Starting phenix.real_space_refine on Mon Jan 20 17:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9brr_44841/01_2025/9brr_44841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9brr_44841/01_2025/9brr_44841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9brr_44841/01_2025/9brr_44841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9brr_44841/01_2025/9brr_44841.map" model { file = "/net/cci-nas-00/data/ceres_data/9brr_44841/01_2025/9brr_44841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9brr_44841/01_2025/9brr_44841.cif" } resolution = 4.5 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 387 5.16 5 C 41973 2.51 5 N 11108 2.21 5 O 12126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65594 Number of models: 1 Model: "" Number of chains: 32 Chain: "b" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1484 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "g" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "1" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "0" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain: "2" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "3" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3610 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Chain: "4" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "5" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "7" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "8" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "9" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "R" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "V" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "X" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "6" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2931 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 9, 'TRANS': 351} Chain breaks: 1 Chain: "U" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3501 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 1 Chain: "d" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "a" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6117 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 31, 'TRANS': 720} Chain breaks: 2 Chain: "e" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 623 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "f" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "p" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Time building chain proxies: 26.85, per 1000 atoms: 0.41 Number of scatterers: 65594 At special positions: 0 Unit cell: (158.215, 182.556, 299.834, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 387 16.00 O 12126 8.00 N 11108 7.00 C 41973 6.00 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=0, symmetry=0 Time building additional restraints: 15.78 Conformation dependent library (CDL) restraints added in 7.5 seconds 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15520 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 43 sheets defined 60.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'b' and resid 7 through 30 removed outlier: 3.797A pdb=" N TYR b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 27 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'b' and resid 36 through 43 Processing helix chain 'b' and resid 45 through 81 removed outlier: 4.068A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 90 Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.558A pdb=" N ALA b 99 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL b 100 " --> pdb=" O PHE b 96 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA b 101 " --> pdb=" O CYS b 97 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE b 102 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE b 111 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN b 113 " --> pdb=" O ILE b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 167 removed outlier: 3.533A pdb=" N GLY b 134 " --> pdb=" O ASN b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 176 Processing helix chain 'b' and resid 177 through 199 removed outlier: 3.529A pdb=" N ILE b 181 " --> pdb=" O LEU b 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 46 removed outlier: 4.418A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 removed outlier: 3.575A pdb=" N ILE g 52 " --> pdb=" O PRO g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 80 removed outlier: 3.919A pdb=" N GLY g 63 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE g 64 " --> pdb=" O VAL g 60 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE g 65 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 121 Processing helix chain 'g' and resid 124 through 126 No H-bonds generated for 'chain 'g' and resid 124 through 126' Processing helix chain 'g' and resid 127 through 155 removed outlier: 4.287A pdb=" N PHE g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA g 138 " --> pdb=" O ILE g 134 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU g 139 " --> pdb=" O LEU g 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU g 141 " --> pdb=" O PHE g 137 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL g 148 " --> pdb=" O TYR g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 45 Processing helix chain 'h' and resid 51 through 63 removed outlier: 3.513A pdb=" N ILE h 57 " --> pdb=" O MET h 53 " (cutoff:3.500A) Proline residue: h 58 - end of helix Processing helix chain 'h' and resid 63 through 80 removed outlier: 3.969A pdb=" N ILE h 67 " --> pdb=" O GLY h 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER h 79 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 122 Processing helix chain 'h' and resid 127 through 155 removed outlier: 4.438A pdb=" N LEU h 141 " --> pdb=" O PHE h 137 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY h 142 " --> pdb=" O ALA h 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU h 143 " --> pdb=" O GLU h 139 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS h 155 " --> pdb=" O ILE h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 45 removed outlier: 3.942A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 56 Processing helix chain 'i' and resid 56 through 79 removed outlier: 3.545A pdb=" N VAL i 60 " --> pdb=" O ILE i 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY i 63 " --> pdb=" O VAL i 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL i 72 " --> pdb=" O TYR i 68 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA i 73 " --> pdb=" O GLY i 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER i 79 " --> pdb=" O LEU i 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 87 through 122 removed outlier: 3.687A pdb=" N ALA i 122 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 126 removed outlier: 6.433A pdb=" N ARG i 126 " --> pdb=" O GLN i 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 123 through 126' Processing helix chain 'i' and resid 127 through 155 removed outlier: 3.850A pdb=" N LYS i 155 " --> pdb=" O ILE i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 45 Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'j' and resid 62 through 79 removed outlier: 4.357A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 124 removed outlier: 4.114A pdb=" N GLN j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 155 removed outlier: 3.876A pdb=" N VAL j 140 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU j 141 " --> pdb=" O PHE j 137 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 45 removed outlier: 4.472A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET k 44 " --> pdb=" O GLY k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 55 Processing helix chain 'k' and resid 56 through 80 removed outlier: 3.643A pdb=" N VAL k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE k 65 " --> pdb=" O MET k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 86 through 122 removed outlier: 3.683A pdb=" N ILE k 112 " --> pdb=" O PHE k 108 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA k 116 " --> pdb=" O ILE k 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA k 122 " --> pdb=" O VAL k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 126 No H-bonds generated for 'chain 'k' and resid 124 through 126' Processing helix chain 'k' and resid 127 through 139 Processing helix chain 'k' and resid 139 through 155 removed outlier: 4.224A pdb=" N LEU k 143 " --> pdb=" O GLU k 139 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU k 152 " --> pdb=" O VAL k 148 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 45 Processing helix chain 'l' and resid 51 through 56 Processing helix chain 'l' and resid 57 through 78 removed outlier: 3.753A pdb=" N MET l 61 " --> pdb=" O ILE l 57 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 122 removed outlier: 4.114A pdb=" N ALA l 122 " --> pdb=" O VAL l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 153 removed outlier: 4.265A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU l 146 " --> pdb=" O GLY l 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 45 Processing helix chain 'm' and resid 48 through 52 Processing helix chain 'm' and resid 57 through 79 removed outlier: 4.003A pdb=" N MET m 61 " --> pdb=" O ILE m 57 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 120 Processing helix chain 'm' and resid 127 through 155 removed outlier: 3.964A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 45 removed outlier: 4.339A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 56 through 79 removed outlier: 4.629A pdb=" N ALA n 62 " --> pdb=" O PRO n 58 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY n 63 " --> pdb=" O VAL n 59 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 122 removed outlier: 3.834A pdb=" N ALA n 122 " --> pdb=" O VAL n 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 155 removed outlier: 4.437A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU n 146 " --> pdb=" O GLY n 142 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS n 155 " --> pdb=" O ILE n 151 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 45 removed outlier: 4.042A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE o 25 " --> pdb=" O SER o 21 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.502A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 122 removed outlier: 3.931A pdb=" N ALA o 122 " --> pdb=" O VAL o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 126 removed outlier: 7.156A pdb=" N ARG o 126 " --> pdb=" O GLN o 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 123 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 4.635A pdb=" N LEU o 133 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU o 135 " --> pdb=" O MET o 131 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 255 through 266 removed outlier: 3.705A pdb=" N ILE 1 259 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 291 removed outlier: 4.352A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 321 through 340 removed outlier: 4.393A pdb=" N ILE 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET 1 340 " --> pdb=" O TYR 1 336 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 366 removed outlier: 3.821A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 387 Processing helix chain '1' and resid 419 through 427 removed outlier: 3.698A pdb=" N GLY 1 427 " --> pdb=" O SER 1 423 " (cutoff:3.500A) Processing helix chain '1' and resid 436 through 442 removed outlier: 3.547A pdb=" N ALA 1 440 " --> pdb=" O ASP 1 436 " (cutoff:3.500A) Processing helix chain '1' and resid 458 through 460 No H-bonds generated for 'chain '1' and resid 458 through 460' Processing helix chain '1' and resid 461 through 469 removed outlier: 3.501A pdb=" N HIS 1 468 " --> pdb=" O TYR 1 464 " (cutoff:3.500A) Processing helix chain '1' and resid 472 through 497 removed outlier: 4.425A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 526 through 530 removed outlier: 3.587A pdb=" N ARG 1 530 " --> pdb=" O PRO 1 527 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 562 removed outlier: 4.075A pdb=" N GLN 1 560 " --> pdb=" O GLU 1 556 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 1 561 " --> pdb=" O THR 1 557 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP 1 562 " --> pdb=" O THR 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 574 through 583 Processing helix chain '1' and resid 584 through 586 No H-bonds generated for 'chain '1' and resid 584 through 586' Processing helix chain '1' and resid 593 through 616 removed outlier: 3.786A pdb=" N LEU 1 615 " --> pdb=" O ALA 1 611 " (cutoff:3.500A) Processing helix chain '0' and resid 106 through 114 Processing helix chain '0' and resid 255 through 266 Processing helix chain '0' and resid 280 through 294 Proline residue: 0 292 - end of helix Processing helix chain '0' and resid 319 through 340 removed outlier: 4.473A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 350 through 366 removed outlier: 4.005A pdb=" N TRP 0 354 " --> pdb=" O SER 0 350 " (cutoff:3.500A) Processing helix chain '0' and resid 377 through 387 Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 436 through 443 Processing helix chain '0' and resid 461 through 469 Processing helix chain '0' and resid 471 through 495 removed outlier: 3.790A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE 0 492 " --> pdb=" O ASP 0 488 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 519 Processing helix chain '0' and resid 533 through 562 removed outlier: 3.663A pdb=" N GLN 0 560 " --> pdb=" O GLU 0 556 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER 0 561 " --> pdb=" O THR 0 557 " (cutoff:3.500A) Processing helix chain '0' and resid 566 through 574 removed outlier: 3.747A pdb=" N ILE 0 570 " --> pdb=" O THR 0 566 " (cutoff:3.500A) Processing helix chain '0' and resid 574 through 584 Processing helix chain '0' and resid 585 through 587 No H-bonds generated for 'chain '0' and resid 585 through 587' Processing helix chain '0' and resid 593 through 616 Processing helix chain '2' and resid 105 through 114 Processing helix chain '2' and resid 256 through 266 removed outlier: 3.839A pdb=" N SER 2 262 " --> pdb=" O VAL 2 258 " (cutoff:3.500A) Processing helix chain '2' and resid 280 through 294 removed outlier: 4.054A pdb=" N MET 2 284 " --> pdb=" O ARG 2 280 " (cutoff:3.500A) Proline residue: 2 292 - end of helix Processing helix chain '2' and resid 319 through 340 removed outlier: 4.401A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 365 removed outlier: 3.882A pdb=" N ARG 2 364 " --> pdb=" O GLU 2 360 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU 2 365 " --> pdb=" O ILE 2 361 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 388 removed outlier: 3.794A pdb=" N ARG 2 388 " --> pdb=" O SER 2 384 " (cutoff:3.500A) Processing helix chain '2' and resid 419 through 429 Processing helix chain '2' and resid 437 through 442 Processing helix chain '2' and resid 457 through 469 removed outlier: 4.656A pdb=" N GLU 2 463 " --> pdb=" O ARG 2 459 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR 2 464 " --> pdb=" O ALA 2 460 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 497 removed outlier: 4.543A pdb=" N GLU 2 491 " --> pdb=" O GLU 2 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE 2 492 " --> pdb=" O ASP 2 488 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 519 Processing helix chain '2' and resid 526 through 530 removed outlier: 3.919A pdb=" N ARG 2 530 " --> pdb=" O PRO 2 527 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 561 removed outlier: 4.013A pdb=" N GLN 2 560 " --> pdb=" O GLU 2 556 " (cutoff:3.500A) Processing helix chain '2' and resid 566 through 574 Processing helix chain '2' and resid 574 through 584 Processing helix chain '2' and resid 593 through 616 Processing helix chain '3' and resid 124 through 128 Processing helix chain '3' and resid 198 through 209 Processing helix chain '3' and resid 237 through 252 removed outlier: 3.607A pdb=" N ASN 3 251 " --> pdb=" O ASP 3 247 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY 3 252 " --> pdb=" O PHE 3 248 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 255 No H-bonds generated for 'chain '3' and resid 253 through 255' Processing helix chain '3' and resid 268 through 271 removed outlier: 3.520A pdb=" N ARG 3 271 " --> pdb=" O THR 3 268 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 268 through 271' Processing helix chain '3' and resid 272 through 289 removed outlier: 4.449A pdb=" N ARG 3 276 " --> pdb=" O ILE 3 272 " (cutoff:3.500A) Processing helix chain '3' and resid 299 through 315 removed outlier: 3.688A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG 3 314 " --> pdb=" O VAL 3 310 " (cutoff:3.500A) Processing helix chain '3' and resid 319 through 323 Processing helix chain '3' and resid 324 through 325 No H-bonds generated for 'chain '3' and resid 324 through 325' Processing helix chain '3' and resid 326 through 336 Processing helix chain '3' and resid 357 through 360 Processing helix chain '3' and resid 363 through 373 Processing helix chain '3' and resid 380 through 386 removed outlier: 3.667A pdb=" N HIS 3 384 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) Processing helix chain '3' and resid 401 through 406 Processing helix chain '3' and resid 414 through 440 removed outlier: 3.831A pdb=" N VAL 3 418 " --> pdb=" O ASP 3 414 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 445 through 462 removed outlier: 3.847A pdb=" N LYS 3 460 " --> pdb=" O GLN 3 456 " (cutoff:3.500A) Processing helix chain '3' and resid 472 through 487 removed outlier: 4.000A pdb=" N PHE 3 487 " --> pdb=" O LEU 3 483 " (cutoff:3.500A) Processing helix chain '3' and resid 496 through 504 Processing helix chain '4' and resid 124 through 128 removed outlier: 3.780A pdb=" N MET 4 127 " --> pdb=" O SER 4 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 4 128 " --> pdb=" O GLU 4 125 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 124 through 128' Processing helix chain '4' and resid 198 through 209 Processing helix chain '4' and resid 218 through 224 removed outlier: 3.628A pdb=" N TYR 4 222 " --> pdb=" O ASP 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 251 Processing helix chain '4' and resid 252 through 255 removed outlier: 4.477A pdb=" N ASP 4 255 " --> pdb=" O GLY 4 252 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 252 through 255' Processing helix chain '4' and resid 268 through 272 Processing helix chain '4' and resid 273 through 290 Processing helix chain '4' and resid 299 through 315 removed outlier: 3.686A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 removed outlier: 3.979A pdb=" N GLY 4 322 " --> pdb=" O GLY 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 324 through 325 No H-bonds generated for 'chain '4' and resid 324 through 325' Processing helix chain '4' and resid 326 through 336 Processing helix chain '4' and resid 357 through 360 Processing helix chain '4' and resid 363 through 373 Processing helix chain '4' and resid 380 through 386 removed outlier: 3.758A pdb=" N HIS 4 384 " --> pdb=" O ASP 4 380 " (cutoff:3.500A) Processing helix chain '4' and resid 401 through 404 Processing helix chain '4' and resid 415 through 439 Processing helix chain '4' and resid 445 through 462 Processing helix chain '4' and resid 472 through 485 Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 124 through 128 removed outlier: 3.507A pdb=" N MET 5 127 " --> pdb=" O SER 5 124 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU 5 128 " --> pdb=" O GLU 5 125 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 124 through 128' Processing helix chain '5' and resid 174 through 179 Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 213 through 217 removed outlier: 3.802A pdb=" N LYS 5 217 " --> pdb=" O LYS 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 220 through 224 Processing helix chain '5' and resid 237 through 252 removed outlier: 3.659A pdb=" N GLY 5 252 " --> pdb=" O PHE 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 267 through 272 Processing helix chain '5' and resid 273 through 288 Processing helix chain '5' and resid 299 through 314 Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 324 through 325 No H-bonds generated for 'chain '5' and resid 324 through 325' Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 357 through 360 Processing helix chain '5' and resid 363 through 373 Processing helix chain '5' and resid 380 through 386 removed outlier: 3.562A pdb=" N HIS 5 384 " --> pdb=" O ASP 5 380 " (cutoff:3.500A) Processing helix chain '5' and resid 401 through 406 removed outlier: 3.526A pdb=" N ILE 5 406 " --> pdb=" O MET 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 440 removed outlier: 3.997A pdb=" N VAL 5 438 " --> pdb=" O ALA 5 434 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY 5 440 " --> pdb=" O LYS 5 436 " (cutoff:3.500A) Processing helix chain '5' and resid 441 through 444 Processing helix chain '5' and resid 445 through 462 Processing helix chain '5' and resid 472 through 485 Processing helix chain '5' and resid 496 through 504 removed outlier: 4.122A pdb=" N GLU 5 502 " --> pdb=" O SER 5 498 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE 5 503 " --> pdb=" O THR 5 499 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 76 removed outlier: 3.513A pdb=" N GLN 7 16 " --> pdb=" O SER 7 12 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR 7 17 " --> pdb=" O ARG 7 13 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU 7 60 " --> pdb=" O MET 7 56 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE 7 74 " --> pdb=" O ALA 7 70 " (cutoff:3.500A) Processing helix chain '7' and resid 79 through 85 Processing helix chain '7' and resid 128 through 215 removed outlier: 4.667A pdb=" N ILE 7 177 " --> pdb=" O GLU 7 173 " (cutoff:3.500A) Proline residue: 7 178 - end of helix removed outlier: 3.645A pdb=" N LYS 7 215 " --> pdb=" O ILE 7 211 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 107 removed outlier: 4.008A pdb=" N LYS 8 52 " --> pdb=" O THR 8 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS 8 107 " --> pdb=" O SER 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 128 removed outlier: 4.218A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU 8 128 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 160 removed outlier: 3.999A pdb=" N ALA 8 146 " --> pdb=" O PRO 8 142 " (cutoff:3.500A) Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 196 through 217 removed outlier: 3.608A pdb=" N GLN 8 206 " --> pdb=" O LEU 8 202 " (cutoff:3.500A) Proline residue: 8 209 - end of helix Processing helix chain '9' and resid 6 through 107 removed outlier: 3.933A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 4.133A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) Processing helix chain '9' and resid 137 through 139 No H-bonds generated for 'chain '9' and resid 137 through 139' Processing helix chain '9' and resid 140 through 160 removed outlier: 3.664A pdb=" N ALA 9 146 " --> pdb=" O PRO 9 142 " (cutoff:3.500A) Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 196 through 207 Processing helix chain '9' and resid 208 through 216 Processing helix chain 'Q' and resid 3 through 20 removed outlier: 3.790A pdb=" N VAL Q 8 " --> pdb=" O SER Q 4 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 43 Processing helix chain 'Q' and resid 44 through 106 Processing helix chain 'Q' and resid 110 through 128 removed outlier: 3.973A pdb=" N VAL Q 114 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 139 No H-bonds generated for 'chain 'Q' and resid 137 through 139' Processing helix chain 'Q' and resid 140 through 159 Proline residue: Q 153 - end of helix Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 207 through 216 Processing helix chain 'R' and resid 5 through 89 removed outlier: 3.956A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 103 removed outlier: 3.991A pdb=" N VAL R 95 " --> pdb=" O ASN R 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 91 removed outlier: 3.617A pdb=" N ASN T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 105 removed outlier: 4.171A pdb=" N GLN T 98 " --> pdb=" O ARG T 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 89 Processing helix chain 'V' and resid 91 through 105 removed outlier: 3.683A pdb=" N VAL V 95 " --> pdb=" O ASN V 91 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 24 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 68 through 74 Processing helix chain 'X' and resid 75 through 80 Processing helix chain 'X' and resid 103 through 109 removed outlier: 3.772A pdb=" N ALA X 109 " --> pdb=" O ILE X 105 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 22 removed outlier: 3.563A pdb=" N TRP 6 19 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) Processing helix chain '6' and resid 23 through 27 Processing helix chain '6' and resid 48 through 79 removed outlier: 4.485A pdb=" N GLY 6 53 " --> pdb=" O ASP 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 117 through 157 removed outlier: 3.601A pdb=" N ASN 6 157 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) Processing helix chain '6' and resid 171 through 175 removed outlier: 3.879A pdb=" N ASP 6 174 " --> pdb=" O LYS 6 171 " (cutoff:3.500A) Processing helix chain '6' and resid 193 through 200 Processing helix chain '6' and resid 200 through 205 Processing helix chain '6' and resid 232 through 242 removed outlier: 3.917A pdb=" N ASP 6 236 " --> pdb=" O LYS 6 232 " (cutoff:3.500A) Processing helix chain '6' and resid 254 through 311 removed outlier: 3.664A pdb=" N MET 6 258 " --> pdb=" O ASN 6 254 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP 6 261 " --> pdb=" O GLU 6 257 " (cutoff:3.500A) Proline residue: 6 278 - end of helix removed outlier: 3.646A pdb=" N GLU 6 289 " --> pdb=" O VAL 6 285 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY 6 311 " --> pdb=" O VAL 6 307 " (cutoff:3.500A) Processing helix chain '6' and resid 327 through 341 removed outlier: 4.589A pdb=" N HIS 6 341 " --> pdb=" O GLU 6 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 removed outlier: 4.030A pdb=" N ALA U 28 " --> pdb=" O ALA U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 52 removed outlier: 3.793A pdb=" N ARG U 52 " --> pdb=" O GLU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 65 Processing helix chain 'U' and resid 66 through 69 Processing helix chain 'U' and resid 76 through 84 removed outlier: 6.554A pdb=" N THR U 82 " --> pdb=" O ILE U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 104 removed outlier: 4.550A pdb=" N MET U 100 " --> pdb=" O MET U 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN U 104 " --> pdb=" O MET U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 Processing helix chain 'U' and resid 158 through 163 removed outlier: 3.623A pdb=" N TYR U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 172 removed outlier: 4.151A pdb=" N ILE U 168 " --> pdb=" O TYR U 164 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR U 170 " --> pdb=" O ASN U 166 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU U 172 " --> pdb=" O ILE U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 209 Processing helix chain 'U' and resid 211 through 221 removed outlier: 3.652A pdb=" N ARG U 215 " --> pdb=" O VAL U 211 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA U 221 " --> pdb=" O ALA U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 233 Processing helix chain 'U' and resid 236 through 251 Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 261 through 263 No H-bonds generated for 'chain 'U' and resid 261 through 263' Processing helix chain 'U' and resid 264 through 276 Processing helix chain 'U' and resid 279 through 296 Processing helix chain 'U' and resid 303 through 311 removed outlier: 3.730A pdb=" N LEU U 307 " --> pdb=" O GLN U 303 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET U 309 " --> pdb=" O TYR U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 313 through 322 removed outlier: 3.664A pdb=" N GLN U 317 " --> pdb=" O LYS U 313 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN U 320 " --> pdb=" O LYS U 316 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 350 removed outlier: 3.585A pdb=" N SER U 332 " --> pdb=" O ASP U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 352 through 362 Processing helix chain 'U' and resid 372 through 378 removed outlier: 3.918A pdb=" N TRP U 376 " --> pdb=" O SER U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 384 Processing helix chain 'U' and resid 388 through 401 Processing helix chain 'U' and resid 403 through 419 Processing helix chain 'U' and resid 421 through 432 Processing helix chain 'U' and resid 432 through 442 removed outlier: 3.809A pdb=" N LEU U 436 " --> pdb=" O GLY U 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS U 442 " --> pdb=" O MET U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 445 through 461 Processing helix chain 'd' and resid 8 through 26 removed outlier: 4.073A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY d 22 " --> pdb=" O GLY d 18 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU d 23 " --> pdb=" O LEU d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 37 removed outlier: 3.698A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 67 through 87 Processing helix chain 'd' and resid 90 through 113 removed outlier: 4.488A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 119 Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 130 through 134 Processing helix chain 'd' and resid 146 through 158 Processing helix chain 'd' and resid 160 through 168 removed outlier: 4.091A pdb=" N ASP d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE d 168 " --> pdb=" O PHE d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 176 removed outlier: 3.629A pdb=" N GLU d 175 " --> pdb=" O GLN d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 200 Processing helix chain 'd' and resid 202 through 228 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 233 through 241 removed outlier: 3.571A pdb=" N PHE d 241 " --> pdb=" O ARG d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 270 removed outlier: 3.945A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 271 through 280 removed outlier: 4.556A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 removed outlier: 3.679A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 339 removed outlier: 4.702A pdb=" N VAL d 319 " --> pdb=" O PHE d 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.819A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 49 Processing helix chain 'a' and resid 51 through 76 removed outlier: 3.830A pdb=" N VAL a 55 " --> pdb=" O PHE a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 134 removed outlier: 3.645A pdb=" N LEU a 97 " --> pdb=" O ASP a 93 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA a 117 " --> pdb=" O THR a 113 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU a 124 " --> pdb=" O ARG a 120 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS a 134 " --> pdb=" O PHE a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 199 Processing helix chain 'a' and resid 233 through 248 Processing helix chain 'a' and resid 259 through 316 removed outlier: 3.955A pdb=" N ASP a 273 " --> pdb=" O ASN a 269 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP a 274 " --> pdb=" O THR a 270 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU a 290 " --> pdb=" O ARG a 286 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN a 291 " --> pdb=" O GLN a 287 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA a 292 " --> pdb=" O ARG a 288 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA a 293 " --> pdb=" O VAL a 289 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG a 298 " --> pdb=" O ALA a 294 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL a 299 " --> pdb=" O LYS a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 351 Processing helix chain 'a' and resid 378 through 387 Processing helix chain 'a' and resid 398 through 414 removed outlier: 4.069A pdb=" N ILE a 404 " --> pdb=" O PRO a 400 " (cutoff:3.500A) Proline residue: a 407 - end of helix Processing helix chain 'a' and resid 416 through 432 removed outlier: 3.823A pdb=" N MET a 430 " --> pdb=" O PHE a 426 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU a 432 " --> pdb=" O VAL a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 439 Processing helix chain 'a' and resid 444 through 453 Processing helix chain 'a' and resid 453 through 472 removed outlier: 3.538A pdb=" N ILE a 457 " --> pdb=" O GLY a 453 " (cutoff:3.500A) Processing helix chain 'a' and resid 527 through 534 removed outlier: 6.251A pdb=" N THR a 534 " --> pdb=" O ASN a 531 " (cutoff:3.500A) Processing helix chain 'a' and resid 535 through 562 removed outlier: 4.003A pdb=" N PHE a 539 " --> pdb=" O ASN a 535 " (cutoff:3.500A) Processing helix chain 'a' and resid 562 through 571 removed outlier: 4.029A pdb=" N ASN a 566 " --> pdb=" O LEU a 562 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 578 removed outlier: 3.809A pdb=" N PHE a 578 " --> pdb=" O LEU a 574 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 605 removed outlier: 4.622A pdb=" N TYR a 593 " --> pdb=" O SER a 589 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU a 594 " --> pdb=" O LEU a 590 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR a 603 " --> pdb=" O PHE a 599 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR a 605 " --> pdb=" O LYS a 601 " (cutoff:3.500A) Processing helix chain 'a' and resid 606 through 610 Processing helix chain 'a' and resid 617 through 626 removed outlier: 3.721A pdb=" N PHE a 624 " --> pdb=" O PHE a 620 " (cutoff:3.500A) Processing helix chain 'a' and resid 639 through 653 removed outlier: 3.737A pdb=" N PHE a 646 " --> pdb=" O GLY a 642 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU a 653 " --> pdb=" O VAL a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 674 removed outlier: 3.843A pdb=" N LYS a 674 " --> pdb=" O TYR a 670 " (cutoff:3.500A) Processing helix chain 'a' and resid 716 through 739 removed outlier: 4.196A pdb=" N ILE a 734 " --> pdb=" O CYS a 730 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER a 735 " --> pdb=" O LEU a 731 " (cutoff:3.500A) Processing helix chain 'a' and resid 741 through 762 Processing helix chain 'a' and resid 769 through 791 removed outlier: 5.046A pdb=" N LEU a 775 " --> pdb=" O LEU a 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY a 776 " --> pdb=" O ALA a 772 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU a 777 " --> pdb=" O GLY a 773 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE a 778 " --> pdb=" O GLY a 774 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE a 779 " --> pdb=" O LEU a 775 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 812 Processing helix chain 'a' and resid 812 through 817 removed outlier: 4.401A pdb=" N PHE a 816 " --> pdb=" O PHE a 812 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 23 removed outlier: 3.894A pdb=" N ILE e 20 " --> pdb=" O PHE e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 70 through 80 Processing helix chain 'f' and resid 8 through 36 removed outlier: 3.616A pdb=" N TRP f 21 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 44 Processing helix chain 'f' and resid 58 through 90 removed outlier: 3.665A pdb=" N TYR f 62 " --> pdb=" O ILE f 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 443 removed outlier: 4.385A pdb=" N GLY c 422 " --> pdb=" O GLY c 418 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET c 439 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 removed outlier: 3.600A pdb=" N ASN p 330 " --> pdb=" O TYR p 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 18 through 25 removed outlier: 6.690A pdb=" N THR 1 30 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL 1 24 " --> pdb=" O VAL 1 28 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL 1 28 " --> pdb=" O VAL 1 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 32 current: chain '1' and resid 50 through 58 removed outlier: 6.693A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 61 through 66 current: chain '0' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 28 through 32 current: chain '0' and resid 50 through 58 removed outlier: 6.586A pdb=" N THR 0 63 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU 0 57 " --> pdb=" O MET 0 61 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '0' and resid 61 through 66 current: chain '3' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 60 current: chain '3' and resid 81 through 90 removed outlier: 6.957A pdb=" N VAL 3 95 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS 3 93 " --> pdb=" O VAL 3 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 93 through 98 current: chain '4' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 57 through 60 current: chain '4' and resid 81 through 90 removed outlier: 6.991A pdb=" N VAL 4 95 " --> pdb=" O LEU 4 87 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL 4 89 " --> pdb=" O LYS 4 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '5' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 57 through 60 current: chain '5' and resid 81 through 90 removed outlier: 6.783A pdb=" N VAL 5 95 " --> pdb=" O LEU 5 87 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL 5 89 " --> pdb=" O LYS 5 93 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS 5 93 " --> pdb=" O VAL 5 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '5' and resid 93 through 98 current: chain '9' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 164 through 167 current: chain '9' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 190 through 195 current: chain 'Q' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 164 through 167 current: chain 'Q' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain '1' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain '1' and resid 98 through 99 removed outlier: 6.540A pdb=" N ILE 1 272 " --> pdb=" O ALA 1 310 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL 1 312 " --> pdb=" O ILE 1 272 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR 1 274 " --> pdb=" O VAL 1 312 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL 1 271 " --> pdb=" O SER 1 345 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET 1 347 " --> pdb=" O VAL 1 271 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE 1 273 " --> pdb=" O MET 1 347 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR 1 246 " --> pdb=" O GLY 1 408 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL 1 410 " --> pdb=" O THR 1 246 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE 1 248 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 164 through 167 removed outlier: 3.745A pdb=" N GLY 1 154 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY 1 183 " --> pdb=" O PHE 1 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 146 through 148 removed outlier: 7.059A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 219 through 220 removed outlier: 3.847A pdb=" N GLU 1 219 " --> pdb=" O LYS 1 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 295 through 296 removed outlier: 3.830A pdb=" N GLU 1 303 " --> pdb=" O MET 1 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '0' and resid 87 through 90 Processing sheet with id=AA9, first strand: chain '0' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 98 through 99 current: chain '0' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 309 through 312 current: chain '0' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 401 through 408 current: chain '0' and resid 454 through 455 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '0' and resid 163 through 167 removed outlier: 3.936A pdb=" N ILE 0 166 " --> pdb=" O GLY 0 154 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN 0 157 " --> pdb=" O GLU 0 134 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU 0 134 " --> pdb=" O ASN 0 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '0' and resid 146 through 147 removed outlier: 6.790A pdb=" N GLU 0 193 " --> pdb=" O THR 0 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain '2' and resid 61 through 66 removed outlier: 4.252A pdb=" N ARG 2 56 " --> pdb=" O THR 2 63 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN 2 65 " --> pdb=" O ILE 2 54 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE 2 54 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG 2 44 " --> pdb=" O LEU 2 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 87 through 90 removed outlier: 3.533A pdb=" N VAL 2 88 " --> pdb=" O TRP 2 209 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP 2 209 " --> pdb=" O VAL 2 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 98 through 99 current: chain '2' and resid 310 through 314 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 310 through 314 current: chain '2' and resid 401 through 410 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '2' and resid 133 through 135 removed outlier: 3.717A pdb=" N GLY 2 183 " --> pdb=" O PHE 2 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 146 through 148 removed outlier: 3.557A pdb=" N SER 2 175 " --> pdb=" O GLU 2 195 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 152 through 156 removed outlier: 6.650A pdb=" N ILE 2 166 " --> pdb=" O TYR 2 153 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE 2 155 " --> pdb=" O HIS 2 164 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS 2 164 " --> pdb=" O ILE 2 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 120 through 123 removed outlier: 3.570A pdb=" N THR 3 121 " --> pdb=" O LEU 3 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 3 151 " --> pdb=" O THR 3 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 131 through 132 removed outlier: 6.162A pdb=" N ILE 3 229 " --> pdb=" O CYS 3 258 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE 3 260 " --> pdb=" O ILE 3 229 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE 3 231 " --> pdb=" O PHE 3 260 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA 3 228 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE 3 296 " --> pdb=" O ALA 3 228 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL 3 230 " --> pdb=" O ILE 3 296 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 3 297 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG 3 340 " --> pdb=" O ILE 3 164 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE 3 164 " --> pdb=" O ARG 3 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 169 through 170 removed outlier: 4.475A pdb=" N ILE 3 183 " --> pdb=" O ILE 3 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 192 through 193 Processing sheet with id=AC5, first strand: chain '3' and resid 375 through 376 Processing sheet with id=AC6, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AC7, first strand: chain '4' and resid 163 through 164 removed outlier: 4.243A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AC9, first strand: chain '4' and resid 191 through 193 removed outlier: 6.035A pdb=" N ILE 4 191 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '4' and resid 257 through 260 removed outlier: 6.894A pdb=" N ILE 4 229 " --> pdb=" O CYS 4 258 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE 4 260 " --> pdb=" O ILE 4 229 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE 4 231 " --> pdb=" O PHE 4 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL 4 293 " --> pdb=" O SER 4 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '4' and resid 375 through 376 Processing sheet with id=AD3, first strand: chain '5' and resid 120 through 123 Processing sheet with id=AD4, first strand: chain '5' and resid 131 through 132 removed outlier: 6.353A pdb=" N PHE 5 132 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU 5 263 " --> pdb=" O PHE 5 132 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY 5 235 " --> pdb=" O ASN 5 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '5' and resid 191 through 193 removed outlier: 6.133A pdb=" N ILE 5 191 " --> pdb=" O LEU 5 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '7' and resid 92 through 101 Processing sheet with id=AD7, first strand: chain '8' and resid 164 through 167 Processing sheet with id=AD8, first strand: chain 'X' and resid 36 through 38 removed outlier: 3.528A pdb=" N LEU X 37 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY X 12 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN X 67 " --> pdb=" O ILE X 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 34 through 37 removed outlier: 3.696A pdb=" N VAL 6 34 " --> pdb=" O GLN 6 322 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL 6 370 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '6' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain '6' and resid 215 through 218 removed outlier: 6.547A pdb=" N VAL 6 215 " --> pdb=" O ASN 6 226 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN 6 226 " --> pdb=" O VAL 6 215 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER 6 217 " --> pdb=" O LEU 6 224 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS 6 225 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 6 186 " --> pdb=" O ARG 6 249 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 325 through 333 removed outlier: 4.250A pdb=" N LEU a 12 " --> pdb=" O MET a 362 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET a 362 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 205 through 209 Processing sheet with id=AE5, first strand: chain 'a' and resid 507 through 509 Processing sheet with id=AE6, first strand: chain 'c' and resid 262 through 264 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 262 through 264 current: chain 'c' and resid 276 through 278 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 276 through 278 current: chain 'c' and resid 387 through 396 No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'c' and resid 295 through 297 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 300 through 302 current: chain 'c' and resid 313 through 326 removed outlier: 4.011A pdb=" N ALA c 322 " --> pdb=" O ALA c 335 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 331 through 335 current: chain 'c' and resid 348 through 350 3877 hydrogen bonds defined for protein. 11370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.90 Time building geometry restraints manager: 18.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10893 1.30 - 1.43: 16533 1.43 - 1.56: 38701 1.56 - 1.69: 8 1.69 - 1.82: 685 Bond restraints: 66820 Sorted by residual: bond pdb=" C ASN d 10 " pdb=" O ASN d 10 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.26e-02 6.30e+03 3.11e+01 bond pdb=" C TYR k 87 " pdb=" O TYR k 87 " ideal model delta sigma weight residual 1.236 1.296 -0.059 1.15e-02 7.56e+03 2.68e+01 bond pdb=" N MET c 446 " pdb=" CA MET c 446 " ideal model delta sigma weight residual 1.458 1.490 -0.032 6.30e-03 2.52e+04 2.52e+01 bond pdb=" C PHE b 12 " pdb=" O PHE b 12 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.09e+01 bond pdb=" C VAL i 60 " pdb=" O VAL i 60 " ideal model delta sigma weight residual 1.237 1.290 -0.054 1.19e-02 7.06e+03 2.02e+01 ... (remaining 66815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 88025 2.36 - 4.72: 2010 4.72 - 7.09: 223 7.09 - 9.45: 42 9.45 - 11.81: 5 Bond angle restraints: 90305 Sorted by residual: angle pdb=" N VAL b 13 " pdb=" CA VAL b 13 " pdb=" C VAL b 13 " ideal model delta sigma weight residual 110.30 102.39 7.91 9.70e-01 1.06e+00 6.65e+01 angle pdb=" N VAL b 13 " pdb=" CA VAL b 13 " pdb=" CB VAL b 13 " ideal model delta sigma weight residual 110.62 119.16 -8.54 1.09e+00 8.42e-01 6.13e+01 angle pdb=" N GLN U 38 " pdb=" CA GLN U 38 " pdb=" C GLN U 38 " ideal model delta sigma weight residual 109.54 100.15 9.39 1.37e+00 5.33e-01 4.69e+01 angle pdb=" N TYR k 87 " pdb=" CA TYR k 87 " pdb=" C TYR k 87 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.20e+00 6.94e-01 4.55e+01 angle pdb=" N TYR m 87 " pdb=" CA TYR m 87 " pdb=" C TYR m 87 " ideal model delta sigma weight residual 111.28 104.15 7.13 1.09e+00 8.42e-01 4.28e+01 ... (remaining 90300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 37307 18.02 - 36.04: 2488 36.04 - 54.06: 458 54.06 - 72.08: 84 72.08 - 90.10: 42 Dihedral angle restraints: 40379 sinusoidal: 16192 harmonic: 24187 Sorted by residual: dihedral pdb=" CA LEU 6 22 " pdb=" C LEU 6 22 " pdb=" N HIS 6 23 " pdb=" CA HIS 6 23 " ideal model delta harmonic sigma weight residual 180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA HIS c 364 " pdb=" C HIS c 364 " pdb=" N CYS c 365 " pdb=" CA CYS c 365 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA THR a 322 " pdb=" C THR a 322 " pdb=" N GLN a 323 " pdb=" CA GLN a 323 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 40376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 8468 0.059 - 0.118: 1490 0.118 - 0.177: 246 0.177 - 0.236: 26 0.236 - 0.295: 6 Chirality restraints: 10236 Sorted by residual: chirality pdb=" CA VAL e 42 " pdb=" N VAL e 42 " pdb=" C VAL e 42 " pdb=" CB VAL e 42 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CG LEU 2 90 " pdb=" CB LEU 2 90 " pdb=" CD1 LEU 2 90 " pdb=" CD2 LEU 2 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB THR n 154 " pdb=" CA THR n 154 " pdb=" OG1 THR n 154 " pdb=" CG2 THR n 154 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 10233 not shown) Planarity restraints: 11580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU k 86 " -0.027 2.00e-02 2.50e+03 5.28e-02 2.78e+01 pdb=" C LEU k 86 " 0.091 2.00e-02 2.50e+03 pdb=" O LEU k 86 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR k 87 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL i 59 " -0.025 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" C VAL i 59 " 0.083 2.00e-02 2.50e+03 pdb=" O VAL i 59 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL i 60 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR o 144 " 0.042 2.00e-02 2.50e+03 3.13e-02 1.96e+01 pdb=" CG TYR o 144 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR o 144 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR o 144 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR o 144 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR o 144 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR o 144 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR o 144 " 0.005 2.00e-02 2.50e+03 ... (remaining 11577 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 16325 2.80 - 3.33: 68443 3.33 - 3.85: 106647 3.85 - 4.38: 122318 4.38 - 4.90: 205039 Nonbonded interactions: 518772 Sorted by model distance: nonbonded pdb=" O GLY 0 278 " pdb=" NH1 ARG 0 353 " model vdw 2.279 3.120 nonbonded pdb=" O CYS b 97 " pdb=" N ALA b 99 " model vdw 2.288 3.120 nonbonded pdb=" O PRO d 92 " pdb=" OG SER d 95 " model vdw 2.315 3.040 nonbonded pdb=" O TYR U 36 " pdb=" C LEU U 37 " model vdw 2.342 3.270 nonbonded pdb=" O ASP c 450 " pdb=" O ASP c 451 " model vdw 2.367 3.040 ... (remaining 518767 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 '0' and resid 17 through 616) selection = chain '1' selection = chain '2' } ncs_group { reference = chain '3' selection = (chain '4' and (resid 39 through 216 or resid 224 through 506)) selection = (chain '5' and (resid 39 through 216 or resid 224 through 506)) } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.270 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: 0.070 Extract box with map and model: 1.890 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 121.410 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.470 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: 0.030 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 0.077 66820 Z= 0.316 Angle : 0.835 11.812 90305 Z= 0.489 Chirality : 0.047 0.295 10236 Planarity : 0.007 0.121 11580 Dihedral : 12.844 90.100 24859 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.95 % Favored : 94.69 % Rotamer: Outliers : 0.42 % Allowed : 0.67 % Favored : 98.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.03 (0.09), residues: 8319 helix: 1.07 (0.08), residues: 4700 sheet: -0.77 (0.20), residues: 671 loop : -1.49 (0.12), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP e 17 HIS 0.027 0.002 HIS X 96 PHE 0.050 0.002 PHE n 90 TYR 0.075 0.002 TYR o 144 ARG 0.032 0.001 ARG 7 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2257 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 2227 time to evaluate : 5.546 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: 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: b 43 GLU cc_start: 0.6784 (tp30) cc_final: 0.6256 (tp30) REVERT: b 172 LEU cc_start: 0.4108 (mt) cc_final: 0.3738 (mt) REVERT: g 14 PHE cc_start: 0.6429 (m-80) cc_final: 0.5807 (m-10) REVERT: h 13 PHE cc_start: 0.8086 (m-10) cc_final: 0.7636 (m-10) REVERT: h 28 MET cc_start: 0.7052 (mmm) cc_final: 0.6637 (mmm) REVERT: h 57 ILE cc_start: 0.7302 (mm) cc_final: 0.6742 (mm) REVERT: h 61 MET cc_start: 0.8198 (mtp) cc_final: 0.7803 (mmm) REVERT: h 131 MET cc_start: 0.7302 (ttp) cc_final: 0.6931 (ttp) REVERT: i 23 MET cc_start: 0.6345 (ttm) cc_final: 0.5779 (ttm) REVERT: i 41 ILE cc_start: 0.7469 (tp) cc_final: 0.7126 (tp) REVERT: i 61 MET cc_start: 0.6690 (mmm) cc_final: 0.6309 (mmt) REVERT: i 82 ASP cc_start: 0.6721 (m-30) cc_final: 0.6169 (t70) REVERT: i 84 ILE cc_start: 0.5175 (tt) cc_final: 0.4828 (pt) REVERT: i 131 MET cc_start: 0.6511 (ttp) cc_final: 0.5982 (ppp) REVERT: i 155 LYS cc_start: 0.5849 (mmtt) cc_final: 0.5287 (mmmt) REVERT: j 12 SER cc_start: 0.7542 (p) cc_final: 0.6777 (m) REVERT: j 28 MET cc_start: 0.8907 (mtp) cc_final: 0.8529 (mtp) REVERT: j 84 ILE cc_start: 0.6890 (mt) cc_final: 0.6238 (mt) REVERT: k 118 VAL cc_start: 0.8263 (t) cc_final: 0.8005 (t) REVERT: k 135 LEU cc_start: 0.4287 (tp) cc_final: 0.4072 (tt) REVERT: l 14 PHE cc_start: 0.7356 (m-80) cc_final: 0.6869 (m-80) REVERT: l 51 LEU cc_start: 0.5879 (mp) cc_final: 0.5420 (mp) REVERT: l 53 MET cc_start: 0.7804 (mmm) cc_final: 0.6277 (tmm) REVERT: l 61 MET cc_start: 0.2359 (mtp) cc_final: 0.1810 (mtp) REVERT: l 76 ILE cc_start: 0.7359 (mt) cc_final: 0.6996 (mt) REVERT: l 102 SER cc_start: 0.8015 (m) cc_final: 0.7800 (p) REVERT: l 128 PHE cc_start: 0.4954 (t80) cc_final: 0.4349 (t80) REVERT: m 16 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.5244 (t) REVERT: m 61 MET cc_start: 0.8068 (mmm) cc_final: 0.7802 (mmm) REVERT: n 45 SER cc_start: 0.6783 (t) cc_final: 0.6427 (t) REVERT: n 82 ASP cc_start: 0.7231 (m-30) cc_final: 0.4271 (m-30) REVERT: n 127 LEU cc_start: 0.6857 (mm) cc_final: 0.6022 (pp) REVERT: n 134 ILE cc_start: 0.6747 (tp) cc_final: 0.6350 (tp) REVERT: o 48 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6332 (mpt180) REVERT: o 127 LEU cc_start: 0.6883 (mm) cc_final: 0.6492 (tp) REVERT: o 144 TYR cc_start: 0.7790 (m-80) cc_final: 0.7274 (m-80) REVERT: 1 86 LEU cc_start: 0.8524 (tp) cc_final: 0.8033 (tp) REVERT: 1 151 ASP cc_start: 0.7131 (m-30) cc_final: 0.6100 (m-30) REVERT: 1 242 GLN cc_start: 0.7752 (tt0) cc_final: 0.7314 (tp40) REVERT: 1 279 GLU cc_start: 0.7531 (pm20) cc_final: 0.5663 (mm-30) REVERT: 1 297 GLU cc_start: 0.4479 (pm20) cc_final: 0.3993 (pm20) REVERT: 1 299 ASP cc_start: 0.5397 (p0) cc_final: 0.4644 (m-30) REVERT: 1 324 GLU cc_start: 0.8530 (tt0) cc_final: 0.7848 (tt0) REVERT: 1 328 TYR cc_start: 0.7669 (m-10) cc_final: 0.7256 (m-80) REVERT: 1 345 SER cc_start: 0.8936 (t) cc_final: 0.8653 (p) REVERT: 1 346 MET cc_start: 0.7669 (ttt) cc_final: 0.7187 (ttt) REVERT: 1 404 VAL cc_start: 0.9311 (t) cc_final: 0.9067 (p) REVERT: 1 494 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7023 (tp40) REVERT: 1 573 HIS cc_start: 0.6928 (m90) cc_final: 0.6559 (t-90) REVERT: 1 588 ASP cc_start: 0.4762 (t70) cc_final: 0.4537 (t70) REVERT: 1 604 LEU cc_start: 0.8243 (tp) cc_final: 0.8042 (tp) REVERT: 0 49 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7336 (mp0) REVERT: 0 53 GLU cc_start: 0.8063 (tp30) cc_final: 0.7777 (tp30) REVERT: 0 308 ARG cc_start: 0.8103 (ptt180) cc_final: 0.7716 (ptt90) REVERT: 0 411 SER cc_start: 0.8708 (t) cc_final: 0.8335 (t) REVERT: 0 456 LYS cc_start: 0.8503 (mmpt) cc_final: 0.7219 (mtmt) REVERT: 2 20 TYR cc_start: 0.5848 (t80) cc_final: 0.5645 (t80) REVERT: 2 34 MET cc_start: 0.7188 (tmm) cc_final: 0.6917 (tmm) REVERT: 2 39 MET cc_start: 0.7194 (pmm) cc_final: 0.6718 (ptp) REVERT: 2 55 ILE cc_start: 0.8115 (mm) cc_final: 0.7068 (mm) REVERT: 2 113 THR cc_start: 0.8692 (p) cc_final: 0.8232 (t) REVERT: 2 155 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7652 (tt) REVERT: 2 167 MET cc_start: 0.8623 (pmm) cc_final: 0.7773 (pmm) REVERT: 2 227 LEU cc_start: 0.8256 (tt) cc_final: 0.8051 (tt) REVERT: 2 335 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6530 (mt-10) REVERT: 2 347 MET cc_start: 0.8598 (ttm) cc_final: 0.8252 (mtt) REVERT: 2 388 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7259 (mmm-85) REVERT: 2 472 PHE cc_start: 0.4850 (t80) cc_final: 0.4473 (t80) REVERT: 2 476 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.6450 (ttm170) REVERT: 2 544 MET cc_start: 0.6615 (mtp) cc_final: 0.6408 (mtp) REVERT: 3 70 GLU cc_start: 0.7700 (pt0) cc_final: 0.7205 (pt0) REVERT: 3 87 LEU cc_start: 0.8968 (mt) cc_final: 0.8301 (mt) REVERT: 3 97 GLN cc_start: 0.9241 (pt0) cc_final: 0.8951 (pt0) REVERT: 3 105 ILE cc_start: 0.8365 (mt) cc_final: 0.8047 (mt) REVERT: 3 183 ILE cc_start: 0.9062 (mt) cc_final: 0.8602 (mt) REVERT: 3 202 ILE cc_start: 0.9021 (mt) cc_final: 0.8767 (mt) REVERT: 3 205 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7482 (tm-30) REVERT: 3 337 ARG cc_start: 0.7489 (mtp180) cc_final: 0.7162 (mtp85) REVERT: 3 374 GLU cc_start: 0.8214 (pm20) cc_final: 0.7471 (pp20) REVERT: 3 392 ILE cc_start: 0.8342 (mt) cc_final: 0.8005 (mt) REVERT: 3 402 MET cc_start: 0.8149 (mtp) cc_final: 0.7885 (ttt) REVERT: 3 423 TYR cc_start: 0.8401 (m-80) cc_final: 0.7549 (m-80) REVERT: 3 469 GLU cc_start: 0.4742 (tm-30) cc_final: 0.4417 (tm-30) REVERT: 3 491 MET cc_start: 0.6059 (mtt) cc_final: 0.5515 (ppp) REVERT: 4 97 GLN cc_start: 0.7449 (pt0) cc_final: 0.7045 (pt0) REVERT: 4 148 GLU cc_start: 0.7964 (tt0) cc_final: 0.7619 (tm-30) REVERT: 4 152 ASP cc_start: 0.7878 (t0) cc_final: 0.7617 (p0) REVERT: 4 153 ILE cc_start: 0.8701 (tt) cc_final: 0.8263 (tt) REVERT: 4 165 TYR cc_start: 0.7746 (t80) cc_final: 0.7521 (t80) REVERT: 4 168 GLU cc_start: 0.7968 (mp0) cc_final: 0.7720 (mp0) REVERT: 4 238 MET cc_start: 0.7957 (mpp) cc_final: 0.7747 (mpp) REVERT: 4 290 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6678 (pt0) REVERT: 4 336 GLU cc_start: 0.7898 (tt0) cc_final: 0.7619 (tt0) REVERT: 4 372 ILE cc_start: 0.8621 (mt) cc_final: 0.8284 (mt) REVERT: 5 78 ASP cc_start: 0.7944 (m-30) cc_final: 0.7729 (m-30) REVERT: 5 202 ILE cc_start: 0.9119 (mt) cc_final: 0.8871 (mm) REVERT: 5 240 THR cc_start: 0.8431 (m) cc_final: 0.8122 (m) REVERT: 5 245 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7956 (ttpt) REVERT: 5 382 GLN cc_start: 0.7932 (mp10) cc_final: 0.7518 (mp10) REVERT: 5 423 TYR cc_start: 0.8161 (t80) cc_final: 0.7829 (t80) REVERT: 5 435 MET cc_start: 0.7026 (mtm) cc_final: 0.6616 (mtm) REVERT: 5 458 PHE cc_start: 0.7427 (t80) cc_final: 0.6714 (t80) REVERT: 5 485 ARG cc_start: 0.7352 (mtp180) cc_final: 0.6991 (mmm160) REVERT: 5 490 GLU cc_start: 0.5800 (tm-30) cc_final: 0.5019 (mt-10) REVERT: 7 23 LEU cc_start: 0.7851 (tp) cc_final: 0.7436 (tp) REVERT: 7 54 THR cc_start: 0.7166 (m) cc_final: 0.6410 (m) REVERT: 8 44 ARG cc_start: 0.6598 (mtp180) cc_final: 0.6367 (ptm160) REVERT: 8 59 LYS cc_start: 0.7692 (mmmm) cc_final: 0.6933 (pptt) REVERT: 8 72 MET cc_start: 0.7994 (mtm) cc_final: 0.7786 (mmt) REVERT: 8 208 MET cc_start: 0.7617 (tmm) cc_final: 0.6908 (tmm) REVERT: 9 54 MET cc_start: 0.7359 (mmt) cc_final: 0.6834 (mmt) REVERT: 9 154 MET cc_start: 0.8090 (mmp) cc_final: 0.7527 (mmt) REVERT: 9 191 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8866 (ttmm) REVERT: 9 197 GLU cc_start: 0.8334 (mp0) cc_final: 0.7754 (mp0) REVERT: Q 67 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7887 (tm-30) REVERT: Q 201 ASP cc_start: 0.8764 (t0) cc_final: 0.8513 (t70) REVERT: R 32 ARG cc_start: 0.6319 (ttp80) cc_final: 0.5997 (ttp80) REVERT: R 58 LYS cc_start: 0.6440 (mttt) cc_final: 0.6055 (mmmt) REVERT: R 79 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8080 (ptp-110) REVERT: R 96 LEU cc_start: 0.9158 (tp) cc_final: 0.8826 (tp) REVERT: T 12 LEU cc_start: 0.6284 (mt) cc_final: 0.6082 (mt) REVERT: T 16 LYS cc_start: 0.8088 (mttt) cc_final: 0.6992 (tttp) REVERT: T 34 LYS cc_start: 0.8148 (tppt) cc_final: 0.7544 (mttt) REVERT: T 42 MET cc_start: 0.7627 (mtm) cc_final: 0.7421 (ppp) REVERT: V 47 TYR cc_start: 0.5890 (m-10) cc_final: 0.5617 (m-10) REVERT: V 87 SER cc_start: 0.8579 (t) cc_final: 0.8223 (p) REVERT: X 27 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7066 (tm-30) REVERT: X 51 THR cc_start: 0.8109 (m) cc_final: 0.7300 (t) REVERT: 6 66 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7233 (mt-10) REVERT: 6 82 ASP cc_start: 0.5324 (t70) cc_final: 0.4866 (m-30) REVERT: 6 109 MET cc_start: 0.7535 (tmm) cc_final: 0.6281 (mtm) REVERT: 6 298 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6586 (mtmt) REVERT: 6 335 LEU cc_start: 0.5569 (pp) cc_final: 0.5185 (pp) REVERT: U 65 MET cc_start: 0.7139 (ppp) cc_final: 0.6393 (ppp) REVERT: U 90 VAL cc_start: 0.3738 (OUTLIER) cc_final: 0.3523 (p) REVERT: U 96 MET cc_start: 0.1426 (ptm) cc_final: 0.0390 (mmt) REVERT: U 127 LEU cc_start: 0.6159 (mt) cc_final: 0.5841 (pt) REVERT: U 147 LYS cc_start: 0.6405 (mmmm) cc_final: 0.5879 (tptt) REVERT: U 156 MET cc_start: 0.6748 (ptm) cc_final: 0.6361 (ptt) REVERT: U 165 PHE cc_start: 0.7393 (m-80) cc_final: 0.7107 (m-80) REVERT: U 234 LYS cc_start: 0.6203 (tttt) cc_final: 0.5720 (mptt) REVERT: U 237 PHE cc_start: 0.6560 (p90) cc_final: 0.5878 (t80) REVERT: U 252 PHE cc_start: 0.4842 (t80) cc_final: 0.4412 (t80) REVERT: U 266 ILE cc_start: 0.5682 (mt) cc_final: 0.5395 (mt) REVERT: U 284 ILE cc_start: 0.7184 (tp) cc_final: 0.6956 (tp) REVERT: U 321 LEU cc_start: 0.8167 (mm) cc_final: 0.7954 (mt) REVERT: U 383 LEU cc_start: 0.7330 (mt) cc_final: 0.6146 (mt) REVERT: U 434 LYS cc_start: 0.5945 (pttm) cc_final: 0.5330 (tttp) REVERT: d 13 ASN cc_start: 0.5256 (OUTLIER) cc_final: 0.4411 (t0) REVERT: d 38 GLN cc_start: 0.6213 (mm-40) cc_final: 0.5123 (pp30) REVERT: d 71 ASP cc_start: 0.6843 (t0) cc_final: 0.6503 (t0) REVERT: d 75 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8032 (mmmt) REVERT: d 78 MET cc_start: 0.8660 (tmm) cc_final: 0.8449 (tmm) REVERT: d 84 HIS cc_start: 0.7939 (t70) cc_final: 0.7597 (t-170) REVERT: d 128 LYS cc_start: 0.8546 (mmpt) cc_final: 0.8267 (mmpt) REVERT: d 135 PHE cc_start: 0.2870 (m-10) cc_final: 0.1739 (m-10) REVERT: d 165 GLN cc_start: 0.7222 (tt0) cc_final: 0.6225 (tp-100) REVERT: d 176 MET cc_start: 0.6950 (mtm) cc_final: 0.6418 (ptp) REVERT: d 189 TYR cc_start: 0.6285 (t80) cc_final: 0.5900 (t80) REVERT: d 261 TYR cc_start: 0.5601 (t80) cc_final: 0.5360 (t80) REVERT: d 276 LEU cc_start: 0.6742 (pp) cc_final: 0.6333 (pp) REVERT: d 294 PHE cc_start: 0.7777 (m-80) cc_final: 0.7359 (m-80) REVERT: d 324 GLN cc_start: 0.7900 (tp40) cc_final: 0.7131 (tp-100) REVERT: d 328 ASN cc_start: 0.7586 (m110) cc_final: 0.7274 (m110) REVERT: d 334 GLU cc_start: 0.4623 (mm-30) cc_final: 0.4299 (mm-30) REVERT: d 339 ARG cc_start: 0.5048 (mpp80) cc_final: 0.4716 (mpp80) REVERT: d 346 ASN cc_start: 0.6965 (t0) cc_final: 0.6706 (t0) REVERT: a 53 ASN cc_start: 0.8004 (m-40) cc_final: 0.7722 (p0) REVERT: a 60 GLU cc_start: 0.7948 (tp30) cc_final: 0.7642 (mm-30) REVERT: a 284 ASP cc_start: 0.7338 (m-30) cc_final: 0.7032 (m-30) REVERT: a 285 HIS cc_start: 0.5939 (t70) cc_final: 0.5379 (t70) REVERT: a 288 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7456 (ttp-170) REVERT: a 329 GLU cc_start: 0.7556 (tt0) cc_final: 0.6718 (mp0) REVERT: a 470 ILE cc_start: 0.7050 (mt) cc_final: 0.6814 (mt) REVERT: a 486 TRP cc_start: 0.4253 (m100) cc_final: 0.3898 (m100) REVERT: a 544 LYS cc_start: 0.7813 (mttt) cc_final: 0.7565 (ptpt) REVERT: a 546 LYS cc_start: 0.8308 (mttt) cc_final: 0.7970 (ptpt) REVERT: a 565 PHE cc_start: 0.7229 (m-80) cc_final: 0.6801 (m-80) REVERT: a 610 SER cc_start: 0.7934 (t) cc_final: 0.7550 (m) REVERT: a 623 MET cc_start: 0.8597 (ttp) cc_final: 0.8044 (tpt) REVERT: a 722 GLN cc_start: 0.8048 (tp40) cc_final: 0.7741 (tp40) REVERT: a 740 TYR cc_start: 0.8266 (m-80) cc_final: 0.7744 (m-80) REVERT: a 769 ARG cc_start: 0.5753 (mtm180) cc_final: 0.5064 (mmt180) REVERT: e 40 MET cc_start: 0.6145 (tmm) cc_final: 0.5791 (tmm) REVERT: e 77 ARG cc_start: 0.4551 (mtp180) cc_final: 0.4163 (tpm170) REVERT: f 29 LEU cc_start: 0.8429 (tp) cc_final: 0.8182 (tp) REVERT: f 63 GLU cc_start: 0.6859 (tp30) cc_final: 0.6235 (tt0) REVERT: c 377 LEU cc_start: 0.7372 (mp) cc_final: 0.7066 (pp) REVERT: c 381 ASN cc_start: 0.6772 (t0) cc_final: 0.6055 (p0) REVERT: c 388 MET cc_start: 0.5854 (tpp) cc_final: 0.5059 (mmt) REVERT: c 429 MET cc_start: 0.7731 (mmm) cc_final: 0.7512 (mmm) outliers start: 30 outliers final: 10 residues processed: 2247 average time/residue: 0.6321 time to fit residues: 2413.5722 Evaluate side-chains 1757 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1743 time to evaluate : 5.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 701 optimal weight: 0.9990 chunk 629 optimal weight: 8.9990 chunk 349 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 651 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 396 optimal weight: 6.9990 chunk 484 optimal weight: 9.9990 chunk 754 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 92 GLN ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 GLN n 124 GLN 1 112 GLN ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN 5 62 HIS 5 209 GLN 5 350 GLN 5 461 ASN 5 482 GLN 8 14 HIS 9 126 GLN Q 77 ASN R 113 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN V 113 ASN ** X 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 252 GLN U 88 GLN U 102 GLN U 324 GLN U 451 ASN d 13 ASN d 84 HIS d 183 ASN a 114 ASN a 494 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 376 ASN ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140598 restraints weight = 149397.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143539 restraints weight = 89865.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145269 restraints weight = 59394.558| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 66820 Z= 0.280 Angle : 0.650 10.527 90305 Z= 0.343 Chirality : 0.043 0.246 10236 Planarity : 0.005 0.120 11580 Dihedral : 4.770 80.896 9108 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 0.23 % Allowed : 3.99 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.30 (0.09), residues: 8319 helix: 1.36 (0.07), residues: 4673 sheet: -0.54 (0.20), residues: 679 loop : -1.50 (0.11), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 16 HIS 0.005 0.001 HIS f 36 PHE 0.049 0.002 PHE e 51 TYR 0.040 0.002 TYR o 144 ARG 0.020 0.001 ARG 7 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2030 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 2014 time to evaluate : 5.549 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: 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: b 39 TRP cc_start: 0.6150 (t60) cc_final: 0.5931 (t60) REVERT: b 50 SER cc_start: 0.7823 (t) cc_final: 0.7555 (p) REVERT: b 89 LYS cc_start: 0.7302 (tttt) cc_final: 0.6382 (tppt) REVERT: b 146 LEU cc_start: 0.7807 (mm) cc_final: 0.7283 (tp) REVERT: b 150 PHE cc_start: 0.8230 (m-80) cc_final: 0.7939 (m-80) REVERT: b 191 VAL cc_start: 0.8618 (p) cc_final: 0.8336 (p) REVERT: g 14 PHE cc_start: 0.5679 (m-80) cc_final: 0.5150 (m-10) REVERT: g 28 MET cc_start: 0.8949 (mtp) cc_final: 0.8739 (mtp) REVERT: g 61 MET cc_start: 0.8450 (mmm) cc_final: 0.8009 (mmm) REVERT: h 28 MET cc_start: 0.7029 (mmm) cc_final: 0.6557 (mmm) REVERT: h 44 MET cc_start: 0.7160 (tmm) cc_final: 0.6800 (ppp) REVERT: h 57 ILE cc_start: 0.7397 (mm) cc_final: 0.6961 (mm) REVERT: h 61 MET cc_start: 0.8348 (mtp) cc_final: 0.7858 (mmm) REVERT: h 131 MET cc_start: 0.7454 (ttp) cc_final: 0.7121 (ttp) REVERT: h 132 ILE cc_start: 0.7078 (mm) cc_final: 0.6872 (mm) REVERT: h 144 TYR cc_start: 0.8449 (m-10) cc_final: 0.8179 (m-10) REVERT: i 61 MET cc_start: 0.6871 (mmm) cc_final: 0.6607 (mmt) REVERT: i 82 ASP cc_start: 0.6894 (m-30) cc_final: 0.6369 (t0) REVERT: i 84 ILE cc_start: 0.5701 (tt) cc_final: 0.5230 (pt) REVERT: i 131 MET cc_start: 0.6387 (ttp) cc_final: 0.6101 (ppp) REVERT: i 155 LYS cc_start: 0.6014 (mmtt) cc_final: 0.5451 (mmmt) REVERT: j 28 MET cc_start: 0.8812 (mtp) cc_final: 0.8565 (mtp) REVERT: j 84 ILE cc_start: 0.6790 (mt) cc_final: 0.6530 (mm) REVERT: j 112 ILE cc_start: 0.5577 (tp) cc_final: 0.5237 (tp) REVERT: k 98 SER cc_start: 0.3854 (p) cc_final: 0.3510 (p) REVERT: l 14 PHE cc_start: 0.7479 (m-80) cc_final: 0.7131 (m-80) REVERT: l 53 MET cc_start: 0.8010 (mmm) cc_final: 0.6449 (tmm) REVERT: m 14 PHE cc_start: 0.7423 (m-80) cc_final: 0.7169 (m-80) REVERT: n 61 MET cc_start: 0.6783 (mmm) cc_final: 0.6452 (mmm) REVERT: n 82 ASP cc_start: 0.7326 (m-30) cc_final: 0.6788 (m-30) REVERT: n 134 ILE cc_start: 0.6706 (tp) cc_final: 0.6114 (tp) REVERT: o 54 LYS cc_start: 0.6148 (tptt) cc_final: 0.5110 (tttt) REVERT: o 144 TYR cc_start: 0.8173 (m-80) cc_final: 0.7816 (m-80) REVERT: 1 86 LEU cc_start: 0.8622 (tp) cc_final: 0.7720 (tp) REVERT: 1 103 GLN cc_start: 0.8118 (tt0) cc_final: 0.7904 (tt0) REVERT: 1 219 GLU cc_start: 0.8974 (pm20) cc_final: 0.8555 (pm20) REVERT: 1 260 SER cc_start: 0.8631 (m) cc_final: 0.8396 (m) REVERT: 1 274 TYR cc_start: 0.9071 (t80) cc_final: 0.8724 (t80) REVERT: 1 279 GLU cc_start: 0.7511 (pm20) cc_final: 0.5578 (mm-30) REVERT: 1 328 TYR cc_start: 0.8110 (m-10) cc_final: 0.7831 (m-80) REVERT: 1 346 MET cc_start: 0.7924 (ttt) cc_final: 0.7356 (ttt) REVERT: 1 508 THR cc_start: 0.6322 (m) cc_final: 0.5919 (p) REVERT: 1 522 GLN cc_start: 0.7875 (tt0) cc_final: 0.7431 (tt0) REVERT: 1 574 MET cc_start: 0.4903 (ptm) cc_final: 0.4676 (mpp) REVERT: 0 49 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7279 (mp0) REVERT: 0 53 GLU cc_start: 0.7957 (tp30) cc_final: 0.7396 (tp30) REVERT: 0 163 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7211 (mmmt) REVERT: 0 224 ASN cc_start: 0.7714 (p0) cc_final: 0.7415 (m-40) REVERT: 0 227 LEU cc_start: 0.8570 (tp) cc_final: 0.8317 (tp) REVERT: 0 286 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: 0 288 LEU cc_start: 0.8389 (mt) cc_final: 0.8170 (mt) REVERT: 0 356 GLU cc_start: 0.7841 (mt-10) cc_final: 0.6952 (tm-30) REVERT: 0 411 SER cc_start: 0.8705 (t) cc_final: 0.8487 (t) REVERT: 0 425 THR cc_start: 0.7826 (m) cc_final: 0.7485 (m) REVERT: 0 445 PHE cc_start: 0.6919 (p90) cc_final: 0.5539 (m-10) REVERT: 0 456 LYS cc_start: 0.8393 (mmpt) cc_final: 0.7661 (mtmt) REVERT: 0 531 PHE cc_start: 0.5721 (t80) cc_final: 0.4813 (t80) REVERT: 2 20 TYR cc_start: 0.6012 (t80) cc_final: 0.5790 (t80) REVERT: 2 34 MET cc_start: 0.7371 (tmm) cc_final: 0.7071 (tmm) REVERT: 2 55 ILE cc_start: 0.8176 (mm) cc_final: 0.7220 (mm) REVERT: 2 113 THR cc_start: 0.8696 (p) cc_final: 0.8178 (t) REVERT: 2 282 ASN cc_start: 0.8081 (t0) cc_final: 0.7670 (t0) REVERT: 2 335 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6278 (mt-10) REVERT: 2 387 GLU cc_start: 0.6757 (tp30) cc_final: 0.6225 (tp30) REVERT: 2 388 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7333 (mmm-85) REVERT: 2 463 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7749 (tm-30) REVERT: 3 70 GLU cc_start: 0.7759 (pt0) cc_final: 0.7338 (pt0) REVERT: 3 127 MET cc_start: 0.7984 (mtp) cc_final: 0.7591 (mtp) REVERT: 3 205 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7372 (tm-30) REVERT: 3 361 ILE cc_start: 0.7340 (tp) cc_final: 0.6854 (tt) REVERT: 3 376 GLN cc_start: 0.7617 (pm20) cc_final: 0.7281 (pm20) REVERT: 3 392 ILE cc_start: 0.8334 (mt) cc_final: 0.7933 (mt) REVERT: 3 394 VAL cc_start: 0.9225 (m) cc_final: 0.8925 (p) REVERT: 3 402 MET cc_start: 0.7971 (mtp) cc_final: 0.7563 (ttp) REVERT: 3 491 MET cc_start: 0.6185 (mtt) cc_final: 0.5561 (ppp) REVERT: 4 70 GLU cc_start: 0.8141 (pt0) cc_final: 0.7416 (pt0) REVERT: 4 97 GLN cc_start: 0.7490 (pt0) cc_final: 0.7102 (pt0) REVERT: 4 105 ILE cc_start: 0.9438 (mm) cc_final: 0.9098 (mm) REVERT: 4 152 ASP cc_start: 0.7762 (t0) cc_final: 0.7442 (p0) REVERT: 4 168 GLU cc_start: 0.7877 (mp0) cc_final: 0.7649 (mp0) REVERT: 4 207 CYS cc_start: 0.7146 (t) cc_final: 0.6936 (t) REVERT: 4 290 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6831 (pt0) REVERT: 4 382 GLN cc_start: 0.7497 (pp30) cc_final: 0.7140 (pp30) REVERT: 5 61 ASP cc_start: 0.8033 (p0) cc_final: 0.7806 (p0) REVERT: 5 100 GLU cc_start: 0.7232 (mp0) cc_final: 0.7002 (tp30) REVERT: 5 119 LEU cc_start: 0.8733 (tp) cc_final: 0.8517 (tp) REVERT: 5 244 PHE cc_start: 0.8390 (m-10) cc_final: 0.8047 (m-10) REVERT: 5 311 SER cc_start: 0.8505 (t) cc_final: 0.8135 (t) REVERT: 5 393 ASN cc_start: 0.8133 (t0) cc_final: 0.6551 (t0) REVERT: 5 423 TYR cc_start: 0.8087 (t80) cc_final: 0.7867 (t80) REVERT: 5 485 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7091 (mmm160) REVERT: 5 490 GLU cc_start: 0.5649 (tm-30) cc_final: 0.5088 (tm-30) REVERT: 7 23 LEU cc_start: 0.7803 (tp) cc_final: 0.7511 (tp) REVERT: 7 163 LYS cc_start: 0.8544 (mmpt) cc_final: 0.7735 (mtpt) REVERT: 7 168 ARG cc_start: 0.5858 (ttt180) cc_final: 0.5584 (ttt180) REVERT: 8 54 MET cc_start: 0.7394 (mpp) cc_final: 0.6753 (mpp) REVERT: 8 72 MET cc_start: 0.8017 (mtm) cc_final: 0.7655 (tpt) REVERT: 8 185 ASN cc_start: 0.8805 (p0) cc_final: 0.8557 (p0) REVERT: 8 208 MET cc_start: 0.6987 (tmm) cc_final: 0.6557 (tmm) REVERT: 9 154 MET cc_start: 0.8204 (mmp) cc_final: 0.7775 (mmm) REVERT: 9 197 GLU cc_start: 0.8444 (mp0) cc_final: 0.8005 (mp0) REVERT: Q 67 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7783 (tm-30) REVERT: R 58 LYS cc_start: 0.6275 (mttt) cc_final: 0.6007 (mmmt) REVERT: R 113 ASN cc_start: 0.8394 (m-40) cc_final: 0.8114 (m-40) REVERT: T 16 LYS cc_start: 0.8237 (mttt) cc_final: 0.7053 (tttp) REVERT: T 34 LYS cc_start: 0.8210 (tppt) cc_final: 0.7405 (mttt) REVERT: V 47 TYR cc_start: 0.5925 (m-10) cc_final: 0.5643 (m-10) REVERT: X 31 ASN cc_start: 0.6317 (m-40) cc_final: 0.6087 (m-40) REVERT: X 51 THR cc_start: 0.8065 (m) cc_final: 0.7636 (t) REVERT: X 55 PHE cc_start: 0.7061 (m-80) cc_final: 0.6780 (m-80) REVERT: 6 66 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7282 (mt-10) REVERT: 6 82 ASP cc_start: 0.5525 (t0) cc_final: 0.5020 (m-30) REVERT: 6 101 TYR cc_start: 0.5834 (t80) cc_final: 0.5623 (t80) REVERT: 6 109 MET cc_start: 0.7509 (tmm) cc_final: 0.6200 (mtm) REVERT: 6 298 LYS cc_start: 0.6897 (mmtt) cc_final: 0.6552 (mtmt) REVERT: U 65 MET cc_start: 0.6762 (ppp) cc_final: 0.6231 (ppp) REVERT: U 96 MET cc_start: 0.1014 (ptm) cc_final: 0.0143 (mmt) REVERT: U 127 LEU cc_start: 0.6122 (mt) cc_final: 0.5770 (pt) REVERT: U 147 LYS cc_start: 0.6220 (mmmm) cc_final: 0.5712 (tptt) REVERT: U 156 MET cc_start: 0.6840 (ptm) cc_final: 0.6456 (ptt) REVERT: U 163 TYR cc_start: 0.6974 (t80) cc_final: 0.6649 (t80) REVERT: U 165 PHE cc_start: 0.7300 (m-80) cc_final: 0.7051 (m-80) REVERT: U 216 PHE cc_start: 0.6864 (m-80) cc_final: 0.6591 (m-10) REVERT: U 218 TRP cc_start: 0.5308 (t-100) cc_final: 0.4750 (t-100) REVERT: U 234 LYS cc_start: 0.6055 (tttt) cc_final: 0.5565 (mptt) REVERT: U 321 LEU cc_start: 0.8113 (mm) cc_final: 0.7747 (mt) REVERT: U 324 GLN cc_start: 0.6978 (mp10) cc_final: 0.6740 (mp10) REVERT: U 434 LYS cc_start: 0.5968 (pttm) cc_final: 0.5318 (tttp) REVERT: U 440 HIS cc_start: 0.6138 (m-70) cc_final: 0.5556 (m90) REVERT: d 38 GLN cc_start: 0.6383 (mm-40) cc_final: 0.5517 (mt0) REVERT: d 85 MET cc_start: 0.8027 (tmm) cc_final: 0.7706 (tmm) REVERT: d 128 LYS cc_start: 0.8540 (mmpt) cc_final: 0.8236 (mptt) REVERT: d 165 GLN cc_start: 0.6975 (tt0) cc_final: 0.5988 (tp40) REVERT: d 176 MET cc_start: 0.6851 (mtm) cc_final: 0.6277 (ptp) REVERT: d 189 TYR cc_start: 0.6596 (t80) cc_final: 0.6127 (t80) REVERT: d 262 GLU cc_start: 0.6456 (tp30) cc_final: 0.5529 (mt-10) REVERT: d 294 PHE cc_start: 0.7773 (m-80) cc_final: 0.7560 (m-80) REVERT: a 53 ASN cc_start: 0.7903 (m-40) cc_final: 0.7588 (p0) REVERT: a 60 GLU cc_start: 0.7985 (tp30) cc_final: 0.7698 (mm-30) REVERT: a 61 MET cc_start: 0.7743 (mtp) cc_final: 0.7332 (mtt) REVERT: a 129 LYS cc_start: 0.7357 (pttp) cc_final: 0.7149 (pttp) REVERT: a 210 GLU cc_start: 0.4974 (tp30) cc_final: 0.4698 (tp30) REVERT: a 290 LEU cc_start: 0.7848 (mt) cc_final: 0.7351 (tt) REVERT: a 316 LEU cc_start: 0.8193 (mm) cc_final: 0.7861 (tp) REVERT: a 329 GLU cc_start: 0.7430 (tt0) cc_final: 0.6420 (mp0) REVERT: a 383 ASN cc_start: 0.8775 (t0) cc_final: 0.8315 (m-40) REVERT: a 470 ILE cc_start: 0.7135 (mt) cc_final: 0.6895 (mt) REVERT: a 486 TRP cc_start: 0.4405 (m100) cc_final: 0.4014 (m100) REVERT: a 546 LYS cc_start: 0.8166 (mttt) cc_final: 0.7840 (ptpt) REVERT: a 565 PHE cc_start: 0.7262 (m-80) cc_final: 0.6782 (m-80) REVERT: a 740 TYR cc_start: 0.8416 (m-80) cc_final: 0.7727 (m-80) REVERT: a 769 ARG cc_start: 0.5704 (mtm180) cc_final: 0.5024 (mmt180) REVERT: e 40 MET cc_start: 0.6452 (tmm) cc_final: 0.6060 (tmm) REVERT: e 77 ARG cc_start: 0.4698 (mtp180) cc_final: 0.4145 (mmm160) REVERT: f 63 GLU cc_start: 0.6690 (tp30) cc_final: 0.6205 (tt0) outliers start: 16 outliers final: 4 residues processed: 2023 average time/residue: 0.6380 time to fit residues: 2216.3129 Evaluate side-chains 1684 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1679 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 9 optimal weight: 0.9990 chunk 690 optimal weight: 5.9990 chunk 659 optimal weight: 7.9990 chunk 701 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 567 optimal weight: 2.9990 chunk 714 optimal weight: 8.9990 chunk 759 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 317 optimal weight: 0.0010 chunk 198 optimal weight: 0.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 124 GLN k 123 GLN l 92 GLN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 441 GLN 4 156 GLN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 385 ASN ** 7 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 11 GLN 8 206 GLN 9 113 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN 6 116 GLN 6 151 GLN 6 296 HIS 6 341 HIS a 114 ASN a 281 GLN a 494 GLN a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 376 ASN ** c 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142793 restraints weight = 149073.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145436 restraints weight = 88969.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147427 restraints weight = 59907.345| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 66820 Z= 0.192 Angle : 0.592 9.888 90305 Z= 0.309 Chirality : 0.042 0.207 10236 Planarity : 0.005 0.151 11580 Dihedral : 4.579 79.124 9108 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.82 % Rotamer: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.56 (0.09), residues: 8319 helix: 1.58 (0.08), residues: 4671 sheet: -0.33 (0.19), residues: 726 loop : -1.45 (0.12), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP U 376 HIS 0.007 0.001 HIS a 285 PHE 0.043 0.002 PHE e 16 TYR 0.028 0.002 TYR i 68 ARG 0.016 0.001 ARG a 806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2001 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1993 time to evaluate : 5.606 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: 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: b 89 LYS cc_start: 0.7114 (tttt) cc_final: 0.6301 (tppt) REVERT: b 105 ILE cc_start: 0.8201 (tp) cc_final: 0.7995 (tp) REVERT: b 146 LEU cc_start: 0.8405 (mm) cc_final: 0.7717 (tp) REVERT: g 28 MET cc_start: 0.8947 (mtp) cc_final: 0.8725 (mtp) REVERT: g 61 MET cc_start: 0.8307 (mmm) cc_final: 0.8073 (mmm) REVERT: h 28 MET cc_start: 0.6879 (mmm) cc_final: 0.6457 (mmp) REVERT: h 57 ILE cc_start: 0.7442 (mm) cc_final: 0.6936 (mm) REVERT: h 61 MET cc_start: 0.8336 (mtp) cc_final: 0.7789 (mmm) REVERT: h 131 MET cc_start: 0.7243 (ttp) cc_final: 0.6901 (ttp) REVERT: h 132 ILE cc_start: 0.6933 (mm) cc_final: 0.6701 (mm) REVERT: h 144 TYR cc_start: 0.8443 (m-10) cc_final: 0.8175 (m-10) REVERT: i 56 ILE cc_start: 0.5912 (pt) cc_final: 0.5621 (tt) REVERT: i 61 MET cc_start: 0.6816 (mmm) cc_final: 0.6566 (mmt) REVERT: i 68 TYR cc_start: 0.8091 (m-80) cc_final: 0.7803 (m-80) REVERT: i 82 ASP cc_start: 0.6896 (m-30) cc_final: 0.6371 (t0) REVERT: i 84 ILE cc_start: 0.5435 (tt) cc_final: 0.4925 (pt) REVERT: i 155 LYS cc_start: 0.5975 (mmtt) cc_final: 0.5414 (mmmt) REVERT: j 17 MET cc_start: 0.5849 (ttm) cc_final: 0.5623 (ttm) REVERT: j 28 MET cc_start: 0.8826 (mtp) cc_final: 0.8516 (mtp) REVERT: j 51 LEU cc_start: 0.8308 (pp) cc_final: 0.7088 (tt) REVERT: l 14 PHE cc_start: 0.7450 (m-80) cc_final: 0.7048 (m-80) REVERT: l 53 MET cc_start: 0.8007 (mmm) cc_final: 0.6278 (tmm) REVERT: l 61 MET cc_start: 0.1642 (mtp) cc_final: 0.1330 (mtp) REVERT: m 14 PHE cc_start: 0.7553 (m-80) cc_final: 0.7240 (m-80) REVERT: n 61 MET cc_start: 0.6714 (mmm) cc_final: 0.6374 (mmm) REVERT: n 127 LEU cc_start: 0.7016 (mm) cc_final: 0.6545 (pt) REVERT: n 134 ILE cc_start: 0.6576 (tp) cc_final: 0.6040 (tp) REVERT: n 137 PHE cc_start: 0.7031 (t80) cc_final: 0.6817 (t80) REVERT: o 32 TYR cc_start: 0.8308 (t80) cc_final: 0.8009 (t80) REVERT: o 48 ARG cc_start: 0.6889 (mmm-85) cc_final: 0.6070 (mpt180) REVERT: o 54 LYS cc_start: 0.6375 (tptt) cc_final: 0.5279 (tttt) REVERT: o 70 LEU cc_start: 0.8547 (mt) cc_final: 0.8270 (mt) REVERT: o 148 VAL cc_start: 0.5247 (t) cc_final: 0.4992 (t) REVERT: 1 103 GLN cc_start: 0.8046 (tt0) cc_final: 0.7683 (tt0) REVERT: 1 232 ARG cc_start: 0.7026 (mtm180) cc_final: 0.6118 (mtm180) REVERT: 1 242 GLN cc_start: 0.7913 (tt0) cc_final: 0.7567 (tp40) REVERT: 1 261 GLN cc_start: 0.8395 (mp10) cc_final: 0.8010 (mp10) REVERT: 1 274 TYR cc_start: 0.9105 (t80) cc_final: 0.8750 (t80) REVERT: 1 279 GLU cc_start: 0.7617 (pm20) cc_final: 0.5694 (mm-30) REVERT: 1 299 ASP cc_start: 0.5598 (p0) cc_final: 0.4809 (m-30) REVERT: 1 306 MET cc_start: 0.7789 (mmm) cc_final: 0.7465 (tpt) REVERT: 1 328 TYR cc_start: 0.8118 (m-10) cc_final: 0.7846 (m-80) REVERT: 1 346 MET cc_start: 0.8043 (ttt) cc_final: 0.7578 (ttt) REVERT: 1 451 LEU cc_start: 0.7659 (mt) cc_final: 0.7034 (mp) REVERT: 1 495 LEU cc_start: 0.8007 (tp) cc_final: 0.7671 (pp) REVERT: 1 508 THR cc_start: 0.6358 (m) cc_final: 0.5913 (p) REVERT: 1 522 GLN cc_start: 0.7712 (tt0) cc_final: 0.7327 (tt0) REVERT: 1 550 MET cc_start: 0.7039 (mtp) cc_final: 0.6691 (mtp) REVERT: 1 600 ASP cc_start: 0.8860 (m-30) cc_final: 0.8617 (m-30) REVERT: 0 49 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7275 (mp0) REVERT: 0 163 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7279 (mmmt) REVERT: 0 227 LEU cc_start: 0.8538 (tp) cc_final: 0.8302 (tp) REVERT: 0 314 ASN cc_start: 0.8650 (t0) cc_final: 0.8325 (t0) REVERT: 0 356 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6848 (tm-30) REVERT: 0 358 LEU cc_start: 0.9215 (mt) cc_final: 0.8943 (mt) REVERT: 0 445 PHE cc_start: 0.6849 (p90) cc_final: 0.5515 (m-10) REVERT: 0 456 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7948 (mtmt) REVERT: 0 572 GLU cc_start: 0.6119 (tm-30) cc_final: 0.5330 (mt-10) REVERT: 2 55 ILE cc_start: 0.8296 (mm) cc_final: 0.7345 (mm) REVERT: 2 113 THR cc_start: 0.8650 (p) cc_final: 0.8104 (t) REVERT: 2 207 GLN cc_start: 0.6324 (pm20) cc_final: 0.6108 (pm20) REVERT: 2 282 ASN cc_start: 0.8195 (t0) cc_final: 0.7878 (t0) REVERT: 2 283 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8188 (pm20) REVERT: 2 387 GLU cc_start: 0.6586 (tp30) cc_final: 0.5869 (tp30) REVERT: 2 388 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6946 (mmm-85) REVERT: 3 70 GLU cc_start: 0.7382 (pt0) cc_final: 0.7098 (pt0) REVERT: 3 87 LEU cc_start: 0.8932 (mt) cc_final: 0.8250 (mt) REVERT: 3 97 GLN cc_start: 0.9042 (pt0) cc_final: 0.8680 (pt0) REVERT: 3 146 LEU cc_start: 0.8173 (tp) cc_final: 0.7850 (tp) REVERT: 3 164 ILE cc_start: 0.8699 (mt) cc_final: 0.8125 (tt) REVERT: 3 202 ILE cc_start: 0.8884 (mt) cc_final: 0.8679 (mt) REVERT: 3 205 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7318 (tm-30) REVERT: 3 206 ILE cc_start: 0.8792 (mt) cc_final: 0.8548 (mt) REVERT: 3 266 ASP cc_start: 0.9037 (m-30) cc_final: 0.8632 (m-30) REVERT: 3 361 ILE cc_start: 0.7262 (tp) cc_final: 0.6753 (tt) REVERT: 3 392 ILE cc_start: 0.8435 (mt) cc_final: 0.8127 (mt) REVERT: 3 402 MET cc_start: 0.7947 (mtp) cc_final: 0.7714 (mtp) REVERT: 3 491 MET cc_start: 0.5984 (mtt) cc_final: 0.5532 (ppp) REVERT: 4 70 GLU cc_start: 0.8100 (pt0) cc_final: 0.7342 (pt0) REVERT: 4 71 ILE cc_start: 0.9358 (mm) cc_final: 0.9139 (mm) REVERT: 4 152 ASP cc_start: 0.7810 (t0) cc_final: 0.7460 (p0) REVERT: 4 164 ILE cc_start: 0.8287 (tp) cc_final: 0.7874 (tp) REVERT: 4 290 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6678 (pt0) REVERT: 4 421 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8208 (mm-40) REVERT: 5 61 ASP cc_start: 0.7843 (p0) cc_final: 0.7632 (p0) REVERT: 5 119 LEU cc_start: 0.8819 (tp) cc_final: 0.8514 (tp) REVERT: 5 148 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7452 (tm-30) REVERT: 5 435 MET cc_start: 0.6648 (mtp) cc_final: 0.6316 (mtp) REVERT: 5 485 ARG cc_start: 0.7571 (mtp180) cc_final: 0.7073 (mmm160) REVERT: 5 490 GLU cc_start: 0.5730 (tm-30) cc_final: 0.5488 (tm-30) REVERT: 7 23 LEU cc_start: 0.7771 (tp) cc_final: 0.7425 (tp) REVERT: 7 168 ARG cc_start: 0.5816 (ttt180) cc_final: 0.5506 (ttt180) REVERT: 7 211 ILE cc_start: 0.6248 (mt) cc_final: 0.6044 (mt) REVERT: 8 50 ARG cc_start: 0.6315 (mmp80) cc_final: 0.5519 (mmp80) REVERT: 8 54 MET cc_start: 0.7623 (mpp) cc_final: 0.7202 (mpp) REVERT: 8 59 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7225 (mmmm) REVERT: 8 72 MET cc_start: 0.8125 (mtm) cc_final: 0.7629 (tpt) REVERT: 8 185 ASN cc_start: 0.8813 (p0) cc_final: 0.8476 (p0) REVERT: 9 31 ASP cc_start: 0.6533 (m-30) cc_final: 0.6293 (m-30) REVERT: 9 154 MET cc_start: 0.8122 (mmp) cc_final: 0.7691 (mmm) REVERT: 9 197 GLU cc_start: 0.8391 (mp0) cc_final: 0.7761 (mp0) REVERT: Q 56 TYR cc_start: 0.5280 (t80) cc_final: 0.4463 (t80) REVERT: Q 125 TYR cc_start: 0.7834 (m-10) cc_final: 0.7633 (m-80) REVERT: Q 132 MET cc_start: 0.7052 (mtt) cc_final: 0.6269 (mtp) REVERT: Q 201 ASP cc_start: 0.8499 (t70) cc_final: 0.8288 (t70) REVERT: R 58 LYS cc_start: 0.6263 (mttt) cc_final: 0.6002 (mmmt) REVERT: R 79 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8239 (ttp80) REVERT: T 16 LYS cc_start: 0.8215 (mttt) cc_final: 0.7054 (tttp) REVERT: T 34 LYS cc_start: 0.8238 (tppt) cc_final: 0.7553 (mttt) REVERT: T 102 MET cc_start: 0.8344 (ttp) cc_final: 0.7976 (ttt) REVERT: T 110 VAL cc_start: 0.8684 (t) cc_final: 0.8345 (t) REVERT: V 47 TYR cc_start: 0.5814 (m-10) cc_final: 0.5553 (m-10) REVERT: X 51 THR cc_start: 0.8065 (m) cc_final: 0.7438 (t) REVERT: 6 66 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7157 (mt-10) REVERT: 6 82 ASP cc_start: 0.5329 (t0) cc_final: 0.4860 (m-30) REVERT: 6 109 MET cc_start: 0.7461 (tmm) cc_final: 0.6201 (mtm) REVERT: 6 292 ILE cc_start: 0.7727 (mt) cc_final: 0.7461 (tt) REVERT: 6 298 LYS cc_start: 0.6657 (mmtt) cc_final: 0.6377 (mtmt) REVERT: 6 335 LEU cc_start: 0.6193 (pp) cc_final: 0.5927 (pp) REVERT: U 41 MET cc_start: 0.0026 (tpp) cc_final: -0.0435 (tpp) REVERT: U 65 MET cc_start: 0.6774 (ppp) cc_final: 0.6386 (ppp) REVERT: U 96 MET cc_start: 0.1342 (ptm) cc_final: 0.0432 (mmt) REVERT: U 127 LEU cc_start: 0.6054 (mt) cc_final: 0.5741 (pt) REVERT: U 147 LYS cc_start: 0.6247 (mmmm) cc_final: 0.5756 (tptt) REVERT: U 156 MET cc_start: 0.6724 (ptm) cc_final: 0.6349 (ptt) REVERT: U 163 TYR cc_start: 0.6943 (t80) cc_final: 0.6667 (t80) REVERT: U 165 PHE cc_start: 0.7486 (m-80) cc_final: 0.7085 (m-80) REVERT: U 234 LYS cc_start: 0.6014 (tttt) cc_final: 0.5480 (mptt) REVERT: U 256 MET cc_start: 0.6065 (mmm) cc_final: 0.5820 (mmm) REVERT: U 321 LEU cc_start: 0.8139 (mm) cc_final: 0.7820 (mt) REVERT: U 324 GLN cc_start: 0.7056 (mp10) cc_final: 0.6709 (mp-120) REVERT: U 364 LEU cc_start: 0.3854 (mp) cc_final: 0.3578 (mp) REVERT: U 434 LYS cc_start: 0.5949 (pttm) cc_final: 0.5346 (tttp) REVERT: U 440 HIS cc_start: 0.6121 (m-70) cc_final: 0.5544 (m-70) REVERT: d 38 GLN cc_start: 0.6455 (mm-40) cc_final: 0.5513 (mt0) REVERT: d 75 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7768 (mmmt) REVERT: d 84 HIS cc_start: 0.7959 (t-90) cc_final: 0.7585 (t-170) REVERT: d 85 MET cc_start: 0.7819 (tmm) cc_final: 0.7469 (tmm) REVERT: d 128 LYS cc_start: 0.8571 (mmpt) cc_final: 0.8308 (mptt) REVERT: d 165 GLN cc_start: 0.7081 (tt0) cc_final: 0.6045 (tp40) REVERT: d 176 MET cc_start: 0.6834 (mtm) cc_final: 0.6296 (ptp) REVERT: d 189 TYR cc_start: 0.6657 (t80) cc_final: 0.6102 (t80) REVERT: d 262 GLU cc_start: 0.6525 (tp30) cc_final: 0.5621 (mt-10) REVERT: d 346 ASN cc_start: 0.7000 (t0) cc_final: 0.6662 (t0) REVERT: d 349 PRO cc_start: 0.7685 (Cg_endo) cc_final: 0.7332 (Cg_exo) REVERT: a 60 GLU cc_start: 0.7815 (tp30) cc_final: 0.7588 (mm-30) REVERT: a 61 MET cc_start: 0.7858 (mtp) cc_final: 0.7495 (mtt) REVERT: a 66 ARG cc_start: 0.8009 (mpt180) cc_final: 0.7752 (mmt-90) REVERT: a 290 LEU cc_start: 0.8015 (mt) cc_final: 0.7433 (tt) REVERT: a 316 LEU cc_start: 0.8107 (mm) cc_final: 0.7863 (tp) REVERT: a 329 GLU cc_start: 0.7412 (tt0) cc_final: 0.6324 (mp0) REVERT: a 345 ARG cc_start: 0.7088 (ptt90) cc_final: 0.6580 (mmt180) REVERT: a 383 ASN cc_start: 0.8746 (t0) cc_final: 0.8386 (m-40) REVERT: a 470 ILE cc_start: 0.7071 (mt) cc_final: 0.6864 (mt) REVERT: a 486 TRP cc_start: 0.4212 (m100) cc_final: 0.3910 (m100) REVERT: a 546 LYS cc_start: 0.8135 (mttt) cc_final: 0.7811 (ptpt) REVERT: a 565 PHE cc_start: 0.7186 (m-80) cc_final: 0.6636 (m-80) REVERT: a 610 SER cc_start: 0.8088 (t) cc_final: 0.7729 (m) REVERT: a 740 TYR cc_start: 0.8419 (m-80) cc_final: 0.7712 (m-80) REVERT: a 769 ARG cc_start: 0.5594 (mtm180) cc_final: 0.4908 (mmt180) REVERT: a 831 HIS cc_start: 0.6534 (p90) cc_final: 0.6092 (p-80) REVERT: e 12 ILE cc_start: 0.6644 (pt) cc_final: 0.6166 (pt) REVERT: e 40 MET cc_start: 0.6499 (tmm) cc_final: 0.6014 (tmm) REVERT: e 52 TRP cc_start: 0.7179 (t-100) cc_final: 0.6850 (t-100) REVERT: f 29 LEU cc_start: 0.8374 (tp) cc_final: 0.8147 (tp) REVERT: c 332 TYR cc_start: 0.5253 (m-80) cc_final: 0.4872 (m-80) REVERT: c 363 PHE cc_start: 0.6182 (t80) cc_final: 0.5465 (t80) REVERT: c 376 ASN cc_start: 0.7414 (m-40) cc_final: 0.7183 (m110) REVERT: c 392 ASN cc_start: 0.7364 (t0) cc_final: 0.6360 (t0) REVERT: c 394 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7164 (mm110) REVERT: c 421 MET cc_start: 0.5502 (mpp) cc_final: 0.5146 (ptp) outliers start: 8 outliers final: 2 residues processed: 1997 average time/residue: 0.6038 time to fit residues: 2051.9737 Evaluate side-chains 1670 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1668 time to evaluate : 5.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 558 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 706 optimal weight: 0.9990 chunk 542 optimal weight: 6.9990 chunk 800 optimal weight: 3.9990 chunk 256 optimal weight: 0.0040 chunk 103 optimal weight: 3.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 124 GLN k 123 GLN l 92 GLN o 123 GLN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 242 GLN 0 573 HIS ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 441 GLN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 161 GLN 5 209 GLN 5 350 GLN 5 482 GLN 9 113 GLN 9 126 GLN Q 77 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN V 59 GLN V 113 ASN 6 116 GLN 6 296 HIS U 442 HIS ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 ASN a 350 HIS a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 ASN c 394 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.172557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143280 restraints weight = 149062.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146116 restraints weight = 89751.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148098 restraints weight = 59966.332| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 66820 Z= 0.181 Angle : 0.576 11.632 90305 Z= 0.301 Chirality : 0.041 0.188 10236 Planarity : 0.004 0.140 11580 Dihedral : 4.460 78.379 9108 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 0.08 % Allowed : 2.52 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.70 (0.09), residues: 8319 helix: 1.67 (0.08), residues: 4679 sheet: -0.23 (0.19), residues: 726 loop : -1.38 (0.12), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP U 376 HIS 0.016 0.001 HIS a 350 PHE 0.064 0.002 PHE c 433 TYR 0.038 0.001 TYR o 144 ARG 0.011 0.000 ARG a 806 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1989 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1983 time to evaluate : 5.557 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 105 ILE cc_start: 0.8344 (tp) cc_final: 0.8129 (tp) REVERT: b 146 LEU cc_start: 0.8667 (mm) cc_final: 0.7706 (mt) REVERT: b 168 GLN cc_start: 0.6885 (pp30) cc_final: 0.6632 (pp30) REVERT: g 61 MET cc_start: 0.8205 (mmm) cc_final: 0.7933 (mmm) REVERT: g 89 SER cc_start: 0.6801 (p) cc_final: 0.4595 (t) REVERT: h 28 MET cc_start: 0.6781 (mmm) cc_final: 0.6322 (mmp) REVERT: h 57 ILE cc_start: 0.7362 (mm) cc_final: 0.6850 (mm) REVERT: h 61 MET cc_start: 0.8415 (mtp) cc_final: 0.7828 (mmm) REVERT: h 131 MET cc_start: 0.7317 (ttp) cc_final: 0.6947 (ttp) REVERT: h 144 TYR cc_start: 0.8458 (m-10) cc_final: 0.8226 (m-10) REVERT: i 23 MET cc_start: 0.6356 (ttm) cc_final: 0.5859 (ttm) REVERT: i 56 ILE cc_start: 0.6011 (pt) cc_final: 0.5722 (tt) REVERT: i 61 MET cc_start: 0.6649 (mmm) cc_final: 0.6404 (mmt) REVERT: i 68 TYR cc_start: 0.8113 (m-80) cc_final: 0.7788 (m-80) REVERT: i 84 ILE cc_start: 0.5532 (tt) cc_final: 0.5090 (pt) REVERT: i 155 LYS cc_start: 0.6021 (mmtt) cc_final: 0.5425 (mmmt) REVERT: j 28 MET cc_start: 0.8777 (mtp) cc_final: 0.8486 (mtp) REVERT: j 51 LEU cc_start: 0.8214 (pp) cc_final: 0.7046 (tt) REVERT: k 28 MET cc_start: 0.5925 (ttt) cc_final: 0.5625 (mtp) REVERT: l 14 PHE cc_start: 0.7387 (m-80) cc_final: 0.7001 (m-80) REVERT: l 44 MET cc_start: 0.6468 (tpp) cc_final: 0.5660 (mmt) REVERT: l 53 MET cc_start: 0.8091 (mmm) cc_final: 0.6477 (tmm) REVERT: l 61 MET cc_start: 0.1751 (mtp) cc_final: 0.1293 (mtp) REVERT: l 92 GLN cc_start: 0.7314 (mm110) cc_final: 0.7101 (mm-40) REVERT: l 131 MET cc_start: 0.7418 (ttp) cc_final: 0.7013 (ttp) REVERT: n 24 VAL cc_start: 0.6344 (m) cc_final: 0.6099 (m) REVERT: n 61 MET cc_start: 0.6678 (mmm) cc_final: 0.6263 (mmm) REVERT: n 70 LEU cc_start: 0.7444 (mt) cc_final: 0.7170 (mt) REVERT: o 32 TYR cc_start: 0.8296 (t80) cc_final: 0.7987 (t80) REVERT: o 48 ARG cc_start: 0.6837 (mmm-85) cc_final: 0.6007 (mpt180) REVERT: o 54 LYS cc_start: 0.6546 (tptt) cc_final: 0.5465 (tttt) REVERT: o 70 LEU cc_start: 0.8622 (mt) cc_final: 0.7915 (mt) REVERT: o 144 TYR cc_start: 0.7945 (m-80) cc_final: 0.7494 (m-80) REVERT: 1 53 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7516 (mt-10) REVERT: 1 103 GLN cc_start: 0.8228 (tt0) cc_final: 0.7746 (tt0) REVERT: 1 242 GLN cc_start: 0.7869 (tt0) cc_final: 0.7471 (tt0) REVERT: 1 261 GLN cc_start: 0.8161 (mp10) cc_final: 0.7828 (mp10) REVERT: 1 274 TYR cc_start: 0.9061 (t80) cc_final: 0.8728 (t80) REVERT: 1 279 GLU cc_start: 0.7642 (pm20) cc_final: 0.5640 (mm-30) REVERT: 1 299 ASP cc_start: 0.5590 (p0) cc_final: 0.5104 (m-30) REVERT: 1 306 MET cc_start: 0.7869 (mmm) cc_final: 0.7606 (tpt) REVERT: 1 328 TYR cc_start: 0.8003 (m-10) cc_final: 0.7684 (m-80) REVERT: 1 346 MET cc_start: 0.7722 (ttt) cc_final: 0.7416 (ttt) REVERT: 1 451 LEU cc_start: 0.7703 (mt) cc_final: 0.7068 (mp) REVERT: 1 495 LEU cc_start: 0.8012 (tp) cc_final: 0.7686 (pp) REVERT: 1 508 THR cc_start: 0.6291 (m) cc_final: 0.5941 (p) REVERT: 1 536 LYS cc_start: 0.8134 (tttt) cc_final: 0.7890 (tttt) REVERT: 1 541 LEU cc_start: 0.8638 (tt) cc_final: 0.8353 (tt) REVERT: 1 600 ASP cc_start: 0.8890 (m-30) cc_final: 0.8652 (m-30) REVERT: 0 49 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7384 (mp0) REVERT: 0 53 GLU cc_start: 0.8189 (tp30) cc_final: 0.7896 (tp30) REVERT: 0 163 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7290 (mmmt) REVERT: 0 314 ASN cc_start: 0.8655 (t0) cc_final: 0.8405 (t0) REVERT: 0 356 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6974 (tm-30) REVERT: 0 358 LEU cc_start: 0.9269 (mt) cc_final: 0.9028 (mt) REVERT: 0 445 PHE cc_start: 0.6813 (p90) cc_final: 0.5424 (m-10) REVERT: 0 456 LYS cc_start: 0.8415 (mmpt) cc_final: 0.7983 (mtmt) REVERT: 0 572 GLU cc_start: 0.5963 (tm-30) cc_final: 0.5175 (mt-10) REVERT: 2 34 MET cc_start: 0.7327 (tmm) cc_final: 0.6856 (tmm) REVERT: 2 55 ILE cc_start: 0.8253 (mm) cc_final: 0.7364 (mm) REVERT: 2 113 THR cc_start: 0.8674 (p) cc_final: 0.8145 (t) REVERT: 2 171 ARG cc_start: 0.7862 (tmm160) cc_final: 0.7602 (tmm160) REVERT: 2 282 ASN cc_start: 0.8133 (t0) cc_final: 0.7870 (t0) REVERT: 3 70 GLU cc_start: 0.7243 (pt0) cc_final: 0.6993 (pt0) REVERT: 3 146 LEU cc_start: 0.8168 (tp) cc_final: 0.7735 (tp) REVERT: 3 202 ILE cc_start: 0.8904 (mt) cc_final: 0.8687 (mt) REVERT: 3 205 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7242 (tm-30) REVERT: 3 206 ILE cc_start: 0.8725 (mt) cc_final: 0.8471 (mt) REVERT: 3 337 ARG cc_start: 0.7420 (mtp85) cc_final: 0.7164 (mtp85) REVERT: 3 361 ILE cc_start: 0.7254 (tp) cc_final: 0.6732 (tt) REVERT: 3 392 ILE cc_start: 0.8579 (mt) cc_final: 0.8315 (mt) REVERT: 3 436 LYS cc_start: 0.6893 (tttp) cc_final: 0.6672 (tttp) REVERT: 3 491 MET cc_start: 0.6149 (mtt) cc_final: 0.5670 (ppp) REVERT: 4 70 GLU cc_start: 0.8028 (pt0) cc_final: 0.7336 (pt0) REVERT: 4 113 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7814 (tm-30) REVERT: 4 152 ASP cc_start: 0.7761 (t0) cc_final: 0.7339 (p0) REVERT: 4 248 PHE cc_start: 0.7390 (m-80) cc_final: 0.7102 (m-80) REVERT: 4 290 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6567 (pt0) REVERT: 4 421 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8281 (mm-40) REVERT: 5 100 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6945 (tm-30) REVERT: 5 270 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7395 (mm-30) REVERT: 5 382 GLN cc_start: 0.7402 (mp10) cc_final: 0.7114 (mp10) REVERT: 5 435 MET cc_start: 0.6395 (mtp) cc_final: 0.6135 (mtp) REVERT: 5 478 ASP cc_start: 0.8102 (m-30) cc_final: 0.7863 (m-30) REVERT: 5 485 ARG cc_start: 0.7688 (mtp180) cc_final: 0.6986 (mmm160) REVERT: 7 23 LEU cc_start: 0.7744 (tp) cc_final: 0.7343 (tp) REVERT: 7 168 ARG cc_start: 0.5776 (ttt180) cc_final: 0.5540 (ttt180) REVERT: 7 190 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7890 (mm-30) REVERT: 8 72 MET cc_start: 0.8172 (mtm) cc_final: 0.7678 (tpt) REVERT: 8 185 ASN cc_start: 0.8807 (p0) cc_final: 0.8391 (p0) REVERT: 9 31 ASP cc_start: 0.6447 (m-30) cc_final: 0.6230 (m-30) REVERT: 9 54 MET cc_start: 0.7636 (mmp) cc_final: 0.6570 (mmm) REVERT: 9 57 TYR cc_start: 0.6198 (t80) cc_final: 0.5900 (t80) REVERT: 9 154 MET cc_start: 0.8153 (mmp) cc_final: 0.7727 (mmm) REVERT: 9 197 GLU cc_start: 0.8323 (mp0) cc_final: 0.7682 (mp0) REVERT: 9 207 MET cc_start: 0.7141 (mmp) cc_final: 0.6655 (mmt) REVERT: Q 56 TYR cc_start: 0.5216 (t80) cc_final: 0.4771 (t80) REVERT: Q 97 GLU cc_start: 0.7684 (pp20) cc_final: 0.7269 (tm-30) REVERT: Q 125 TYR cc_start: 0.7769 (m-10) cc_final: 0.7488 (m-80) REVERT: Q 132 MET cc_start: 0.7022 (mtt) cc_final: 0.6242 (mtp) REVERT: Q 201 ASP cc_start: 0.8499 (t70) cc_final: 0.8234 (t70) REVERT: R 58 LYS cc_start: 0.6208 (mttt) cc_final: 0.5941 (mmmt) REVERT: R 96 LEU cc_start: 0.9085 (tp) cc_final: 0.8847 (tp) REVERT: T 16 LYS cc_start: 0.8171 (mttt) cc_final: 0.6999 (tttp) REVERT: T 34 LYS cc_start: 0.8220 (tppt) cc_final: 0.7559 (mttt) REVERT: V 47 TYR cc_start: 0.5728 (m-10) cc_final: 0.5453 (m-10) REVERT: X 27 GLU cc_start: 0.7519 (pp20) cc_final: 0.7136 (pp20) REVERT: X 51 THR cc_start: 0.8122 (m) cc_final: 0.7870 (t) REVERT: 6 66 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7075 (mt-10) REVERT: 6 82 ASP cc_start: 0.5708 (t0) cc_final: 0.5219 (m-30) REVERT: 6 109 MET cc_start: 0.7516 (tmm) cc_final: 0.6357 (mtm) REVERT: 6 301 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6568 (ttm170) REVERT: 6 319 MET cc_start: 0.4920 (ttp) cc_final: 0.4707 (ttp) REVERT: 6 335 LEU cc_start: 0.6215 (pp) cc_final: 0.5995 (pp) REVERT: U 65 MET cc_start: 0.6641 (ppp) cc_final: 0.6288 (ppp) REVERT: U 96 MET cc_start: 0.1516 (ptm) cc_final: 0.0673 (mmt) REVERT: U 127 LEU cc_start: 0.6143 (mt) cc_final: 0.5871 (pt) REVERT: U 147 LYS cc_start: 0.6183 (mmmm) cc_final: 0.5732 (tptt) REVERT: U 156 MET cc_start: 0.6692 (ptm) cc_final: 0.6306 (ptt) REVERT: U 163 TYR cc_start: 0.6833 (t80) cc_final: 0.6628 (t80) REVERT: U 218 TRP cc_start: 0.4991 (t-100) cc_final: 0.4746 (t-100) REVERT: U 234 LYS cc_start: 0.6132 (tttt) cc_final: 0.5562 (mptt) REVERT: U 256 MET cc_start: 0.5983 (mmm) cc_final: 0.5705 (mmm) REVERT: U 293 LEU cc_start: 0.8395 (mm) cc_final: 0.8038 (mp) REVERT: U 321 LEU cc_start: 0.8164 (mm) cc_final: 0.7927 (mt) REVERT: U 324 GLN cc_start: 0.7072 (mp10) cc_final: 0.6701 (mp-120) REVERT: U 364 LEU cc_start: 0.3432 (mp) cc_final: 0.3149 (mp) REVERT: U 434 LYS cc_start: 0.5943 (pttm) cc_final: 0.5366 (tttp) REVERT: U 440 HIS cc_start: 0.6155 (m-70) cc_final: 0.5558 (m-70) REVERT: d 38 GLN cc_start: 0.6337 (mm-40) cc_final: 0.5509 (mt0) REVERT: d 75 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7926 (mmmt) REVERT: d 128 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8330 (mptt) REVERT: d 189 TYR cc_start: 0.6760 (t80) cc_final: 0.6126 (t80) REVERT: d 262 GLU cc_start: 0.6525 (tp30) cc_final: 0.5713 (mt-10) REVERT: d 346 ASN cc_start: 0.6873 (t0) cc_final: 0.6535 (t0) REVERT: d 349 PRO cc_start: 0.7684 (Cg_endo) cc_final: 0.7322 (Cg_exo) REVERT: a 60 GLU cc_start: 0.7807 (tp30) cc_final: 0.7546 (mm-30) REVERT: a 61 MET cc_start: 0.7620 (mtp) cc_final: 0.7286 (mtt) REVERT: a 111 ILE cc_start: 0.8704 (tp) cc_final: 0.8484 (tt) REVERT: a 124 GLU cc_start: 0.6413 (tp30) cc_final: 0.5157 (pp20) REVERT: a 125 LEU cc_start: 0.6586 (mt) cc_final: 0.5994 (mt) REVERT: a 128 LEU cc_start: 0.8158 (tp) cc_final: 0.7943 (tp) REVERT: a 290 LEU cc_start: 0.7973 (mt) cc_final: 0.7507 (tt) REVERT: a 329 GLU cc_start: 0.7435 (tt0) cc_final: 0.6332 (mp0) REVERT: a 383 ASN cc_start: 0.8746 (t0) cc_final: 0.8359 (m-40) REVERT: a 470 ILE cc_start: 0.6986 (mt) cc_final: 0.6779 (mt) REVERT: a 565 PHE cc_start: 0.7290 (m-80) cc_final: 0.6768 (m-80) REVERT: a 610 SER cc_start: 0.8118 (t) cc_final: 0.7771 (m) REVERT: a 623 MET cc_start: 0.8557 (ttp) cc_final: 0.8223 (tpp) REVERT: a 635 MET cc_start: 0.4647 (mmt) cc_final: 0.3877 (tpt) REVERT: a 740 TYR cc_start: 0.8475 (m-80) cc_final: 0.7778 (m-80) REVERT: a 769 ARG cc_start: 0.5654 (mtm180) cc_final: 0.4947 (mmt180) REVERT: a 831 HIS cc_start: 0.6737 (p90) cc_final: 0.6213 (p-80) REVERT: e 40 MET cc_start: 0.6470 (tmm) cc_final: 0.5966 (tmm) REVERT: e 52 TRP cc_start: 0.7129 (t-100) cc_final: 0.6860 (t-100) REVERT: e 57 LEU cc_start: 0.7896 (mt) cc_final: 0.7573 (mt) REVERT: c 363 PHE cc_start: 0.6460 (t80) cc_final: 0.6027 (t80) REVERT: c 374 LYS cc_start: 0.6404 (mtpp) cc_final: 0.6100 (mtpp) REVERT: c 376 ASN cc_start: 0.7432 (m-40) cc_final: 0.7140 (m110) REVERT: c 392 ASN cc_start: 0.7310 (t0) cc_final: 0.6577 (t0) REVERT: c 429 MET cc_start: 0.7870 (mmm) cc_final: 0.7560 (mmm) outliers start: 6 outliers final: 1 residues processed: 1987 average time/residue: 0.5939 time to fit residues: 2015.5085 Evaluate side-chains 1648 residues out of total 7059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1647 time to evaluate : 5.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 485 optimal weight: 4.9990 chunk 530 optimal weight: 0.9990 chunk 434 optimal weight: 0.0470 chunk 221 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 643 optimal weight: 2.9990 chunk 639 optimal weight: 6.9990 chunk 770 optimal weight: 0.9980 chunk 581 optimal weight: 9.9990 chunk 749 optimal weight: 0.4980 chunk 37 optimal weight: 20.0000 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 124 GLN k 123 GLN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 573 HIS ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 441 GLN 3 97 GLN 4 156 GLN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 206 GLN ** Q 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN V 56 GLN V 113 ASN 6 116 GLN 6 296 HIS U 259 HIS U 443 HIS U 451 ASN d 13 ASN a 285 HIS a 494 GLN a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.173856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145132 restraints weight = 146987.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148297 restraints weight = 89846.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150278 restraints weight = 58749.378| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2722 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: