> pdb=" O ASP Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 249 Processing helix chain 'Q' and resid 255 through 260 Processing helix chain 'Q' and resid 271 through 276 Processing helix chain 'Q' and resid 279 through 289 removed outlier: 3.524A pdb=" N VAL Q 283 " --> pdb=" O ILE Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 304 through 307 Processing helix chain 'Q' and resid 308 through 320 removed outlier: 3.522A pdb=" N HIS Q 316 " --> pdb=" O PHE Q 312 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 350 Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'Q' and resid 367 through 383 Processing helix chain 'Q' and resid 387 through 401 removed outlier: 3.726A pdb=" N LYS Q 400 " --> pdb=" O GLU Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 402 through 409 Processing helix chain 'Q' and resid 409 through 420 Processing helix chain 'Q' and resid 426 through 437 removed outlier: 3.736A pdb=" N VAL Q 430 " --> pdb=" O GLU Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 450 Processing helix chain 'R' and resid 49 through 66 Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 106 through 109 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'R' and resid 175 through 184 Processing helix chain 'R' and resid 212 through 216 removed outlier: 3.717A pdb=" N ASP R 216 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 251 removed outlier: 3.512A pdb=" N ASN R 251 " --> pdb=" O ASP R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 260 Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 274 through 287 Processing helix chain 'R' and resid 300 through 304 Processing helix chain 'R' and resid 305 through 317 removed outlier: 3.935A pdb=" N ARG R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 352 Processing helix chain 'R' and resid 363 through 379 removed outlier: 4.015A pdb=" N LYS R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 395 Processing helix chain 'R' and resid 398 through 416 removed outlier: 3.801A pdb=" N ALA R 402 " --> pdb=" O SER R 398 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 403 " --> pdb=" O LEU R 399 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 406 " --> pdb=" O ALA R 402 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR R 407 " --> pdb=" O ILE R 403 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG R 416 " --> pdb=" O VAL R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 431 removed outlier: 3.561A pdb=" N LYS R 427 " --> pdb=" O VAL R 423 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 442 Processing helix chain 'S' and resid 55 through 60 Processing helix chain 'S' and resid 78 through 92 Processing helix chain 'S' and resid 97 through 101 Processing helix chain 'S' and resid 112 through 126 Processing helix chain 'S' and resid 137 through 145 Processing helix chain 'S' and resid 181 through 196 Processing helix chain 'S' and resid 202 through 217 removed outlier: 3.847A pdb=" N GLU S 207 " --> pdb=" O THR S 203 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS S 217 " --> pdb=" O LYS S 213 " (cutoff:3.500A) Processing helix chain 'S' and resid 222 through 233 Processing helix chain 'S' and resid 252 through 257 Processing helix chain 'S' and resid 258 through 262 Processing helix chain 'S' and resid 263 through 268 Processing helix chain 'S' and resid 273 through 284 Processing helix chain 'S' and resid 286 through 296 removed outlier: 4.325A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 305 Processing helix chain 'S' and resid 308 through 321 Processing helix chain 'S' and resid 337 through 349 removed outlier: 3.722A pdb=" N GLY S 343 " --> pdb=" O VAL S 339 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 355 removed outlier: 3.726A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 366 Processing helix chain 'S' and resid 369 through 374 Processing helix chain 'T' and resid 95 through 110 Processing helix chain 'T' and resid 129 through 144 Processing helix chain 'T' and resid 154 through 162 Processing helix chain 'T' and resid 189 through 192 Processing helix chain 'T' and resid 198 through 213 Processing helix chain 'T' and resid 219 through 221 No H-bonds generated for 'chain 'T' and resid 219 through 221' Processing helix chain 'T' and resid 247 through 266 Processing helix chain 'T' and resid 275 through 282 Processing helix chain 'T' and resid 299 through 310 Proline residue: T 305 - end of helix removed outlier: 4.367A pdb=" N LEU T 308 " --> pdb=" O ILE T 304 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE T 309 " --> pdb=" O PRO T 305 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 314 removed outlier: 3.591A pdb=" N VAL T 314 " --> pdb=" O PRO T 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 311 through 314' Processing helix chain 'T' and resid 324 through 335 Processing helix chain 'T' and resid 340 through 346 Processing helix chain 'T' and resid 352 through 357 Processing helix chain 'T' and resid 359 through 372 Processing helix chain 'T' and resid 385 through 401 removed outlier: 6.415A pdb=" N SER T 393 " --> pdb=" O ARG T 389 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TRP T 394 " --> pdb=" O ARG T 390 " (cutoff:3.500A) Processing helix chain 'T' and resid 402 through 407 removed outlier: 7.007A pdb=" N THR T 405 " --> pdb=" O SER T 402 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 420 Processing helix chain 'T' and resid 422 through 427 removed outlier: 3.524A pdb=" N ARG T 426 " --> pdb=" O GLN T 422 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 63 removed outlier: 4.272A pdb=" N GLY U 63 " --> pdb=" O SER U 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 60 through 63' Processing helix chain 'U' and resid 79 through 92 removed outlier: 3.810A pdb=" N TYR U 91 " --> pdb=" O HIS U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 126 removed outlier: 3.977A pdb=" N GLU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS U 118 " --> pdb=" O ALA U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 removed outlier: 3.797A pdb=" N TYR U 143 " --> pdb=" O VAL U 139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA U 144 " --> pdb=" O LEU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 182 through 193 Processing helix chain 'U' and resid 202 through 210 removed outlier: 4.161A pdb=" N ILE U 208 " --> pdb=" O ALA U 204 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 215 Processing helix chain 'U' and resid 224 through 231 removed outlier: 3.639A pdb=" N ALA U 230 " --> pdb=" O GLU U 226 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA U 231 " --> pdb=" O MET U 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 251 through 255 Processing helix chain 'U' and resid 257 through 262 Processing helix chain 'U' and resid 263 through 267 Processing helix chain 'U' and resid 273 through 284 Processing helix chain 'U' and resid 289 through 296 removed outlier: 3.579A pdb=" N LEU U 293 " --> pdb=" O ILE U 289 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 306 removed outlier: 4.036A pdb=" N TYR U 306 " --> pdb=" O THR U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 319 removed outlier: 4.017A pdb=" N ASP U 311 " --> pdb=" O PRO U 307 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE U 317 " --> pdb=" O MET U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 337 through 348 Processing helix chain 'U' and resid 352 through 356 Processing helix chain 'U' and resid 359 through 366 Processing helix chain 'V' and resid 54 through 63 Processing helix chain 'V' and resid 139 through 147 Processing helix chain 'V' and resid 153 through 167 removed outlier: 3.920A pdb=" N HIS V 159 " --> pdb=" O ALA V 155 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU V 160 " --> pdb=" O GLU V 156 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE V 161 " --> pdb=" O THR V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 170 through 177 removed outlier: 3.793A pdb=" N HIS V 175 " --> pdb=" O PHE V 171 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP V 176 " --> pdb=" O VAL V 172 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG V 177 " --> pdb=" O VAL V 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 187 through 207 removed outlier: 3.649A pdb=" N ARG V 206 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 220 through 235 removed outlier: 3.759A pdb=" N LEU V 230 " --> pdb=" O ARG V 226 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU V 231 " --> pdb=" O LYS V 227 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU V 233 " --> pdb=" O GLN V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 255 removed outlier: 3.921A pdb=" N LEU V 247 " --> pdb=" O GLU V 243 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG V 252 " --> pdb=" O LEU V 248 " (cutoff:3.500A) Processing helix chain 'V' and resid 261 through 275 Processing helix chain 'W' and resid 58 through 61 Processing helix chain 'W' and resid 123 through 129 Processing helix chain 'W' and resid 148 through 157 Processing helix chain 'W' and resid 171 through 204 removed outlier: 3.779A pdb=" N LYS W 182 " --> pdb=" O LYS W 178 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.976A pdb=" N ILE A 79 " --> pdb=" O GLY B 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.903A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.206A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 695 through 698 removed outlier: 6.459A pdb=" N LEU I 696 " --> pdb=" O ILE I 722 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N SER I 724 " --> pdb=" O LEU I 696 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N TYR I 698 " --> pdb=" O SER I 724 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU I 671 " --> pdb=" O ILE I 744 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP I 746 " --> pdb=" O LEU I 671 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE I 673 " --> pdb=" O ASP I 746 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG I 741 " --> pdb=" O ARG I 769 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU I 771 " --> pdb=" O ARG I 741 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU I 743 " --> pdb=" O LEU I 771 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU I 773 " --> pdb=" O LEU I 743 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU I 745 " --> pdb=" O LEU I 773 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY I 639 " --> pdb=" O LEU I 772 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE I 640 " --> pdb=" O LEU I 838 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 852 through 859 removed outlier: 3.763A pdb=" N ARG I2165 " --> pdb=" O HIS I 855 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU I2063 " --> pdb=" O VAL I2134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 916 through 917 removed outlier: 5.903A pdb=" N PHE I 916 " --> pdb=" O GLU I1984 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 923 through 925 Processing sheet with id=AB3, first strand: chain 'J' and resid 213 through 217 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 263 through 267 current: chain 'P' and resid 158 through 165 removed outlier: 4.139A pdb=" N GLY P 159 " --> pdb=" O LEU P 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 168 through 174 current: chain 'P' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 202 through 207 current: chain 'Q' and resid 153 through 162 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 167 through 172 current: chain 'Q' and resid 200 through 205 Processing sheet with id=AB4, first strand: chain 'J' and resid 301 through 302 Processing sheet with id=AB5, first strand: chain 'K' and resid 4 through 5 removed outlier: 5.855A pdb=" N LEU K 4 " --> pdb=" O ILE K 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'K' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'K' and resid 146 through 149 Processing sheet with id=AB8, first strand: chain 'K' and resid 236 through 237 removed outlier: 3.848A pdb=" N PHE K 248 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 126 through 127 Processing sheet with id=AC1, first strand: chain 'M' and resid 93 through 97 removed outlier: 6.100A pdb=" N CYS M 94 " --> pdb=" O PHE M 300 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP M 302 " --> pdb=" O CYS M 94 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET M 96 " --> pdb=" O ASP M 302 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL M 66 " --> pdb=" O PHE M 329 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER M 331 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU M 68 " --> pdb=" O SER M 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 237 through 239 Processing sheet with id=AC3, first strand: chain 'M' and resid 126 through 141 removed outlier: 6.258A pdb=" N GLY M 160 " --> pdb=" O THR M 136 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU M 138 " --> pdb=" O ILE M 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE M 158 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS M 156 " --> pdb=" O PRO M 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 166 through 172 current: chain 'M' and resid 202 through 205 Processing sheet with id=AC4, first strand: chain 'M' and resid 336 through 337 Processing sheet with id=AC5, first strand: chain 'M' and resid 385 through 386 removed outlier: 7.414A pdb=" N ASN M 385 " --> pdb=" O ILE M 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'N' and resid 33 through 34 Processing sheet with id=AC7, first strand: chain 'N' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'N' and resid 100 through 104 removed outlier: 6.472A pdb=" N THR N 101 " --> pdb=" O PHE N 297 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP N 299 " --> pdb=" O THR N 101 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE N 103 " --> pdb=" O ASP N 299 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR N 328 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 127 through 145 removed outlier: 6.529A pdb=" N THR N 162 " --> pdb=" O VAL N 143 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE N 145 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS N 160 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY N 159 " --> pdb=" O LEU N 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 168 through 174 current: chain 'N' and resid 202 through 207 Processing sheet with id=AD1, first strand: chain 'N' and resid 332 through 334 Processing sheet with id=AD2, first strand: chain 'O' and resid 93 through 97 removed outlier: 6.524A pdb=" N CYS O 94 " --> pdb=" O PHE O 300 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP O 302 " --> pdb=" O CYS O 94 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET O 96 " --> pdb=" O ASP O 302 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU O 299 " --> pdb=" O ILE O 328 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA O 330 " --> pdb=" O LEU O 299 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL O 301 " --> pdb=" O ALA O 330 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL O 66 " --> pdb=" O PHE O 329 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER O 331 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU O 68 " --> pdb=" O SER O 331 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA O 65 " --> pdb=" O MET O 359 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE O 361 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU O 67 " --> pdb=" O ILE O 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'O' and resid 120 through 142 removed outlier: 5.680A pdb=" N VAL O 135 " --> pdb=" O LYS O 162 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS O 162 " --> pdb=" O VAL O 135 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU O 137 " --> pdb=" O GLY O 160 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS O 156 " --> pdb=" O CYS O 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 166 through 172 current: chain 'O' and resid 199 through 206 removed outlier: 5.441A pdb=" N VAL O 221 " --> pdb=" O GLN O 203 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ARG O 205 " --> pdb=" O VAL O 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 335 through 337 Processing sheet with id=AD5, first strand: chain 'P' and resid 100 through 104 removed outlier: 3.706A pdb=" N GLY P 77 " --> pdb=" O THR P 328 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA P 72 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL P 357 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU P 74 " --> pdb=" O VAL P 357 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR P 359 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA P 76 " --> pdb=" O THR P 359 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 333 through 334 Processing sheet with id=AD7, first strand: chain 'Q' and resid 93 through 97 Processing sheet with id=AD8, first strand: chain 'Q' and resid 336 through 337 Processing sheet with id=AD9, first strand: chain 'R' and resid 100 through 104 removed outlier: 6.617A pdb=" N THR R 101 " --> pdb=" O PHE R 297 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP R 299 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE R 103 " --> pdb=" O ASP R 299 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY R 77 " --> pdb=" O THR R 328 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA R 72 " --> pdb=" O LEU R 355 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL R 357 " --> pdb=" O ALA R 72 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU R 74 " --> pdb=" O VAL R 357 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR R 359 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA R 76 " --> pdb=" O THR R 359 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 127 through 145 removed outlier: 6.653A pdb=" N THR R 162 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE R 145 " --> pdb=" O LYS R 160 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS R 160 " --> pdb=" O ILE R 145 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY R 159 " --> pdb=" O LEU R 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 168 through 174 current: chain 'R' and resid 202 through 206 Processing sheet with id=AE2, first strand: chain 'R' and resid 332 through 334 Processing sheet with id=AE3, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.610A pdb=" N LEU S 8 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR S 106 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL S 10 " --> pdb=" O THR S 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'S' and resid 71 through 72 Processing sheet with id=AE6, first strand: chain 'S' and resid 150 through 155 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 169 through 170 current: chain 'S' and resid 329 through 330 Processing sheet with id=AE7, first strand: chain 'S' and resid 238 through 241 Processing sheet with id=AE8, first strand: chain 'T' and resid 35 through 38 removed outlier: 6.252A pdb=" N LEU T 14 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N SER T 123 " --> pdb=" O LEU T 14 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE T 16 " --> pdb=" O SER T 123 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL T 120 " --> pdb=" O PHE T 150 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N CYS T 152 " --> pdb=" O VAL T 120 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET T 122 " --> pdb=" O CYS T 152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 42 through 44 Processing sheet with id=AF1, first strand: chain 'T' and resid 88 through 89 Processing sheet with id=AF2, first strand: chain 'T' and resid 167 through 172 Processing sheet with id=AF3, first strand: chain 'T' and resid 223 through 227 removed outlier: 3.758A pdb=" N SER T 225 " --> pdb=" O LYS T 238 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN T 236 " --> pdb=" O GLU T 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 285 through 288 Processing sheet with id=AF5, first strand: chain 'U' and resid 20 through 21 Processing sheet with id=AF6, first strand: chain 'U' and resid 35 through 38 Processing sheet with id=AF7, first strand: chain 'U' and resid 160 through 161 Processing sheet with id=AF8, first strand: chain 'V' and resid 96 through 101 Processing sheet with id=AF9, first strand: chain 'W' and resid 86 through 92 Processing sheet with id=AG1, first strand: chain 'W' and resid 78 through 81 removed outlier: 3.571A pdb=" N LYS W 65 " --> pdb=" O PHE W 103 " (cutoff:3.500A) 2251 hydrogen bonds defined for protein. 6378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 634 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 26.86 Time building geometry restraints manager: 13.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8897 1.31 - 1.44: 16115 1.44 - 1.56: 32274 1.56 - 1.69: 622 1.69 - 1.82: 426 Bond restraints: 58334 Sorted by residual: bond pdb=" C ASP L 12 " pdb=" O ASP L 12 " ideal model delta sigma weight residual 1.234 1.187 0.048 5.00e-03 4.00e+04 9.11e+01 bond pdb=" C LEU I 124 " pdb=" O LEU I 124 " ideal model delta sigma weight residual 1.234 1.203 0.032 5.00e-03 4.00e+04 4.00e+01 bond pdb=" C ARG J 165 " pdb=" O ARG J 165 " ideal model delta sigma weight residual 1.238 1.313 -0.075 1.28e-02 6.10e+03 3.45e+01 bond pdb=" CD1 PHE V 183 " pdb=" CE1 PHE V 183 " ideal model delta sigma weight residual 1.382 1.551 -0.169 3.00e-02 1.11e+03 3.19e+01 bond pdb=" CA ARG V 261 " pdb=" C ARG V 261 " ideal model delta sigma weight residual 1.524 1.564 -0.039 7.00e-03 2.04e+04 3.15e+01 ... (remaining 58329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 79079 2.95 - 5.89: 888 5.89 - 8.84: 74 8.84 - 11.78: 12 11.78 - 14.73: 8 Bond angle restraints: 80061 Sorted by residual: angle pdb=" N PRO I1995 " pdb=" CA PRO I1995 " pdb=" C PRO I1995 " ideal model delta sigma weight residual 110.70 122.49 -11.79 1.22e+00 6.72e-01 9.34e+01 angle pdb=" N TYR R 215 " pdb=" CA TYR R 215 " pdb=" C TYR R 215 " ideal model delta sigma weight residual 111.71 100.60 11.11 1.15e+00 7.56e-01 9.34e+01 angle pdb=" CB GLU V 156 " pdb=" CG GLU V 156 " pdb=" CD GLU V 156 " ideal model delta sigma weight residual 112.60 127.33 -14.73 1.70e+00 3.46e-01 7.51e+01 angle pdb=" N ARG M 317 " pdb=" CA ARG M 317 " pdb=" C ARG M 317 " ideal model delta sigma weight residual 113.50 103.75 9.75 1.23e+00 6.61e-01 6.28e+01 angle pdb=" C GLU V 260 " pdb=" N ARG V 261 " pdb=" CA ARG V 261 " ideal model delta sigma weight residual 122.44 114.43 8.01 1.19e+00 7.06e-01 4.54e+01 ... (remaining 80056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.78: 31870 31.78 - 63.55: 2809 63.55 - 95.33: 175 95.33 - 127.11: 7 127.11 - 158.89: 3 Dihedral angle restraints: 34864 sinusoidal: 16418 harmonic: 18446 Sorted by residual: dihedral pdb=" CA THR W 170 " pdb=" C THR W 170 " pdb=" N GLU W 171 " pdb=" CA GLU W 171 " ideal model delta harmonic sigma weight residual -180.00 -62.82 -117.18 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CD ARG G 134 " pdb=" NE ARG G 134 " pdb=" CZ ARG G 134 " pdb=" NH1 ARG G 134 " ideal model delta sinusoidal sigma weight residual 0.00 72.94 -72.94 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CD ARG V 257 " pdb=" NE ARG V 257 " pdb=" CZ ARG V 257 " pdb=" NH1 ARG V 257 " ideal model delta sinusoidal sigma weight residual 0.00 71.34 -71.34 1 1.00e+01 1.00e-02 6.53e+01 ... (remaining 34861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 7785 0.065 - 0.129: 1081 0.129 - 0.194: 134 0.194 - 0.258: 10 0.258 - 0.323: 8 Chirality restraints: 9018 Sorted by residual: chirality pdb=" CG LEU K 89 " pdb=" CB LEU K 89 " pdb=" CD1 LEU K 89 " pdb=" CD2 LEU K 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ATP T 501 " pdb=" C2' ATP T 501 " pdb=" C4' ATP T 501 " pdb=" O3' ATP T 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.95 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C3' ATP U 401 " pdb=" C2' ATP U 401 " pdb=" C4' ATP U 401 " pdb=" O3' ATP U 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 9015 not shown) Planarity restraints: 9229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 134 " -1.054 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG G 134 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 134 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 134 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 134 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 257 " 1.031 9.50e-02 1.11e+02 4.62e-01 1.29e+02 pdb=" NE ARG V 257 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG V 257 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG V 257 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG V 257 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 18 " 0.589 9.50e-02 1.11e+02 2.64e-01 4.26e+01 pdb=" NE ARG P 18 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG P 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG P 18 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG P 18 " 0.018 2.00e-02 2.50e+03 ... (remaining 9226 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 49 2.18 - 2.86: 20380 2.86 - 3.54: 83053 3.54 - 4.22: 145145 4.22 - 4.90: 235848 Nonbonded interactions: 484475 Sorted by model distance: nonbonded pdb=" CD2 LEU I2014 " pdb=" CD1 ILE Q 256 " model vdw 1.500 3.880 nonbonded pdb=" CE2 TYR I 633 " pdb=" OH TYR I 742 " model vdw 1.503 3.340 nonbonded pdb=" OE2 GLU O 126 " pdb=" CE LYS O 128 " model vdw 1.512 3.440 nonbonded pdb=" OE2 GLU A 62 " pdb=" OE1 GLN L 15 " model vdw 1.586 3.040 nonbonded pdb=" CD GLU A 62 " pdb=" OE1 GLN L 15 " model vdw 1.627 3.270 ... (remaining 484470 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 'A' and resid 15 through 119) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 28 through 121) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 41 through 134) selection = (chain 'G' and resid 41 through 134) } ncs_group { reference = (chain 'D' and resid 23 through 102) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 15 through 451 or resid 501)) selection = (chain 'O' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) selection = (chain 'Q' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) } ncs_group { reference = (chain 'N' and (resid 18 through 148 or resid 157 through 447 or resid 501)) selection = (chain 'P' and (resid 18 through 148 or resid 157 through 208 or resid 225 throu \ gh 447 or resid 501)) selection = (chain 'R' and (resid 18 through 208 or resid 225 through 447 or resid 501)) } ncs_group { reference = (chain 'S' and (resid 2 through 40 or resid 52 through 371)) selection = (chain 'U' and resid 2 through 371) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 3.010 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: 0.090 Extract box with map and model: 1.780 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 118.050 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4709 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 : 0.005 0.169 58334 Z= 0.302 Angle : 0.834 14.730 80061 Z= 0.479 Chirality : 0.046 0.323 9018 Planarity : 0.011 0.473 9229 Dihedral : 20.515 158.885 22956 Min Nonbonded Distance : 1.500 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 7.61 % Allowed : 8.91 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.10), residues: 6298 helix: -1.13 (0.09), residues: 2913 sheet: -0.46 (0.19), residues: 685 loop : -1.71 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 68 HIS 0.011 0.001 HIS M 316 PHE 0.054 0.002 PHE V 183 TYR 0.024 0.002 TYR K 64 ARG 0.013 0.001 ARG V 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 416 poor density : 1240 time to evaluate : 4.893 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4739 (OUTLIER) cc_final: 0.4237 (mt) REVERT: B 28 ARG cc_start: 0.1816 (OUTLIER) cc_final: 0.1479 (mtp-110) REVERT: B 98 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6332 (mm) REVERT: E 73 ASN cc_start: 0.6531 (t160) cc_final: 0.6270 (t0) REVERT: F 28 ARG cc_start: 0.1037 (OUTLIER) cc_final: 0.0027 (mmt180) REVERT: I 825 LEU cc_start: 0.5794 (mp) cc_final: 0.5575 (mt) REVERT: I 2036 ARG cc_start: 0.7172 (mmm160) cc_final: 0.6321 (mtm110) REVERT: I 2073 ASP cc_start: 0.6724 (t0) cc_final: 0.6471 (m-30) REVERT: I 2109 LYS cc_start: 0.7565 (tppp) cc_final: 0.7228 (mppt) REVERT: J 174 ARG cc_start: 0.5065 (ttm-80) cc_final: 0.4827 (tmm-80) REVERT: K 34 THR cc_start: 0.3636 (OUTLIER) cc_final: 0.3428 (p) REVERT: K 38 LYS cc_start: 0.3265 (OUTLIER) cc_final: 0.3004 (mtpp) REVERT: K 69 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6050 (p0) REVERT: K 106 GLN cc_start: 0.6749 (mt0) cc_final: 0.6282 (mt0) REVERT: K 109 MET cc_start: 0.6252 (ttm) cc_final: 0.5917 (ttp) REVERT: K 138 ASP cc_start: 0.5721 (OUTLIER) cc_final: 0.5173 (p0) REVERT: K 185 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.6917 (ttpp) REVERT: K 186 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6400 (tp30) REVERT: K 274 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5580 (ptm160) REVERT: K 289 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5795 (pt) REVERT: K 310 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: K 319 LEU cc_start: 0.6913 (mt) cc_final: 0.6671 (mp) REVERT: K 326 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: K 383 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6074 (mt-10) REVERT: M 96 MET cc_start: 0.7535 (ttp) cc_final: 0.7282 (ttm) REVERT: M 306 MET cc_start: 0.7950 (mmm) cc_final: 0.7748 (mmp) REVERT: M 323 ILE cc_start: 0.8448 (pt) cc_final: 0.7915 (mt) REVERT: M 346 SER cc_start: 0.8911 (m) cc_final: 0.8300 (t) REVERT: N 267 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8135 (mp0) REVERT: N 381 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7269 (mp0) REVERT: N 436 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7305 (tm-30) REVERT: O 37 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8034 (p) REVERT: O 259 MET cc_start: 0.7933 (mmm) cc_final: 0.7670 (tpt) REVERT: O 269 THR cc_start: 0.6820 (p) cc_final: 0.5837 (p) REVERT: O 270 GLU cc_start: 0.7230 (pt0) cc_final: 0.6980 (pp20) REVERT: O 271 ILE cc_start: 0.6472 (tt) cc_final: 0.6240 (tp) REVERT: O 323 ILE cc_start: 0.7839 (pt) cc_final: 0.7358 (mt) REVERT: O 392 ASN cc_start: 0.7582 (t0) cc_final: 0.7080 (m-40) REVERT: P 113 MET cc_start: 0.8142 (ptt) cc_final: 0.7756 (ptp) REVERT: P 117 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6419 (tp30) REVERT: P 168 MET cc_start: 0.7848 (ptm) cc_final: 0.6697 (ptp) REVERT: P 188 GLN cc_start: 0.8018 (pt0) cc_final: 0.7770 (pm20) REVERT: P 236 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8101 (pttm) REVERT: P 257 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.4753 (m-10) REVERT: P 261 PHE cc_start: 0.7122 (t80) cc_final: 0.6792 (t80) REVERT: P 267 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6857 (mm-30) REVERT: P 284 ARG cc_start: 0.6797 (ttt90) cc_final: 0.6541 (ttp-110) REVERT: Q 61 MET cc_start: 0.8283 (mmm) cc_final: 0.7976 (mmm) REVERT: Q 159 ILE cc_start: 0.7952 (tt) cc_final: 0.7674 (mt) REVERT: Q 165 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7150 (tptp) REVERT: Q 181 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7682 (tp-100) REVERT: Q 271 ILE cc_start: 0.7218 (mm) cc_final: 0.6971 (tt) REVERT: Q 308 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6349 (t70) REVERT: R 67 LYS cc_start: 0.8003 (mttt) cc_final: 0.7519 (mmtt) REVERT: R 88 MET cc_start: 0.8179 (mmm) cc_final: 0.7794 (mmm) REVERT: R 145 ILE cc_start: 0.8332 (mt) cc_final: 0.8057 (mt) REVERT: R 225 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6851 (m) REVERT: R 246 GLU cc_start: 0.4324 (OUTLIER) cc_final: 0.2864 (pt0) REVERT: R 374 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5812 (mmp-170) REVERT: R 387 TYR cc_start: 0.6956 (m-80) cc_final: 0.6655 (m-80) REVERT: S 44 MET cc_start: 0.0289 (mtp) cc_final: -0.0563 (tpp) REVERT: S 229 THR cc_start: 0.2688 (m) cc_final: 0.2339 (p) REVERT: S 296 ASN cc_start: 0.2884 (m-40) cc_final: 0.2342 (m-40) REVERT: T 303 LYS cc_start: 0.3733 (ttmt) cc_final: 0.3522 (ptpt) REVERT: U 24 ASP cc_start: 0.2822 (p0) cc_final: 0.2434 (p0) REVERT: U 227 MET cc_start: 0.0538 (mmt) cc_final: -0.1197 (ttp) REVERT: U 330 ILE cc_start: 0.0557 (OUTLIER) cc_final: -0.0141 (tt) REVERT: V 91 LYS cc_start: -0.0129 (OUTLIER) cc_final: -0.2210 (mtmm) REVERT: V 98 MET cc_start: -0.1640 (mtt) cc_final: -0.2624 (ppp) REVERT: V 111 PHE cc_start: -0.1785 (m-80) cc_final: -0.1991 (m-80) REVERT: V 120 GLU cc_start: 0.1759 (OUTLIER) cc_final: -0.0333 (mt-10) REVERT: V 134 GLN cc_start: 0.0108 (OUTLIER) cc_final: -0.0512 (pp30) REVERT: V 202 LEU cc_start: 0.2127 (OUTLIER) cc_final: 0.1669 (tp) REVERT: V 206 ARG cc_start: -0.0794 (OUTLIER) cc_final: -0.1372 (mpt180) REVERT: V 217 VAL cc_start: -0.0825 (OUTLIER) cc_final: -0.1054 (m) REVERT: V 229 GLN cc_start: 0.1605 (pm20) cc_final: 0.1013 (pp30) REVERT: V 239 GLU cc_start: 0.2299 (OUTLIER) cc_final: 0.1088 (pt0) REVERT: V 255 GLU cc_start: 0.3145 (OUTLIER) cc_final: 0.2681 (tp30) REVERT: V 267 ASP cc_start: 0.1145 (OUTLIER) cc_final: 0.0642 (m-30) REVERT: V 270 LYS cc_start: 0.1166 (OUTLIER) cc_final: 0.0686 (ptpt) outliers start: 416 outliers final: 84 residues processed: 1547 average time/residue: 0.6208 time to fit residues: 1528.9474 Evaluate side-chains 705 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 585 time to evaluate : 4.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 174 ASN Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 309 MET Chi-restraints excluded: chain K residue 310 GLN Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 326 PHE Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 379 ARG Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain M residue 192 TYR Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 211 THR Chi-restraints excluded: chain Q residue 237 ASP Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 215 TYR Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 374 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 120 GLU Chi-restraints excluded: chain V residue 134 GLN Chi-restraints excluded: chain V residue 156 GLU Chi-restraints excluded: chain V residue 202 LEU Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 206 ARG Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain V residue 222 HIS Chi-restraints excluded: chain V residue 223 GLU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain V residue 265 SER Chi-restraints excluded: chain V residue 267 ASP Chi-restraints excluded: chain V residue 270 LYS Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 553 optimal weight: 7.9990 chunk 496 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 169 optimal weight: 0.0980 chunk 334 optimal weight: 0.0970 chunk 265 optimal weight: 0.9980 chunk 513 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 594 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN D 75 HIS E 73 ASN E 94 ASN G 85 GLN G 108 ASN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1896 GLN I1963 GLN I1964 GLN ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I2082 HIS K 19 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 HIS K 174 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 GLN ** K 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 ASN L 39 ASN L 41 GLN ** M 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN M 429 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN N 277 ASN N 302 HIS N 329 ASN O 18 HIS P 240 HIS ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 313 ASN P 447 GLN Q 236 GLN Q 284 ASN Q 408 GLN Q 429 HIS T 408 GLN U 101 HIS U 173 HIS U 296 ASN U 353 GLN ** V 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 204 ASN ** V 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 269 GLN W 29 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.172262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.126154 restraints weight = 122549.792| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.15 r_work: 0.3566 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 58334 Z= 0.243 Angle : 0.731 13.300 80061 Z= 0.385 Chirality : 0.046 0.472 9018 Planarity : 0.006 0.079 9229 Dihedral : 22.383 160.734 10594 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.19 % Favored : 94.46 % Rotamer: Outliers : 4.57 % Allowed : 14.12 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 6298 helix: -0.27 (0.09), residues: 2932 sheet: -0.34 (0.18), residues: 744 loop : -1.52 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 96 HIS 0.019 0.001 HIS I 102 PHE 0.025 0.002 PHE N 261 TYR 0.032 0.002 TYR A 58 ARG 0.008 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 666 time to evaluate : 4.850 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: A 109 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5761 (mp) REVERT: B 28 ARG cc_start: 0.2658 (OUTLIER) cc_final: 0.2184 (mtp-110) REVERT: B 59 MET cc_start: 0.6230 (mmm) cc_final: 0.5761 (mmp) REVERT: C 65 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6449 (mt) REVERT: C 79 LYS cc_start: 0.4322 (OUTLIER) cc_final: 0.4098 (tttt) REVERT: D 72 TYR cc_start: 0.6422 (m-80) cc_final: 0.6048 (m-80) REVERT: E 73 ASN cc_start: 0.6498 (t0) cc_final: 0.5685 (t0) REVERT: E 74 LYS cc_start: 0.8246 (mttt) cc_final: 0.7622 (mtpt) REVERT: F 28 ARG cc_start: -0.0868 (OUTLIER) cc_final: -0.1695 (mmt180) REVERT: F 40 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7217 (ttpt) REVERT: G 81 ASP cc_start: 0.6899 (m-30) cc_final: 0.6693 (m-30) REVERT: G 123 ASP cc_start: 0.6925 (m-30) cc_final: 0.6512 (m-30) REVERT: G 129 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7314 (mmm160) REVERT: H 52 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: H 53 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7605 (tm-30) REVERT: H 80 THR cc_start: 0.7668 (p) cc_final: 0.7328 (p) REVERT: I 144 MET cc_start: 0.0163 (tmm) cc_final: -0.0140 (ppp) REVERT: I 895 MET cc_start: 0.8239 (tpp) cc_final: 0.8034 (tpt) REVERT: I 1895 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7974 (ttm-80) REVERT: I 2067 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: J 187 LEU cc_start: 0.6575 (mt) cc_final: 0.6126 (tp) REVERT: J 310 TYR cc_start: 0.5164 (p90) cc_final: 0.4764 (p90) REVERT: J 314 ARG cc_start: 0.7811 (ptt-90) cc_final: 0.7590 (ttm110) REVERT: K 14 LYS cc_start: 0.2260 (OUTLIER) cc_final: 0.1892 (mptt) REVERT: K 64 TYR cc_start: 0.1860 (m-80) cc_final: 0.1180 (m-10) REVERT: K 69 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5896 (p0) REVERT: K 95 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6117 (mp) REVERT: K 138 ASP cc_start: 0.6181 (OUTLIER) cc_final: 0.5749 (p0) REVERT: K 319 LEU cc_start: 0.7171 (mt) cc_final: 0.6956 (mt) REVERT: K 383 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6190 (mt-10) REVERT: M 260 MET cc_start: 0.7839 (ttt) cc_final: 0.7065 (mpp) REVERT: M 268 LYS cc_start: 0.7055 (mtpt) cc_final: 0.6844 (mtpt) REVERT: N 116 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (p) REVERT: N 132 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: N 326 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8046 (mtm) REVERT: O 18 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7143 (t70) REVERT: O 106 ILE cc_start: 0.8622 (tt) cc_final: 0.8307 (tt) REVERT: O 215 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7404 (tt) REVERT: O 259 MET cc_start: 0.8327 (mmm) cc_final: 0.7974 (tpt) REVERT: O 359 MET cc_start: 0.8108 (mtm) cc_final: 0.7867 (mtm) REVERT: P 188 GLN cc_start: 0.8260 (pt0) cc_final: 0.7884 (pm20) REVERT: P 232 LEU cc_start: 0.7819 (tp) cc_final: 0.7593 (tp) REVERT: P 236 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8388 (pttm) REVERT: P 257 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.5467 (m-10) REVERT: Q 61 MET cc_start: 0.8637 (mmm) cc_final: 0.8278 (mmm) REVERT: Q 147 MET cc_start: 0.5567 (mmt) cc_final: 0.5211 (mtp) REVERT: Q 165 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7495 (tptp) REVERT: Q 170 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7850 (mp) REVERT: Q 180 LEU cc_start: 0.8591 (mt) cc_final: 0.8369 (mp) REVERT: R 90 MET cc_start: 0.8525 (mtp) cc_final: 0.8077 (mtm) REVERT: R 246 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.5659 (pm20) REVERT: S 1 MET cc_start: 0.0456 (ttp) cc_final: -0.0694 (tpp) REVERT: S 123 MET cc_start: 0.2965 (mmm) cc_final: 0.2559 (ttm) REVERT: S 354 GLN cc_start: 0.4440 (mt0) cc_final: 0.4088 (pm20) REVERT: T 250 TRP cc_start: 0.1786 (t60) cc_final: 0.1299 (t60) REVERT: T 303 LYS cc_start: 0.4388 (ttmt) cc_final: 0.3907 (ptpt) REVERT: U 28 ARG cc_start: 0.4699 (mmm160) cc_final: 0.4389 (mmm160) REVERT: U 227 MET cc_start: 0.0333 (mmt) cc_final: -0.1055 (ttp) REVERT: U 285 CYS cc_start: 0.3172 (m) cc_final: 0.2842 (p) REVERT: U 330 ILE cc_start: 0.1445 (OUTLIER) cc_final: 0.1224 (tt) REVERT: V 90 LYS cc_start: 0.1272 (pttm) cc_final: 0.0228 (mtmt) REVERT: V 91 LYS cc_start: 0.0251 (OUTLIER) cc_final: -0.2160 (mtmm) REVERT: V 98 MET cc_start: 0.0982 (mtt) cc_final: 0.0477 (ppp) REVERT: V 223 GLU cc_start: 0.0988 (OUTLIER) cc_final: 0.0737 (tp30) REVERT: V 239 GLU cc_start: 0.2950 (OUTLIER) cc_final: 0.2280 (pt0) REVERT: W 128 MET cc_start: 0.3339 (ptm) cc_final: 0.1406 (mmp) REVERT: W 178 LYS cc_start: 0.1469 (tppp) cc_final: 0.1264 (pttt) outliers start: 250 outliers final: 97 residues processed: 854 average time/residue: 0.5661 time to fit residues: 817.1200 Evaluate side-chains 621 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 496 time to evaluate : 4.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain E residue 25 PHE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1980 MET Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2067 GLN Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2196 PHE Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 383 GLU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 215 LEU Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 267 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 170 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain Q residue 402 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 132 MET Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 101 HIS Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 223 GLU Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 249 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 122 optimal weight: 0.0020 chunk 481 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 501 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 519 optimal weight: 10.0000 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 795 HIS ** I 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 967 HIS I1963 GLN ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I2084 HIS I2153 HIS K 156 HIS K 272 ASN K 387 HIS M 181 GLN M 280 ASN M 305 HIS N 25 HIS N 240 HIS O 289 GLN ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 404 GLN Q 229 HIS S 137 GLN T 251 HIS U 296 ASN V 204 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.167874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.125641 restraints weight = 120765.957| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.52 r_work: 0.3496 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 58334 Z= 0.344 Angle : 0.734 13.615 80061 Z= 0.383 Chirality : 0.047 0.446 9018 Planarity : 0.006 0.072 9229 Dihedral : 21.916 158.731 10451 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.49 % Favored : 94.22 % Rotamer: Outliers : 4.48 % Allowed : 16.51 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 6298 helix: 0.09 (0.09), residues: 2958 sheet: -0.40 (0.18), residues: 800 loop : -1.45 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 96 HIS 0.010 0.002 HIS I 102 PHE 0.032 0.002 PHE I 923 TYR 0.026 0.002 TYR D 88 ARG 0.013 0.001 ARG U 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 516 time to evaluate : 4.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.5963 (mt) cc_final: 0.5600 (mm) REVERT: B 28 ARG cc_start: 0.1669 (OUTLIER) cc_final: 0.1120 (mtp-110) REVERT: B 59 MET cc_start: 0.6262 (mmm) cc_final: 0.5979 (mmm) REVERT: B 90 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: D 72 TYR cc_start: 0.6668 (m-80) cc_final: 0.6285 (m-80) REVERT: E 58 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8633 (mm) REVERT: F 28 ARG cc_start: 0.1281 (OUTLIER) cc_final: 0.0659 (mmt180) REVERT: G 123 ASP cc_start: 0.7099 (m-30) cc_final: 0.6865 (m-30) REVERT: I 849 MET cc_start: 0.6951 (tpt) cc_final: 0.6620 (tpt) REVERT: I 1895 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7762 (ttm-80) REVERT: J 187 LEU cc_start: 0.6346 (mt) cc_final: 0.5902 (tp) REVERT: K 1 MET cc_start: 0.3155 (OUTLIER) cc_final: 0.2291 (ppp) REVERT: K 12 ASN cc_start: 0.5802 (OUTLIER) cc_final: 0.4644 (p0) REVERT: K 69 ASP cc_start: 0.5508 (OUTLIER) cc_final: 0.5096 (p0) REVERT: K 83 MET cc_start: 0.4101 (mmm) cc_final: 0.3799 (mmp) REVERT: K 90 ASP cc_start: 0.4968 (OUTLIER) cc_final: 0.3908 (m-30) REVERT: K 138 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.6053 (p0) REVERT: K 185 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7393 (mtpt) REVERT: K 196 MET cc_start: 0.5869 (ptm) cc_final: 0.5541 (ptm) REVERT: K 219 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: K 302 ILE cc_start: 0.7003 (mm) cc_final: 0.6734 (mm) REVERT: K 314 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.4811 (p90) REVERT: K 335 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.7238 (m) REVERT: K 350 VAL cc_start: 0.5761 (OUTLIER) cc_final: 0.5497 (m) REVERT: K 374 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7263 (t70) REVERT: M 260 MET cc_start: 0.7373 (ttt) cc_final: 0.7043 (mpp) REVERT: M 268 LYS cc_start: 0.7394 (mtpt) cc_final: 0.7089 (mttm) REVERT: N 116 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8702 (p) REVERT: N 132 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: O 18 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7572 (t70) REVERT: O 342 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: P 188 GLN cc_start: 0.8246 (pt0) cc_final: 0.7864 (pm20) REVERT: P 236 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8256 (pttm) REVERT: P 257 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.5700 (m-10) REVERT: P 349 ASP cc_start: 0.7799 (t0) cc_final: 0.7401 (t0) REVERT: Q 61 MET cc_start: 0.8526 (mmm) cc_final: 0.8015 (mmm) REVERT: Q 147 MET cc_start: 0.5447 (mmt) cc_final: 0.5152 (mtp) REVERT: Q 165 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7498 (tptp) REVERT: Q 433 ILE cc_start: 0.8801 (mm) cc_final: 0.8554 (mm) REVERT: R 90 MET cc_start: 0.8676 (mtp) cc_final: 0.8310 (mtm) REVERT: R 232 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7923 (tp) REVERT: R 246 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6322 (pp20) REVERT: R 253 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6976 (ttm110) REVERT: R 317 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6915 (mm-30) REVERT: R 441 GLN cc_start: 0.8669 (tp40) cc_final: 0.8411 (tp40) REVERT: S 47 MET cc_start: 0.0206 (tpt) cc_final: -0.0134 (ptp) REVERT: S 190 MET cc_start: 0.1503 (tpp) cc_final: 0.1145 (mmm) REVERT: S 354 GLN cc_start: 0.4202 (mt0) cc_final: 0.3856 (pm20) REVERT: T 105 HIS cc_start: 0.3746 (OUTLIER) cc_final: 0.3470 (t-90) REVERT: T 250 TRP cc_start: 0.1678 (t60) cc_final: 0.1206 (t60) REVERT: U 227 MET cc_start: 0.0388 (mmt) cc_final: -0.1237 (ttp) REVERT: U 330 ILE cc_start: 0.1954 (OUTLIER) cc_final: 0.1466 (tt) REVERT: V 90 LYS cc_start: 0.1474 (pttm) cc_final: 0.0659 (mtmt) REVERT: V 239 GLU cc_start: 0.2565 (OUTLIER) cc_final: 0.1502 (pt0) REVERT: W 128 MET cc_start: 0.4250 (ptm) cc_final: 0.3689 (ppp) outliers start: 245 outliers final: 133 residues processed: 717 average time/residue: 0.5426 time to fit residues: 663.1843 Evaluate side-chains 598 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 437 time to evaluate : 4.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 25 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 657 LEU Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2138 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 219 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 274 ARG Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 374 ASP Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 431 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 165 LYS Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 96 TRP Chi-restraints excluded: chain T residue 105 HIS Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 335 optimal weight: 0.4980 chunk 539 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 429 optimal weight: 4.9990 chunk 407 optimal weight: 5.9990 chunk 569 optimal weight: 5.9990 chunk 639 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 628 optimal weight: 20.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 105 GLN B 60 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN G 39 HIS ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 623 HIS ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 702 GLN ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 ASN I 865 GLN ** I 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 HIS ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS K 283 ASN K 316 ASN ** K 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 113 GLN O 316 HIS O 348 HIS ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 335 ASN Q 348 HIS S 161 HIS S 173 HIS T 143 HIS ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 353 GLN ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 180 HIS ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.114424 restraints weight = 119237.608| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.97 r_work: 0.3347 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 58334 Z= 0.522 Angle : 0.836 14.675 80061 Z= 0.434 Chirality : 0.051 0.519 9018 Planarity : 0.007 0.084 9229 Dihedral : 21.858 154.699 10417 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.24 % Favored : 93.51 % Rotamer: Outliers : 5.60 % Allowed : 17.78 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.10), residues: 6298 helix: -0.08 (0.09), residues: 2937 sheet: -0.61 (0.17), residues: 814 loop : -1.66 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 667 HIS 0.028 0.002 HIS I 936 PHE 0.035 0.003 PHE I 923 TYR 0.033 0.002 TYR D 88 ARG 0.014 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 481 time to evaluate : 4.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6223 (mm) REVERT: B 28 ARG cc_start: 0.1183 (OUTLIER) cc_final: 0.0580 (mtp-110) REVERT: B 59 MET cc_start: 0.6353 (mmm) cc_final: 0.5882 (mmm) REVERT: B 90 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: E 58 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8670 (mm) REVERT: F 59 MET cc_start: 0.9083 (mmp) cc_final: 0.8668 (mmt) REVERT: F 108 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7999 (p) REVERT: G 129 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7665 (mmm160) REVERT: H 53 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7441 (tm-30) REVERT: I 144 MET cc_start: 0.0170 (ppp) cc_final: -0.0971 (tmm) REVERT: I 849 MET cc_start: 0.7436 (tpt) cc_final: 0.7076 (tpt) REVERT: I 2028 MET cc_start: 0.9158 (ttm) cc_final: 0.8907 (mtp) REVERT: J 173 LEU cc_start: 0.6914 (mm) cc_final: 0.6694 (mm) REVERT: J 187 LEU cc_start: 0.6221 (mt) cc_final: 0.5840 (tp) REVERT: J 214 TYR cc_start: 0.8318 (t80) cc_final: 0.7767 (t80) REVERT: K 1 MET cc_start: 0.2620 (pp-130) cc_final: 0.1986 (ppp) REVERT: K 12 ASN cc_start: 0.7083 (OUTLIER) cc_final: 0.6746 (t0) REVERT: K 64 TYR cc_start: 0.2171 (m-80) cc_final: 0.1671 (m-80) REVERT: K 138 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6145 (p0) REVERT: K 185 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7326 (mtpt) REVERT: K 196 MET cc_start: 0.6310 (ptm) cc_final: 0.5985 (tmm) REVERT: K 220 MET cc_start: 0.7500 (mtp) cc_final: 0.6624 (mmm) REVERT: K 255 MET cc_start: 0.0917 (tpp) cc_final: 0.0210 (mmm) REVERT: K 313 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6569 (t80) REVERT: K 314 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.5380 (p90) REVERT: K 325 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6682 (mm) REVERT: K 374 ASP cc_start: 0.7945 (m-30) cc_final: 0.7427 (t70) REVERT: L 146 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6161 (pt0) REVERT: M 260 MET cc_start: 0.8007 (ttt) cc_final: 0.7323 (mpp) REVERT: M 264 MET cc_start: 0.8210 (tmm) cc_final: 0.7805 (tmm) REVERT: N 116 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8729 (p) REVERT: N 354 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8203 (pp) REVERT: N 400 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7290 (mtm-85) REVERT: O 18 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7005 (t70) REVERT: O 342 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: P 19 ILE cc_start: 0.6727 (mt) cc_final: 0.6299 (tt) REVERT: P 236 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8357 (pttm) REVERT: P 257 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.5479 (m-10) REVERT: P 349 ASP cc_start: 0.8231 (t0) cc_final: 0.7923 (t0) REVERT: P 382 MET cc_start: 0.8028 (mtm) cc_final: 0.7751 (mtm) REVERT: P 448 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8031 (t0) REVERT: Q 61 MET cc_start: 0.8702 (mmm) cc_final: 0.8068 (mmm) REVERT: Q 192 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6068 (t80) REVERT: R 37 LEU cc_start: 0.8884 (mp) cc_final: 0.8634 (mt) REVERT: R 232 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8129 (tp) REVERT: R 246 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: R 253 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7257 (ttm170) REVERT: R 291 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8980 (tt) REVERT: R 317 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: R 346 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8094 (pt) REVERT: S 87 HIS cc_start: 0.5045 (m-70) cc_final: 0.4793 (m90) REVERT: S 190 MET cc_start: 0.1347 (tpp) cc_final: 0.1138 (mmm) REVERT: S 354 GLN cc_start: 0.4605 (mt0) cc_final: 0.4314 (pm20) REVERT: T 250 TRP cc_start: 0.1740 (t60) cc_final: 0.1191 (t60) REVERT: U 82 MET cc_start: -0.0066 (tpp) cc_final: -0.0448 (ttt) REVERT: U 227 MET cc_start: 0.0252 (mmt) cc_final: -0.1102 (ttp) REVERT: U 285 CYS cc_start: 0.3868 (m) cc_final: 0.3495 (p) REVERT: U 330 ILE cc_start: 0.1923 (OUTLIER) cc_final: 0.1337 (tt) REVERT: V 239 GLU cc_start: 0.4372 (OUTLIER) cc_final: 0.3543 (pt0) REVERT: W 44 THR cc_start: 0.0832 (p) cc_final: 0.0564 (t) outliers start: 306 outliers final: 179 residues processed: 742 average time/residue: 0.6193 time to fit residues: 780.6617 Evaluate side-chains 631 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 424 time to evaluate : 4.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 232 HIS Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 649 LYS Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 776 THR Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 862 SER Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1960 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2037 LEU Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2118 THR Chi-restraints excluded: chain I residue 2138 SER Chi-restraints excluded: chain I residue 2154 ARG Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 273 GLU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 312 HIS Chi-restraints excluded: chain K residue 313 PHE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 333 VAL Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 372 PHE Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 210 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 330 ARG Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 170 LEU Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 370 ILE Chi-restraints excluded: chain R residue 396 GLU Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 132 MET Chi-restraints excluded: chain T residue 96 TRP Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 201 THR Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 535 optimal weight: 7.9990 chunk 319 optimal weight: 30.0000 chunk 508 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 345 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 513 optimal weight: 10.0000 chunk 530 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN C 55 GLN F 46 HIS ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 HIS K 200 HIS K 283 ASN ** K 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 HIS T 81 ASN T 183 HIS ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.165280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115085 restraints weight = 119414.058| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.12 r_work: 0.3391 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 58334 Z= 0.306 Angle : 0.691 14.825 80061 Z= 0.358 Chirality : 0.045 0.576 9018 Planarity : 0.005 0.096 9229 Dihedral : 21.603 155.219 10399 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.57 % Favored : 94.17 % Rotamer: Outliers : 4.54 % Allowed : 19.28 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 6298 helix: 0.30 (0.10), residues: 2927 sheet: -0.53 (0.18), residues: 793 loop : -1.54 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 250 HIS 0.020 0.001 HIS I 936 PHE 0.032 0.002 PHE I 923 TYR 0.027 0.002 TYR D 88 ARG 0.014 0.001 ARG N 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 474 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6150 (mm) REVERT: B 28 ARG cc_start: 0.0808 (OUTLIER) cc_final: 0.0132 (mtp-110) REVERT: B 59 MET cc_start: 0.6343 (mmm) cc_final: 0.5918 (mmm) REVERT: B 90 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: C 65 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7000 (mt) REVERT: C 90 MET cc_start: 0.8051 (mmm) cc_final: 0.7309 (mmm) REVERT: E 58 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8579 (mm) REVERT: G 129 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7692 (mtp85) REVERT: H 53 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7545 (tm-30) REVERT: H 54 THR cc_start: 0.8927 (m) cc_final: 0.8508 (m) REVERT: I 144 MET cc_start: 0.0353 (ppp) cc_final: -0.1011 (tmm) REVERT: I 615 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6621 (ptp90) REVERT: I 849 MET cc_start: 0.7098 (tpt) cc_final: 0.6750 (tpt) REVERT: I 931 ARG cc_start: 0.7086 (tpm170) cc_final: 0.6833 (tpm170) REVERT: I 2028 MET cc_start: 0.8928 (ttm) cc_final: 0.8666 (mtp) REVERT: J 173 LEU cc_start: 0.6986 (mm) cc_final: 0.6716 (mm) REVERT: J 177 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6578 (mptt) REVERT: J 187 LEU cc_start: 0.6305 (mt) cc_final: 0.5968 (tp) REVERT: J 214 TYR cc_start: 0.8311 (t80) cc_final: 0.8110 (t80) REVERT: K 1 MET cc_start: 0.2773 (OUTLIER) cc_final: 0.1690 (ppp) REVERT: K 12 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.4913 (p0) REVERT: K 64 TYR cc_start: 0.1891 (m-80) cc_final: 0.1471 (m-80) REVERT: K 117 TYR cc_start: 0.4587 (m-80) cc_final: 0.4143 (m-10) REVERT: K 138 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6202 (p0) REVERT: K 220 MET cc_start: 0.7643 (mtp) cc_final: 0.7419 (mmm) REVERT: K 255 MET cc_start: 0.0835 (tpp) cc_final: -0.0123 (mmm) REVERT: K 283 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (t0) REVERT: K 314 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.5635 (p90) REVERT: K 325 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6674 (mm) REVERT: K 374 ASP cc_start: 0.7794 (m-30) cc_final: 0.7306 (t70) REVERT: K 375 MET cc_start: 0.5923 (tmm) cc_final: 0.5710 (tmm) REVERT: L 146 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6064 (pt0) REVERT: M 260 MET cc_start: 0.7742 (ttt) cc_final: 0.7074 (mpp) REVERT: M 264 MET cc_start: 0.7907 (tmm) cc_final: 0.7670 (tmm) REVERT: M 308 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7931 (t0) REVERT: N 116 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8704 (p) REVERT: N 132 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8113 (mmtm) REVERT: N 168 MET cc_start: 0.6982 (ptp) cc_final: 0.6705 (ptp) REVERT: N 354 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8106 (pp) REVERT: O 18 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7105 (t70) REVERT: O 159 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8032 (mm) REVERT: O 342 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: P 19 ILE cc_start: 0.6500 (mt) cc_final: 0.6073 (tt) REVERT: P 236 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8228 (pttm) REVERT: P 257 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.5352 (m-10) REVERT: P 448 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7831 (t0) REVERT: Q 61 MET cc_start: 0.8743 (mmm) cc_final: 0.8188 (mmm) REVERT: Q 147 MET cc_start: 0.4383 (mtp) cc_final: 0.4020 (ttm) REVERT: Q 192 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6060 (t80) REVERT: R 37 LEU cc_start: 0.8801 (mp) cc_final: 0.8556 (mt) REVERT: R 232 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8134 (tp) REVERT: R 246 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: R 317 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: R 428 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7899 (tpt90) REVERT: S 87 HIS cc_start: 0.5342 (m-70) cc_final: 0.5074 (m90) REVERT: S 190 MET cc_start: 0.1095 (tpp) cc_final: 0.0832 (mmm) REVERT: S 354 GLN cc_start: 0.4565 (mt0) cc_final: 0.4261 (pm20) REVERT: T 230 ARG cc_start: 0.5422 (mtt180) cc_final: 0.4466 (tpt170) REVERT: U 16 MET cc_start: 0.4641 (ptt) cc_final: 0.4429 (pmm) REVERT: U 82 MET cc_start: 0.0714 (tpp) cc_final: 0.0387 (ttt) REVERT: U 88 HIS cc_start: 0.4513 (t-90) cc_final: 0.4223 (t70) REVERT: U 227 MET cc_start: 0.0258 (mmt) cc_final: -0.1141 (ttp) REVERT: U 285 CYS cc_start: 0.4661 (m) cc_final: 0.4376 (p) REVERT: U 330 ILE cc_start: 0.1767 (OUTLIER) cc_final: 0.1143 (tt) REVERT: V 239 GLU cc_start: 0.3872 (OUTLIER) cc_final: 0.3209 (pt0) REVERT: W 44 THR cc_start: 0.0886 (p) cc_final: 0.0613 (t) outliers start: 248 outliers final: 151 residues processed: 679 average time/residue: 0.5645 time to fit residues: 644.7926 Evaluate side-chains 617 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 435 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 615 ARG Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 656 LEU Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 727 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 900 VAL Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1960 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2037 LEU Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2138 SER Chi-restraints excluded: chain I residue 2154 ARG Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 273 GLU Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain O residue 450 GLN Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 316 HIS Chi-restraints excluded: chain Q residue 353 ASP Chi-restraints excluded: chain Q residue 402 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 428 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 132 MET Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 235 optimal weight: 0.9990 chunk 451 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 446 optimal weight: 2.9990 chunk 280 optimal weight: 0.2980 chunk 548 optimal weight: 0.0980 chunk 386 optimal weight: 0.5980 chunk 404 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 442 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 HIS ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2067 GLN K 200 HIS ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN P 245 HIS ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN T 383 ASN V 229 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.167499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.117926 restraints weight = 120388.741| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.09 r_work: 0.3451 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 58334 Z= 0.181 Angle : 0.634 24.563 80061 Z= 0.326 Chirality : 0.042 0.341 9018 Planarity : 0.004 0.097 9229 Dihedral : 21.335 156.020 10392 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.16 % Favored : 94.60 % Rotamer: Outliers : 3.68 % Allowed : 20.19 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 6298 helix: 0.66 (0.10), residues: 2924 sheet: -0.46 (0.18), residues: 800 loop : -1.37 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 277 HIS 0.023 0.001 HIS I 936 PHE 0.036 0.001 PHE N 261 TYR 0.022 0.001 TYR K 261 ARG 0.035 0.000 ARG N 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 479 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.5980 (m) REVERT: A 94 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6189 (mm) REVERT: B 28 ARG cc_start: 0.0531 (OUTLIER) cc_final: -0.0290 (mtp-110) REVERT: B 43 LYS cc_start: 0.5582 (mmtt) cc_final: 0.5341 (mmpt) REVERT: B 59 MET cc_start: 0.6206 (mmm) cc_final: 0.5803 (mmm) REVERT: C 90 MET cc_start: 0.7952 (mmm) cc_final: 0.7249 (mmm) REVERT: E 58 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8629 (mm) REVERT: E 114 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6865 (p) REVERT: G 112 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7884 (pp) REVERT: G 120 MET cc_start: 0.7830 (ptp) cc_final: 0.7435 (pmm) REVERT: G 129 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7744 (mtp85) REVERT: H 54 THR cc_start: 0.8885 (m) cc_final: 0.8525 (m) REVERT: I 144 MET cc_start: -0.0152 (ppp) cc_final: -0.0894 (tmm) REVERT: I 803 PHE cc_start: 0.7643 (m-80) cc_final: 0.7418 (m-10) REVERT: I 849 MET cc_start: 0.7000 (tpt) cc_final: 0.6569 (tpp) REVERT: I 860 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6855 (ttp80) REVERT: I 1895 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8157 (ttm-80) REVERT: I 1939 ARG cc_start: 0.7720 (tpm170) cc_final: 0.7453 (tpm170) REVERT: I 2026 CYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8846 (t) REVERT: J 173 LEU cc_start: 0.7003 (mm) cc_final: 0.6742 (mm) REVERT: J 177 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6814 (mptt) REVERT: J 187 LEU cc_start: 0.6311 (mt) cc_final: 0.6103 (mm) REVERT: K 1 MET cc_start: 0.2156 (OUTLIER) cc_final: 0.1717 (ppp) REVERT: K 12 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.5312 (p0) REVERT: K 64 TYR cc_start: 0.1550 (m-80) cc_final: 0.1117 (m-80) REVERT: K 185 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7416 (mtpt) REVERT: K 196 MET cc_start: 0.6363 (ptm) cc_final: 0.5930 (tmm) REVERT: K 220 MET cc_start: 0.7660 (mtp) cc_final: 0.7419 (mmm) REVERT: K 255 MET cc_start: 0.0353 (tpp) cc_final: 0.0013 (mmm) REVERT: K 314 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.5805 (p90) REVERT: K 374 ASP cc_start: 0.7800 (m-30) cc_final: 0.7309 (t70) REVERT: M 260 MET cc_start: 0.7804 (ttt) cc_final: 0.7076 (mpp) REVERT: M 308 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8018 (t0) REVERT: N 132 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8109 (mmtm) REVERT: N 168 MET cc_start: 0.7123 (ptp) cc_final: 0.6825 (ptp) REVERT: N 326 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: N 354 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8105 (pp) REVERT: N 436 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7605 (tm-30) REVERT: O 18 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.6974 (t70) REVERT: O 159 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7888 (mm) REVERT: O 223 LEU cc_start: 0.7637 (tp) cc_final: 0.7122 (tp) REVERT: O 364 MET cc_start: 0.8298 (mmm) cc_final: 0.8073 (mmm) REVERT: P 19 ILE cc_start: 0.6074 (mt) cc_final: 0.5771 (tt) REVERT: P 236 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8278 (pttm) REVERT: P 257 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.5316 (m-10) REVERT: Q 61 MET cc_start: 0.8695 (mmm) cc_final: 0.8147 (mmm) REVERT: Q 113 MET cc_start: 0.8498 (tpt) cc_final: 0.8225 (tpt) REVERT: Q 147 MET cc_start: 0.4366 (mtp) cc_final: 0.4162 (ttm) REVERT: Q 173 ASP cc_start: 0.7517 (m-30) cc_final: 0.6723 (p0) REVERT: R 37 LEU cc_start: 0.8756 (mp) cc_final: 0.8520 (mt) REVERT: R 116 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8757 (p) REVERT: R 246 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6613 (pp20) REVERT: R 364 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7589 (tm-30) REVERT: R 428 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7971 (tpt170) REVERT: S 1 MET cc_start: 0.0465 (ttp) cc_final: -0.0938 (tpp) REVERT: S 87 HIS cc_start: 0.5156 (m-70) cc_final: 0.4891 (m90) REVERT: S 123 MET cc_start: 0.1967 (mmm) cc_final: 0.1756 (mmm) REVERT: S 354 GLN cc_start: 0.4707 (mt0) cc_final: 0.4401 (pm20) REVERT: S 355 MET cc_start: 0.2790 (mtp) cc_final: 0.2131 (mtt) REVERT: T 250 TRP cc_start: 0.1204 (t60) cc_final: 0.0997 (t60) REVERT: U 34 ILE cc_start: 0.0417 (OUTLIER) cc_final: -0.0285 (mt) REVERT: U 82 MET cc_start: 0.0354 (tpp) cc_final: 0.0022 (ttt) REVERT: U 88 HIS cc_start: 0.4361 (t-90) cc_final: 0.4101 (t70) REVERT: U 99 GLU cc_start: 0.3637 (mm-30) cc_final: 0.2654 (pp20) REVERT: U 227 MET cc_start: 0.0236 (mmt) cc_final: -0.1064 (ttp) REVERT: U 285 CYS cc_start: 0.4773 (m) cc_final: 0.4428 (p) REVERT: U 330 ILE cc_start: 0.2278 (OUTLIER) cc_final: 0.1931 (tt) REVERT: V 239 GLU cc_start: 0.3685 (OUTLIER) cc_final: 0.3194 (pt0) REVERT: W 44 THR cc_start: 0.0723 (p) cc_final: 0.0478 (t) outliers start: 201 outliers final: 102 residues processed: 648 average time/residue: 0.5622 time to fit residues: 617.3485 Evaluate side-chains 559 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 430 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 727 LEU Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2052 LEU Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 132 LYS Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 259 MET Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 402 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 428 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 92 optimal weight: 3.9990 chunk 629 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 487 optimal weight: 5.9990 chunk 346 optimal weight: 0.8980 chunk 482 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 396 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 241 optimal weight: 0.3980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN G 125 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.166312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3868 r_free = 0.3868 target = 0.117809 restraints weight = 119113.819| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.05 r_work: 0.3432 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 58334 Z= 0.242 Angle : 0.656 21.777 80061 Z= 0.337 Chirality : 0.043 0.368 9018 Planarity : 0.005 0.186 9229 Dihedral : 21.248 155.061 10379 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.35 % Favored : 94.43 % Rotamer: Outliers : 3.93 % Allowed : 20.06 % Favored : 76.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6298 helix: 0.71 (0.10), residues: 2935 sheet: -0.38 (0.18), residues: 799 loop : -1.30 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 277 HIS 0.021 0.001 HIS I 936 PHE 0.033 0.002 PHE N 261 TYR 0.030 0.001 TYR V 246 ARG 0.037 0.000 ARG N 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 453 time to evaluate : 4.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6291 (mm) REVERT: B 28 ARG cc_start: 0.0436 (OUTLIER) cc_final: -0.0456 (mtp-110) REVERT: B 59 MET cc_start: 0.6390 (mmm) cc_final: 0.5981 (mmm) REVERT: C 90 MET cc_start: 0.7943 (mmm) cc_final: 0.7211 (mmm) REVERT: E 58 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8579 (mm) REVERT: E 114 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6883 (p) REVERT: G 112 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (pp) REVERT: G 120 MET cc_start: 0.7751 (ptp) cc_final: 0.7336 (pmm) REVERT: G 129 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (mtp85) REVERT: I 144 MET cc_start: -0.0143 (ppp) cc_final: -0.0927 (tmm) REVERT: I 803 PHE cc_start: 0.7651 (m-80) cc_final: 0.7415 (m-10) REVERT: I 849 MET cc_start: 0.7100 (tpt) cc_final: 0.6602 (tpt) REVERT: I 860 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6930 (ttp80) REVERT: I 1895 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8272 (ttm-80) REVERT: I 1939 ARG cc_start: 0.7828 (tpm170) cc_final: 0.7579 (tpm170) REVERT: I 2028 MET cc_start: 0.8930 (mtp) cc_final: 0.8620 (mtp) REVERT: J 173 LEU cc_start: 0.6979 (mm) cc_final: 0.6650 (mm) REVERT: J 177 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6945 (mptt) REVERT: J 215 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.8252 (m-70) REVERT: J 271 ASP cc_start: 0.7742 (p0) cc_final: 0.7524 (p0) REVERT: K 1 MET cc_start: 0.2487 (OUTLIER) cc_final: 0.1956 (ppp) REVERT: K 12 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.5346 (p0) REVERT: K 64 TYR cc_start: 0.1741 (m-80) cc_final: 0.1462 (m-10) REVERT: K 109 MET cc_start: 0.6435 (ttp) cc_final: 0.5870 (tpt) REVERT: K 196 MET cc_start: 0.6441 (ptm) cc_final: 0.5954 (ptt) REVERT: K 220 MET cc_start: 0.7714 (mtp) cc_final: 0.7458 (mmm) REVERT: K 314 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.5731 (p90) REVERT: K 374 ASP cc_start: 0.7686 (m-30) cc_final: 0.7259 (t70) REVERT: M 260 MET cc_start: 0.7874 (ttt) cc_final: 0.7200 (mpp) REVERT: M 302 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8792 (t0) REVERT: M 308 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8094 (t0) REVERT: N 78 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: N 119 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8216 (mt) REVERT: N 168 MET cc_start: 0.7114 (ptp) cc_final: 0.6902 (ptp) REVERT: N 326 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8293 (mtm) REVERT: O 18 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7076 (t70) REVERT: O 159 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7869 (mm) REVERT: O 223 LEU cc_start: 0.7670 (tp) cc_final: 0.7135 (tp) REVERT: O 249 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7856 (mtt180) REVERT: O 265 LYS cc_start: 0.7893 (tptm) cc_final: 0.7412 (tppt) REVERT: P 19 ILE cc_start: 0.6224 (mt) cc_final: 0.5706 (tt) REVERT: P 236 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8357 (pttm) REVERT: P 257 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.5453 (m-10) REVERT: P 448 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.7758 (t0) REVERT: Q 61 MET cc_start: 0.8753 (mmm) cc_final: 0.8269 (mmm) REVERT: Q 113 MET cc_start: 0.8543 (tpt) cc_final: 0.8261 (tpt) REVERT: Q 147 MET cc_start: 0.4543 (mtp) cc_final: 0.4303 (ttm) REVERT: Q 173 ASP cc_start: 0.7598 (m-30) cc_final: 0.6911 (p0) REVERT: Q 192 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.5897 (t80) REVERT: R 37 LEU cc_start: 0.8802 (mp) cc_final: 0.8568 (mt) REVERT: R 232 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7874 (tp) REVERT: R 246 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6711 (pp20) REVERT: R 317 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: R 346 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8085 (pt) REVERT: R 428 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8012 (tpt90) REVERT: S 87 HIS cc_start: 0.5168 (m-70) cc_final: 0.4942 (m90) REVERT: S 119 MET cc_start: 0.5087 (mtp) cc_final: 0.4808 (mtm) REVERT: S 190 MET cc_start: 0.1933 (mmm) cc_final: 0.1153 (mmm) REVERT: S 354 GLN cc_start: 0.4841 (mt0) cc_final: 0.4512 (pm20) REVERT: S 355 MET cc_start: 0.2887 (mtp) cc_final: 0.2158 (mtt) REVERT: T 230 ARG cc_start: 0.5361 (mtt180) cc_final: 0.4366 (tpt170) REVERT: U 88 HIS cc_start: 0.4475 (t-90) cc_final: 0.4264 (t70) REVERT: U 227 MET cc_start: 0.0258 (mmt) cc_final: -0.1087 (ttp) REVERT: U 285 CYS cc_start: 0.3879 (m) cc_final: 0.3517 (p) REVERT: U 330 ILE cc_start: 0.2218 (OUTLIER) cc_final: 0.1861 (tt) REVERT: V 239 GLU cc_start: 0.3658 (OUTLIER) cc_final: 0.3173 (pt0) REVERT: W 44 THR cc_start: 0.0755 (p) cc_final: 0.0505 (t) REVERT: W 128 MET cc_start: 0.3693 (ptt) cc_final: 0.1509 (mmp) outliers start: 215 outliers final: 130 residues processed: 633 average time/residue: 0.5367 time to fit residues: 578.5654 Evaluate side-chains 589 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 430 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 969 LEU Chi-restraints excluded: chain I residue 1971 GLU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain I residue 2154 ARG Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 314 PHE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 233 GLU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 302 ASP Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 15 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 326 MET Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 428 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 470 optimal weight: 3.9990 chunk 398 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 206 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 326 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 241 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.120064 restraints weight = 119926.014| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.10 r_work: 0.3467 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 58334 Z= 0.177 Angle : 0.628 19.941 80061 Z= 0.322 Chirality : 0.042 0.299 9018 Planarity : 0.006 0.425 9229 Dihedral : 21.123 156.314 10376 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.02 % Favored : 94.76 % Rotamer: Outliers : 3.31 % Allowed : 20.83 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 6298 helix: 0.83 (0.10), residues: 2928 sheet: -0.35 (0.18), residues: 802 loop : -1.23 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 277 HIS 0.017 0.001 HIS I 936 PHE 0.033 0.001 PHE N 261 TYR 0.020 0.001 TYR D 88 ARG 0.042 0.000 ARG N 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 460 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.0742 (OUTLIER) cc_final: -0.0251 (mtp-110) REVERT: B 43 LYS cc_start: 0.5669 (mmtt) cc_final: 0.5408 (mmpt) REVERT: B 59 MET cc_start: 0.6440 (mmm) cc_final: 0.6033 (mmm) REVERT: C 90 MET cc_start: 0.7935 (mmm) cc_final: 0.7194 (mmm) REVERT: C 99 TYR cc_start: 0.7436 (t80) cc_final: 0.7178 (t80) REVERT: E 58 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8573 (mm) REVERT: G 112 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7905 (pp) REVERT: G 120 MET cc_start: 0.7655 (ptp) cc_final: 0.7346 (pmm) REVERT: G 129 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7830 (mtp85) REVERT: I 144 MET cc_start: -0.0194 (ppp) cc_final: -0.0875 (tmm) REVERT: I 803 PHE cc_start: 0.7619 (m-80) cc_final: 0.7411 (m-10) REVERT: I 860 ARG cc_start: 0.6884 (ttp80) cc_final: 0.6670 (ttp80) REVERT: I 1939 ARG cc_start: 0.7866 (tpm170) cc_final: 0.7663 (tpm170) REVERT: I 2026 CYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8856 (t) REVERT: J 173 LEU cc_start: 0.6979 (mm) cc_final: 0.6641 (mm) REVERT: J 215 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8267 (m-70) REVERT: K 1 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.1880 (ppp) REVERT: K 12 ASN cc_start: 0.6884 (OUTLIER) cc_final: 0.5135 (p0) REVERT: K 64 TYR cc_start: 0.1797 (m-80) cc_final: 0.1504 (m-10) REVERT: K 185 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7432 (mtpt) REVERT: K 196 MET cc_start: 0.6379 (ptm) cc_final: 0.5958 (tmm) REVERT: K 206 LYS cc_start: 0.4737 (OUTLIER) cc_final: 0.4276 (pttp) REVERT: K 220 MET cc_start: 0.7668 (mtp) cc_final: 0.7444 (mmm) REVERT: K 374 ASP cc_start: 0.7549 (m-30) cc_final: 0.7271 (t70) REVERT: M 260 MET cc_start: 0.7778 (ttt) cc_final: 0.7069 (mpp) REVERT: M 308 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7951 (t0) REVERT: N 78 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: N 119 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8273 (mt) REVERT: N 168 MET cc_start: 0.7063 (ptp) cc_final: 0.6775 (ptp) REVERT: N 169 GLU cc_start: 0.7184 (mp0) cc_final: 0.6731 (mp0) REVERT: N 326 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8325 (mtm) REVERT: N 354 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8042 (pp) REVERT: O 18 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.6957 (t70) REVERT: O 223 LEU cc_start: 0.7601 (tp) cc_final: 0.7054 (tp) REVERT: P 19 ILE cc_start: 0.6055 (mt) cc_final: 0.5685 (tt) REVERT: P 188 GLN cc_start: 0.8278 (pt0) cc_final: 0.7978 (pm20) REVERT: P 236 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8346 (pttm) REVERT: P 257 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.5450 (m-10) REVERT: Q 61 MET cc_start: 0.8679 (mmm) cc_final: 0.8175 (mmm) REVERT: Q 113 MET cc_start: 0.8442 (tpt) cc_final: 0.8186 (tpt) REVERT: Q 173 ASP cc_start: 0.7459 (m-30) cc_final: 0.6790 (p0) REVERT: Q 192 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.5789 (t80) REVERT: R 37 LEU cc_start: 0.8737 (mp) cc_final: 0.8518 (mt) REVERT: R 116 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (p) REVERT: R 246 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: R 317 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: R 364 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7551 (tm-30) REVERT: R 428 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7820 (tpt170) REVERT: S 1 MET cc_start: 0.0316 (ttp) cc_final: -0.1031 (tpp) REVERT: S 82 MET cc_start: 0.4956 (tpp) cc_final: 0.4637 (tpt) REVERT: S 86 TRP cc_start: 0.4355 (m-10) cc_final: 0.3674 (m-10) REVERT: S 87 HIS cc_start: 0.5221 (m-70) cc_final: 0.4965 (m90) REVERT: S 190 MET cc_start: 0.1180 (mmm) cc_final: 0.0544 (mmt) REVERT: S 354 GLN cc_start: 0.4944 (mt0) cc_final: 0.4560 (pm20) REVERT: S 355 MET cc_start: 0.3031 (mtp) cc_final: 0.2272 (mtt) REVERT: T 230 ARG cc_start: 0.5423 (mtt180) cc_final: 0.4433 (tpt170) REVERT: U 88 HIS cc_start: 0.4588 (t-90) cc_final: 0.4292 (t70) REVERT: U 227 MET cc_start: 0.0382 (mmt) cc_final: -0.1085 (ttp) REVERT: U 285 CYS cc_start: 0.3865 (m) cc_final: 0.3300 (p) REVERT: U 330 ILE cc_start: 0.1555 (OUTLIER) cc_final: 0.1323 (tt) REVERT: V 184 LYS cc_start: 0.4680 (pttt) cc_final: 0.4011 (tptt) REVERT: V 239 GLU cc_start: 0.3858 (OUTLIER) cc_final: 0.3481 (pt0) REVERT: W 44 THR cc_start: 0.0779 (p) cc_final: 0.0505 (t) REVERT: W 128 MET cc_start: 0.3843 (ptt) cc_final: 0.1418 (mmp) outliers start: 181 outliers final: 111 residues processed: 615 average time/residue: 0.5330 time to fit residues: 556.5643 Evaluate side-chains 567 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 431 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 727 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 922 CYS Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 1894 LYS Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2052 LEU Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 355 LEU Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 419 ILE Chi-restraints excluded: chain O residue 450 GLN Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 428 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 69 TYR Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Chi-restraints excluded: chain V residue 271 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 379 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 224 optimal weight: 0.0770 chunk 470 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 524 optimal weight: 2.9990 chunk 627 optimal weight: 20.0000 chunk 436 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 HIS ** I 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS K 303 GLN K 310 GLN ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 383 ASN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.167399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.120360 restraints weight = 120308.320| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.12 r_work: 0.3468 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58334 Z= 0.184 Angle : 0.631 17.244 80061 Z= 0.323 Chirality : 0.041 0.251 9018 Planarity : 0.006 0.419 9229 Dihedral : 21.002 156.569 10374 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.05 % Favored : 94.74 % Rotamer: Outliers : 3.02 % Allowed : 21.09 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 6298 helix: 0.91 (0.10), residues: 2914 sheet: -0.34 (0.18), residues: 814 loop : -1.18 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 277 HIS 0.010 0.001 HIS I 936 PHE 0.032 0.001 PHE N 261 TYR 0.036 0.001 TYR D 88 ARG 0.042 0.000 ARG N 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 459 time to evaluate : 5.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.0468 (OUTLIER) cc_final: -0.0457 (mtp-110) REVERT: B 59 MET cc_start: 0.6385 (mmm) cc_final: 0.6027 (mmm) REVERT: C 90 MET cc_start: 0.7957 (mmm) cc_final: 0.7211 (mmm) REVERT: C 99 TYR cc_start: 0.7430 (t80) cc_final: 0.7191 (t80) REVERT: E 58 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8560 (mm) REVERT: G 129 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7835 (mtp85) REVERT: I 144 MET cc_start: -0.0247 (ppp) cc_final: -0.1061 (tmm) REVERT: I 860 ARG cc_start: 0.6805 (ttp80) cc_final: 0.6351 (ttp80) REVERT: I 1895 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8015 (ttp-170) REVERT: I 2026 CYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (t) REVERT: J 146 LEU cc_start: 0.7455 (tp) cc_final: 0.7197 (mp) REVERT: J 215 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8271 (m-70) REVERT: K 1 MET cc_start: 0.2670 (OUTLIER) cc_final: 0.1960 (ppp) REVERT: K 12 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.5094 (p0) REVERT: K 117 TYR cc_start: 0.4817 (m-80) cc_final: 0.4225 (m-10) REVERT: K 185 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7442 (mtpt) REVERT: K 196 MET cc_start: 0.6407 (ptm) cc_final: 0.6015 (tmm) REVERT: K 206 LYS cc_start: 0.4815 (OUTLIER) cc_final: 0.4361 (pttp) REVERT: K 269 ARG cc_start: 0.5305 (tpt-90) cc_final: 0.4183 (mtp85) REVERT: K 374 ASP cc_start: 0.7474 (m-30) cc_final: 0.7152 (t70) REVERT: K 391 GLU cc_start: 0.3982 (mm-30) cc_final: 0.3775 (mm-30) REVERT: L 33 GLU cc_start: 0.7977 (tp30) cc_final: 0.7430 (pt0) REVERT: M 257 LEU cc_start: 0.8471 (tp) cc_final: 0.7980 (tt) REVERT: M 260 MET cc_start: 0.7822 (ttt) cc_final: 0.6914 (mpp) REVERT: N 78 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: N 119 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (mt) REVERT: N 168 MET cc_start: 0.6966 (ptp) cc_final: 0.6694 (ptp) REVERT: N 169 GLU cc_start: 0.7248 (mp0) cc_final: 0.6807 (mp0) REVERT: N 326 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8377 (mtm) REVERT: N 354 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8098 (pp) REVERT: N 364 GLU cc_start: 0.8111 (mp0) cc_final: 0.7747 (mt-10) REVERT: O 18 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.6830 (t70) REVERT: O 223 LEU cc_start: 0.7630 (tp) cc_final: 0.7073 (tp) REVERT: P 19 ILE cc_start: 0.6352 (mt) cc_final: 0.5887 (tt) REVERT: P 46 MET cc_start: 0.8250 (ttp) cc_final: 0.8024 (ttp) REVERT: P 188 GLN cc_start: 0.8278 (pt0) cc_final: 0.7984 (pm20) REVERT: P 236 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8354 (pttm) REVERT: Q 61 MET cc_start: 0.8685 (mmm) cc_final: 0.8233 (mmm) REVERT: Q 113 MET cc_start: 0.8494 (tpt) cc_final: 0.8255 (tpt) REVERT: Q 173 ASP cc_start: 0.7598 (m-30) cc_final: 0.6907 (p0) REVERT: Q 192 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.5762 (t80) REVERT: R 37 LEU cc_start: 0.8723 (mp) cc_final: 0.8518 (mt) REVERT: R 116 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8751 (p) REVERT: R 246 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6577 (pp20) REVERT: R 317 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: R 364 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7742 (tm-30) REVERT: R 428 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7856 (tpt170) REVERT: S 1 MET cc_start: 0.0512 (ttp) cc_final: -0.0895 (tpp) REVERT: S 87 HIS cc_start: 0.5205 (m-70) cc_final: 0.4854 (m90) REVERT: S 354 GLN cc_start: 0.4949 (mt0) cc_final: 0.4565 (pm20) REVERT: S 355 MET cc_start: 0.3042 (mtp) cc_final: 0.2254 (mtt) REVERT: T 230 ARG cc_start: 0.5382 (mtt180) cc_final: 0.4350 (tpt170) REVERT: U 16 MET cc_start: 0.3356 (pmm) cc_final: 0.3027 (ptt) REVERT: U 88 HIS cc_start: 0.4610 (t-90) cc_final: 0.4347 (t70) REVERT: U 227 MET cc_start: 0.0585 (mmt) cc_final: -0.0882 (ttp) REVERT: U 285 CYS cc_start: 0.3880 (m) cc_final: 0.3295 (p) REVERT: U 330 ILE cc_start: 0.1386 (OUTLIER) cc_final: 0.1151 (tt) REVERT: V 184 LYS cc_start: 0.4679 (pttt) cc_final: 0.4008 (tptt) REVERT: V 239 GLU cc_start: 0.3770 (OUTLIER) cc_final: 0.3472 (pt0) REVERT: W 44 THR cc_start: 0.0765 (p) cc_final: 0.0493 (t) REVERT: W 128 MET cc_start: 0.3838 (ptt) cc_final: 0.1408 (mmp) outliers start: 165 outliers final: 113 residues processed: 602 average time/residue: 0.5434 time to fit residues: 554.7554 Evaluate side-chains 565 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 430 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 822 ASN Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 922 CYS Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 1894 LYS Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2026 CYS Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain N residue 447 GLN Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 419 ILE Chi-restraints excluded: chain O residue 450 GLN Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 200 VAL Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain R residue 428 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 69 TYR Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 289 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 482 optimal weight: 20.0000 chunk 452 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 617 optimal weight: 6.9990 chunk 397 optimal weight: 1.9990 chunk 486 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 HIS ** I 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.164010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116188 restraints weight = 118884.912| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.03 r_work: 0.3372 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 58334 Z= 0.412 Angle : 0.758 14.366 80061 Z= 0.388 Chirality : 0.047 0.362 9018 Planarity : 0.006 0.101 9229 Dihedral : 21.249 168.766 10374 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.02 % Favored : 93.78 % Rotamer: Outliers : 2.87 % Allowed : 21.31 % Favored : 75.82 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 6298 helix: 0.59 (0.10), residues: 2958 sheet: -0.38 (0.18), residues: 810 loop : -1.38 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 806 HIS 0.019 0.002 HIS I 936 PHE 0.033 0.002 PHE N 261 TYR 0.032 0.002 TYR D 88 ARG 0.016 0.001 ARG N 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12596 Ramachandran restraints generated. 6298 Oldfield, 0 Emsley, 6298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 413 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.0742 (OUTLIER) cc_final: -0.0331 (mtp-110) REVERT: B 59 MET cc_start: 0.6624 (mmm) cc_final: 0.6229 (mmm) REVERT: C 90 MET cc_start: 0.8032 (mmm) cc_final: 0.7311 (mmm) REVERT: D 93 GLN cc_start: 0.7793 (mm110) cc_final: 0.7587 (mm-40) REVERT: D 98 TYR cc_start: 0.6933 (m-10) cc_final: 0.6653 (m-80) REVERT: E 15 LYS cc_start: 0.3749 (OUTLIER) cc_final: 0.3537 (mtpp) REVERT: E 58 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8549 (mm) REVERT: F 59 MET cc_start: 0.9131 (mmp) cc_final: 0.8638 (mmt) REVERT: G 120 MET cc_start: 0.7881 (ptp) cc_final: 0.7405 (pmm) REVERT: G 129 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7831 (mtp85) REVERT: I 198 MET cc_start: 0.4776 (ptt) cc_final: 0.4374 (ptt) REVERT: I 615 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6857 (ptp90) REVERT: I 742 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6472 (m-80) REVERT: I 782 LEU cc_start: 0.7498 (tp) cc_final: 0.7296 (tp) REVERT: J 146 LEU cc_start: 0.7419 (tp) cc_final: 0.7179 (mp) REVERT: J 214 TYR cc_start: 0.7991 (t80) cc_final: 0.7740 (t80) REVERT: J 215 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8304 (m-70) REVERT: K 1 MET cc_start: 0.4010 (OUTLIER) cc_final: 0.1735 (ppp) REVERT: K 185 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7598 (mtpt) REVERT: K 196 MET cc_start: 0.6582 (ptm) cc_final: 0.6124 (tmm) REVERT: K 313 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6263 (t80) REVERT: K 325 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7184 (mm) REVERT: K 374 ASP cc_start: 0.7799 (m-30) cc_final: 0.7394 (t70) REVERT: M 260 MET cc_start: 0.7987 (ttt) cc_final: 0.7306 (mpp) REVERT: M 308 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8116 (t0) REVERT: N 78 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: N 354 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8028 (pp) REVERT: O 18 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7225 (t70) REVERT: P 19 ILE cc_start: 0.6164 (mt) cc_final: 0.5898 (tt) REVERT: P 236 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8319 (pttm) REVERT: P 448 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7502 (t0) REVERT: Q 61 MET cc_start: 0.8750 (mmm) cc_final: 0.8222 (mmm) REVERT: Q 113 MET cc_start: 0.8712 (tpt) cc_final: 0.8426 (tpt) REVERT: Q 173 ASP cc_start: 0.7873 (m-30) cc_final: 0.7325 (p0) REVERT: Q 192 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6020 (t80) REVERT: R 37 LEU cc_start: 0.8825 (mp) cc_final: 0.8596 (mt) REVERT: R 246 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6908 (pp20) REVERT: R 317 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: R 364 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7768 (tm-30) REVERT: R 428 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8025 (tpt170) REVERT: S 87 HIS cc_start: 0.5198 (m-70) cc_final: 0.4845 (m90) REVERT: S 166 TYR cc_start: 0.5285 (t80) cc_final: 0.4928 (t80) REVERT: S 190 MET cc_start: 0.1454 (mmt) cc_final: 0.0734 (mmt) REVERT: T 230 ARG cc_start: 0.5282 (mtt180) cc_final: 0.4228 (tpt170) REVERT: U 86 TRP cc_start: -0.0252 (m-10) cc_final: -0.0510 (m-10) REVERT: U 227 MET cc_start: 0.0479 (mmt) cc_final: -0.0960 (ttp) REVERT: U 285 CYS cc_start: 0.3846 (m) cc_final: 0.3347 (p) REVERT: U 330 ILE cc_start: 0.1479 (OUTLIER) cc_final: 0.1230 (tt) REVERT: V 239 GLU cc_start: 0.4066 (OUTLIER) cc_final: 0.3683 (pt0) REVERT: W 44 THR cc_start: 0.0863 (p) cc_final: 0.0575 (t) REVERT: W 128 MET cc_start: 0.3774 (ptt) cc_final: 0.1383 (mmp) REVERT: W 142 MET cc_start: 0.0732 (mmp) cc_final: 0.0466 (mmt) outliers start: 157 outliers final: 113 residues processed: 545 average time/residue: 0.5832 time to fit residues: 541.1015 Evaluate side-chains 539 residues out of total 5487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 403 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 615 ARG Chi-restraints excluded: chain I residue 720 VAL Chi-restraints excluded: chain I residue 722 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 774 THR Chi-restraints excluded: chain I residue 856 VAL Chi-restraints excluded: chain I residue 884 THR Chi-restraints excluded: chain I residue 891 ILE Chi-restraints excluded: chain I residue 922 CYS Chi-restraints excluded: chain I residue 927 SER Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 974 LEU Chi-restraints excluded: chain I residue 1989 SER Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2087 LEU Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 14 LYS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 119 PHE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 313 PHE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 129 GLU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 298 VAL Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 401 THR Chi-restraints excluded: chain M residue 403 LEU Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 227 CYS Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 429 VAL Chi-restraints excluded: chain N residue 442 TYR Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 228 VAL Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 419 ILE Chi-restraints excluded: chain O residue 450 GLN Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 323 VAL Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 221 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 263 LEU Chi-restraints excluded: chain Q residue 264 MET Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain R residue 428 ARG Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 329 VAL Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 173 HIS Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 350 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain V residue 205 VAL Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 233 LEU Chi-restraints excluded: chain V residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 361 optimal weight: 0.9990 chunk 180 optimal weight: 0.1980 chunk 217 optimal weight: 5.9990 chunk 198 optimal weight: 0.0470 chunk 165 optimal weight: 0.0020 chunk 384 optimal weight: 0.7980 chunk 652 optimal weight: 10.0000 chunk 618 optimal weight: 7.9990 chunk 497 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 GLN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.167234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3923 r_free = 0.3923 target = 0.121577 restraints weight = 119676.679| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.37 r_work: 0.3459 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 58334 Z= 0.171 Angle : 0.644 16.045 80061 Z= 0.329 Chirality : 0.042 0.260 9018 Planarity : 0.005 0.254 9229 Dihedral : 20.985 154.579 10372 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.87 % Favored : 94.93 % Rotamer: Outliers : 2.29 % Allowed : 21.96 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 6298 helix: 0.86 (0.10), residues: 2949 sheet: -0.43 (0.18), residues: 814 loop : -1.22 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 283 HIS 0.009 0.001 HIS I 936 PHE 0.037 0.001 PHE N 261 TYR 0.042 0.001 TYR F 80 ARG 0.018 0.000 ARG N 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41702.12 seconds wall clock time: 711 minutes 46.61 seconds (42706.61 seconds total)