Starting phenix.real_space_refine on Sat Sep 28 04:20:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/09_2024/3j7a_2660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/09_2024/3j7a_2660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/09_2024/3j7a_2660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/09_2024/3j7a_2660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/09_2024/3j7a_2660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/09_2024/3j7a_2660.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1681 5.49 5 Mg 67 5.21 5 S 141 5.16 5 C 37011 2.51 5 N 12467 2.21 5 O 17498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 68866 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 34277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1608, 34277 Classifications: {'RNA': 1608} Modifications used: {'rna2p_pur': 137, 'rna2p_pyr': 92, 'rna3p_pur': 738, 'rna3p_pyr': 641} Link IDs: {'rna2p': 228, 'rna3p': 1379} Chain breaks: 22 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1713 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1228 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 3 Chain: "E" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1508 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2061 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1757 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1424 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1528 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "K" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1392 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 2 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1098 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "N" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 772 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "O" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 686 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "P" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 953 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "Q" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "R" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 746 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain breaks: 2 Chain: "S" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1042 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 404 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "U" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain: "V" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1206 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain breaks: 1 Chain: "W" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Chain: "X" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain breaks: 1 Chain: "Y" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1266 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "Z" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 556 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "1" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 981 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 320 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 2 Chain: "3" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 781 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "4" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 586 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "5" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 451 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 345 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "7" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1571 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 62} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 102 Unusual residues: {' MG': 67, '34G': 1} Classifications: {'undetermined': 68} Link IDs: {None: 67} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57636 SG CYS T 19 55.402 88.444 75.019 1.00119.06 S ATOM 57660 SG CYS T 22 58.256 92.212 74.720 1.00187.39 S ATOM 57784 SG CYS T 37 58.819 87.359 76.500 1.00132.78 S ATOM 57810 SG CYS T 40 58.234 90.449 77.786 1.00141.95 S Time building chain proxies: 27.24, per 1000 atoms: 0.40 Number of scatterers: 68866 At special positions: 0 Unit cell: (218.42, 226.46, 192.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 141 16.00 P 1681 15.00 Mg 67 11.99 O 17498 8.00 N 12467 7.00 C 37011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 3 26 " - pdb=" SG CYS 3 77 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.86 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 100 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 40 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 37 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 22 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 19 " Number of angles added : 6 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 42 sheets defined 39.3% alpha, 13.4% beta 482 base pairs and 897 stacking pairs defined. Time for finding SS restraints: 23.74 Creating SS restraints... Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.562A pdb=" N GLN B 79 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.939A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.624A pdb=" N GLN B 149 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR B 150 " --> pdb=" O GLN B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 157 through 179 removed outlier: 4.374A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.542A pdb=" N LYS B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.544A pdb=" N ARG C 35 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 67 removed outlier: 3.530A pdb=" N ILE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.586A pdb=" N VAL C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 185 Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 66 through 78 Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.838A pdb=" N GLN D 102 " --> pdb=" O CYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'D' and resid 162 through 168 removed outlier: 3.684A pdb=" N LYS D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 35 Processing helix chain 'E' and resid 39 through 62 removed outlier: 3.538A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 100 through 107 removed outlier: 3.735A pdb=" N LEU E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.538A pdb=" N GLY E 165 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 166 " --> pdb=" O PRO E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 162 through 166' Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 37 through 41 removed outlier: 3.528A pdb=" N SER F 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 57 through 67 Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.582A pdb=" N LYS F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 257 Processing helix chain 'G' and resid 45 through 53 removed outlier: 3.690A pdb=" N GLU G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 65 removed outlier: 3.896A pdb=" N ILE G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 removed outlier: 4.187A pdb=" N ILE G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 193 through 204 Processing helix chain 'G' and resid 218 through 233 Processing helix chain 'G' and resid 238 through 243 removed outlier: 3.817A pdb=" N TRP G 242 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS G 243 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 255 through 260 Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.846A pdb=" N LEU H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 180 through 213 removed outlier: 3.806A pdb=" N LEU H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 30 Processing helix chain 'I' and resid 52 through 56 Processing helix chain 'I' and resid 58 through 68 Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 76 through 94 Processing helix chain 'I' and resid 98 through 111 removed outlier: 3.854A pdb=" N GLY I 111 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 154 Processing helix chain 'I' and resid 159 through 174 Processing helix chain 'I' and resid 178 through 195 removed outlier: 3.746A pdb=" N LYS I 182 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 31 Processing helix chain 'J' and resid 66 through 72 Processing helix chain 'J' and resid 76 through 88 Processing helix chain 'J' and resid 118 through 131 Processing helix chain 'J' and resid 164 through 181 Processing helix chain 'K' and resid 5 through 21 Processing helix chain 'K' and resid 31 through 44 Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.617A pdb=" N ILE K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 120 Processing helix chain 'L' and resid 87 through 94 removed outlier: 3.820A pdb=" N VAL L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 117 removed outlier: 3.818A pdb=" N THR L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 178 removed outlier: 3.547A pdb=" N GLN L 178 " --> pdb=" O GLU L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'L' and resid 202 through 213 Processing helix chain 'M' and resid 45 through 57 removed outlier: 4.044A pdb=" N VAL M 49 " --> pdb=" O LEU M 45 " (cutoff:3.500A) Proline residue: M 52 - end of helix Processing helix chain 'M' and resid 75 through 98 removed outlier: 3.529A pdb=" N ILE M 91 " --> pdb=" O GLY M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 114 removed outlier: 3.859A pdb=" N LYS M 103 " --> pdb=" O ASP M 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 44 removed outlier: 3.505A pdb=" N GLU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 102 Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 49 through 64 Processing helix chain 'O' and resid 80 through 89 removed outlier: 4.151A pdb=" N GLU O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 123 removed outlier: 4.225A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 24 removed outlier: 4.433A pdb=" N TRP Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 34 Processing helix chain 'Q' and resid 35 through 40 removed outlier: 3.819A pdb=" N LYS Q 39 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 138 Processing helix chain 'R' and resid 23 through 36 removed outlier: 4.191A pdb=" N LYS R 27 " --> pdb=" O THR R 23 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 50 Processing helix chain 'R' and resid 66 through 78 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'R' and resid 128 through 135 removed outlier: 3.701A pdb=" N SER R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 34 Processing helix chain 'S' and resid 40 through 51 Processing helix chain 'S' and resid 57 through 61 removed outlier: 3.729A pdb=" N GLU S 60 " --> pdb=" O ARG S 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU S 61 " --> pdb=" O ALA S 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 57 through 61' Processing helix chain 'S' and resid 62 through 74 Processing helix chain 'S' and resid 101 through 120 removed outlier: 3.825A pdb=" N ASP S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'T' and resid 30 through 34 removed outlier: 3.839A pdb=" N ASN T 33 " --> pdb=" O ARG T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 49 removed outlier: 5.230A pdb=" N ASP T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE T 47 " --> pdb=" O GLU T 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 43 Processing helix chain 'U' and resid 46 through 57 Processing helix chain 'U' and resid 62 through 67 Processing helix chain 'U' and resid 70 through 79 Processing helix chain 'U' and resid 85 through 105 Processing helix chain 'U' and resid 108 through 132 Processing helix chain 'U' and resid 145 through 150 removed outlier: 3.917A pdb=" N LEU U 149 " --> pdb=" O THR U 145 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE U 150 " --> pdb=" O ALA U 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 145 through 150' Processing helix chain 'V' and resid 48 through 53 removed outlier: 3.508A pdb=" N LYS V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 157 Processing helix chain 'W' and resid 6 through 19 removed outlier: 4.215A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU W 18 " --> pdb=" O ARG W 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 39 Processing helix chain 'W' and resid 44 through 61 Processing helix chain 'W' and resid 71 through 83 removed outlier: 3.999A pdb=" N GLU W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 110 Processing helix chain 'X' and resid 22 through 28 Processing helix chain 'X' and resid 29 through 37 Processing helix chain 'X' and resid 38 through 48 Processing helix chain 'X' and resid 49 through 67 removed outlier: 4.128A pdb=" N ALA X 53 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS X 54 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 90 removed outlier: 3.928A pdb=" N VAL X 90 " --> pdb=" O PRO X 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 33 through 49 Processing helix chain 'Y' and resid 55 through 60 removed outlier: 3.680A pdb=" N THR Y 58 " --> pdb=" O LYS Y 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Y 60 " --> pdb=" O CYS Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 67 removed outlier: 3.738A pdb=" N LYS Y 67 " --> pdb=" O LYS Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 90 removed outlier: 3.532A pdb=" N ILE Y 78 " --> pdb=" O ASP Y 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 102 removed outlier: 3.747A pdb=" N LEU Y 98 " --> pdb=" O GLY Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 134 removed outlier: 4.270A pdb=" N LEU Y 123 " --> pdb=" O SER Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 168 Processing helix chain 'Z' and resid 25 through 29 removed outlier: 3.648A pdb=" N GLU Z 28 " --> pdb=" O PRO Z 25 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS Z 29 " --> pdb=" O ALA Z 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 25 through 29' Processing helix chain 'Z' and resid 55 through 62 removed outlier: 3.545A pdb=" N ARG Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 75 Processing helix chain '1' and resid 36 through 48 removed outlier: 3.509A pdb=" N VAL 1 40 " --> pdb=" O ALA 1 36 " (cutoff:3.500A) Processing helix chain '1' and resid 52 through 54 No H-bonds generated for 'chain '1' and resid 52 through 54' Processing helix chain '1' and resid 79 through 86 Processing helix chain '1' and resid 88 through 96 Processing helix chain '1' and resid 107 through 114 Processing helix chain '2' and resid 60 through 69 Processing helix chain '2' and resid 71 through 84 Processing helix chain '3' and resid 47 through 57 Processing helix chain '3' and resid 74 through 81 Processing helix chain '3' and resid 88 through 94 removed outlier: 4.056A pdb=" N ARG 3 93 " --> pdb=" O ARG 3 89 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL 3 94 " --> pdb=" O GLU 3 90 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 18 removed outlier: 3.723A pdb=" N ASN 6 16 " --> pdb=" O GLY 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 32 through 44 Processing sheet with id=A, first strand: chain 'B' and resid 42 through 48 removed outlier: 4.194A pdb=" N GLY B 44 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.475A pdb=" N LYS B 85 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 126 through 128 removed outlier: 6.812A pdb=" N HIS B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'C' and resid 24 through 25 removed outlier: 7.060A pdb=" N ILE C 47 " --> pdb=" O TYR C 38 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.398A pdb=" N LEU C 121 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'D' and resid 151 through 154 removed outlier: 3.651A pdb=" N GLY D 134 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'E' and resid 139 through 140 removed outlier: 4.191A pdb=" N GLN E 139 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.389A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.056A pdb=" N LYS F 75 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.508A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR F 159 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N HIS F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG F 161 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'F' and resid 192 through 193 Processing sheet with id=L, first strand: chain 'F' and resid 197 through 198 Processing sheet with id=M, first strand: chain 'G' and resid 89 through 99 removed outlier: 5.184A pdb=" N ASP G 90 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY G 117 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL G 92 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA G 115 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS G 94 " --> pdb=" O PHE G 113 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'G' and resid 170 through 174 Processing sheet with id=O, first strand: chain 'H' and resid 12 through 17 removed outlier: 7.867A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER H 6 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'H' and resid 63 through 64 Processing sheet with id=Q, first strand: chain 'I' and resid 114 through 116 Processing sheet with id=R, first strand: chain 'J' and resid 46 through 51 removed outlier: 7.042A pdb=" N LYS J 58 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N VAL J 93 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE J 60 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL J 95 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE J 62 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS J 97 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE J 64 " --> pdb=" O LYS J 97 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'J' and resid 136 through 138 removed outlier: 6.982A pdb=" N MET J 154 " --> pdb=" O ILE J 137 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'J' and resid 184 through 185 removed outlier: 7.763A pdb=" N VAL J 185 " --> pdb=" O ARG J 149 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE J 151 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG J 140 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER K 49 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL K 62 " --> pdb=" O GLU K 51 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'K' and resid 72 through 74 removed outlier: 6.709A pdb=" N ILE K 103 " --> pdb=" O LEU K 126 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE K 128 " --> pdb=" O HIS K 101 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS K 101 " --> pdb=" O PHE K 128 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'L' and resid 37 through 38 removed outlier: 6.738A pdb=" N GLN L 42 " --> pdb=" O ILE L 58 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'L' and resid 72 through 75 removed outlier: 6.262A pdb=" N SER L 64 " --> pdb=" O GLY L 197 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE L 199 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER L 66 " --> pdb=" O ILE L 199 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE L 101 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L 80 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP L 105 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE L 78 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'M' and resid 7 through 11 Processing sheet with id=Y, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=Z, first strand: chain 'N' and resid 59 through 65 removed outlier: 3.513A pdb=" N THR N 64 " --> pdb=" O ASP N 77 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS T 51 " --> pdb=" O GLU N 80 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'O' and resid 31 through 32 Processing sheet with id=AB, first strand: chain 'P' and resid 52 through 55 removed outlier: 6.608A pdb=" N VAL P 44 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'Q' and resid 48 through 60 removed outlier: 5.522A pdb=" N VAL Q 53 " --> pdb=" O GLN Q 75 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN Q 75 " --> pdb=" O VAL Q 53 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE Q 122 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU Q 103 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL Q 127 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU Q 101 " --> pdb=" O VAL Q 127 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.796A pdb=" N VAL R 56 " --> pdb=" O VAL R 119 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'T' and resid 28 through 29 removed outlier: 3.593A pdb=" N ILE T 36 " --> pdb=" O ILE T 29 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'V' and resid 73 through 80 removed outlier: 17.719A pdb=" N ILE V 73 " --> pdb=" O LEU V 94 " (cutoff:3.500A) removed outlier: 14.560A pdb=" N LEU V 94 " --> pdb=" O ILE V 73 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS V 75 " --> pdb=" O ASN V 92 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN V 92 " --> pdb=" O LYS V 75 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE V 88 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE V 140 " --> pdb=" O PRO V 111 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR V 127 " --> pdb=" O LEU V 143 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL V 145 " --> pdb=" O ILE V 125 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE V 125 " --> pdb=" O VAL V 145 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'X' and resid 93 through 94 Processing sheet with id=AH, first strand: chain 'Y' and resid 104 through 108 removed outlier: 4.709A pdb=" N ARG Y 108 " --> pdb=" O PRO Y 112 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'Y' and resid 136 through 137 Processing sheet with id=AJ, first strand: chain 'Z' and resid 32 through 39 removed outlier: 6.016A pdb=" N LYS Z 48 " --> pdb=" O MET Z 38 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain '1' and resid 6 through 15 removed outlier: 4.479A pdb=" N TYR 1 12 " --> pdb=" O GLN 1 22 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN 1 22 " --> pdb=" O TYR 1 12 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER 1 14 " --> pdb=" O ARG 1 20 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG 1 20 " --> pdb=" O SER 1 14 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS 1 71 " --> pdb=" O PHE 1 61 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE 1 61 " --> pdb=" O LYS 1 71 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain '3' and resid 20 through 22 Processing sheet with id=AM, first strand: chain '3' and resid 36 through 38 Processing sheet with id=AN, first strand: chain '3' and resid 41 through 43 Processing sheet with id=AO, first strand: chain '4' and resid 44 through 45 removed outlier: 3.537A pdb=" N SER 4 76 " --> pdb=" O LYS 4 34 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain '5' and resid 40 through 44 removed outlier: 6.641A pdb=" N GLN 5 24 " --> pdb=" O LEU 5 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS 5 11 " --> pdb=" O ARG 5 26 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN 5 28 " --> pdb=" O VAL 5 9 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL 5 9 " --> pdb=" O GLN 5 28 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA 5 7 " --> pdb=" O LEU 5 54 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1143 hydrogen bonds 1864 hydrogen bond angles 0 basepair planarities 482 basepair parallelities 897 stacking parallelities Total time for adding SS restraints: 60.05 Time building geometry restraints manager: 15.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7756 1.32 - 1.45: 29017 1.45 - 1.57: 33241 1.57 - 1.70: 3343 1.70 - 1.83: 208 Bond restraints: 73565 Sorted by residual: bond pdb=" C1' U A 789 " pdb=" N1 U A 789 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.08e+01 bond pdb=" O3' A A 788 " pdb=" P U A 789 " ideal model delta sigma weight residual 1.607 1.703 -0.096 1.50e-02 4.44e+03 4.11e+01 bond pdb=" CAM 34G A2168 " pdb=" CAX 34G A2168 " ideal model delta sigma weight residual 1.504 1.377 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C1' A A 788 " pdb=" N9 A A 788 " ideal model delta sigma weight residual 1.475 1.391 0.084 1.50e-02 4.44e+03 3.13e+01 bond pdb=" CAL 34G A2168 " pdb=" CAW 34G A2168 " ideal model delta sigma weight residual 1.505 1.412 0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 73560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 103505 3.41 - 6.83: 3512 6.83 - 10.24: 198 10.24 - 13.66: 18 13.66 - 17.07: 5 Bond angle restraints: 107238 Sorted by residual: angle pdb=" O3' U A2053 " pdb=" C3' U A2053 " pdb=" C2' U A2053 " ideal model delta sigma weight residual 109.50 126.57 -17.07 1.50e+00 4.44e-01 1.30e+02 angle pdb=" O3' U A1386 " pdb=" C3' U A1386 " pdb=" C2' U A1386 " ideal model delta sigma weight residual 109.50 125.28 -15.78 1.50e+00 4.44e-01 1.11e+02 angle pdb=" O3' G A 465 " pdb=" C3' G A 465 " pdb=" C2' G A 465 " ideal model delta sigma weight residual 109.50 123.81 -14.31 1.50e+00 4.44e-01 9.09e+01 angle pdb=" C3' A A 788 " pdb=" O3' A A 788 " pdb=" P U A 789 " ideal model delta sigma weight residual 120.20 106.69 13.51 1.50e+00 4.44e-01 8.12e+01 angle pdb=" C4' A A1897 " pdb=" C3' A A1897 " pdb=" O3' A A1897 " ideal model delta sigma weight residual 109.40 122.36 -12.96 1.50e+00 4.44e-01 7.46e+01 ... (remaining 107233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 41120 35.91 - 71.82: 4764 71.82 - 107.72: 437 107.72 - 143.63: 20 143.63 - 179.54: 54 Dihedral angle restraints: 46395 sinusoidal: 34520 harmonic: 11875 Sorted by residual: dihedral pdb=" CA SER K 76 " pdb=" C SER K 76 " pdb=" N PRO K 77 " pdb=" CA PRO K 77 " ideal model delta harmonic sigma weight residual -180.00 -128.59 -51.41 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" O4' C A1702 " pdb=" C1' C A1702 " pdb=" N1 C A1702 " pdb=" C2 C A1702 " ideal model delta sinusoidal sigma weight residual 200.00 22.80 177.20 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1069 " pdb=" C1' C A1069 " pdb=" N1 C A1069 " pdb=" C2 C A1069 " ideal model delta sinusoidal sigma weight residual 200.00 24.67 175.33 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 46392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 11543 0.160 - 0.319: 1806 0.319 - 0.479: 70 0.479 - 0.639: 11 0.639 - 0.798: 4 Chirality restraints: 13434 Sorted by residual: chirality pdb=" C3' U A2053 " pdb=" C4' U A2053 " pdb=" O3' U A2053 " pdb=" C2' U A2053 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C3' U A1386 " pdb=" C4' U A1386 " pdb=" O3' U A1386 " pdb=" C2' U A1386 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C3' A A 105 " pdb=" C4' A A 105 " pdb=" O3' A A 105 " pdb=" C2' A A 105 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 13431 not shown) Planarity restraints: 7296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 76 " -0.101 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO K 77 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO K 77 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO K 77 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 427 " 0.060 2.00e-02 2.50e+03 2.71e-02 2.02e+01 pdb=" N9 A A 427 " -0.062 2.00e-02 2.50e+03 pdb=" C8 A A 427 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A A 427 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 427 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 427 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A A 427 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 427 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 427 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 427 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A A 427 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1209 " -0.063 2.00e-02 2.50e+03 2.51e-02 1.90e+01 pdb=" N9 G A1209 " 0.047 2.00e-02 2.50e+03 pdb=" C8 G A1209 " 0.013 2.00e-02 2.50e+03 pdb=" N7 G A1209 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A1209 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G A1209 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A1209 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G A1209 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A1209 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G A1209 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G A1209 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A1209 " 0.017 2.00e-02 2.50e+03 ... (remaining 7293 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 94 2.35 - 2.99: 31999 2.99 - 3.63: 116812 3.63 - 4.26: 191505 4.26 - 4.90: 271533 Nonbonded interactions: 611943 Sorted by model distance: nonbonded pdb=" OP1 A A 169 " pdb="MG MG A2155 " model vdw 1.715 2.170 nonbonded pdb=" O ILE S 35 " pdb=" CG1 ILE S 38 " model vdw 1.757 3.440 nonbonded pdb=" OP2 A A 998 " pdb="MG MG A2140 " model vdw 1.822 2.170 nonbonded pdb=" O2 C A 759 " pdb=" C2 A A 788 " model vdw 1.841 3.340 nonbonded pdb=" O2' A A1447 " pdb=" OP2 U A1448 " model vdw 1.847 3.040 ... (remaining 611938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.970 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 176.410 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 73565 Z= 0.496 Angle : 1.394 17.070 107238 Z= 0.941 Chirality : 0.103 0.798 13434 Planarity : 0.007 0.153 7296 Dihedral : 24.278 179.539 38712 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 4.16 % Allowed : 10.46 % Favored : 85.38 % Rotamer: Outliers : 15.41 % Allowed : 15.77 % Favored : 68.83 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4014 helix: 1.04 (0.11), residues: 1421 sheet: -2.97 (0.17), residues: 597 loop : -3.42 (0.12), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP O 72 HIS 0.015 0.002 HIS K 101 PHE 0.038 0.003 PHE L 65 TYR 0.032 0.003 TYR G 234 ARG 0.012 0.001 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1645 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 556 poor density : 1089 time to evaluate : 3.577 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: B 39 LEU cc_start: 0.6384 (tt) cc_final: 0.6084 (tt) REVERT: B 51 THR cc_start: 0.4861 (m) cc_final: 0.4268 (m) REVERT: B 129 THR cc_start: 0.3581 (OUTLIER) cc_final: 0.3205 (m) REVERT: B 130 LEU cc_start: 0.4932 (mt) cc_final: 0.4640 (mm) REVERT: B 137 MET cc_start: 0.4079 (mmt) cc_final: 0.3488 (mmt) REVERT: B 169 VAL cc_start: 0.4410 (t) cc_final: 0.4190 (t) REVERT: C 20 CYS cc_start: 0.4991 (OUTLIER) cc_final: 0.4782 (t) REVERT: C 28 ASN cc_start: 0.2206 (m-40) cc_final: 0.1575 (m-40) REVERT: C 40 ARG cc_start: 0.4220 (OUTLIER) cc_final: 0.4003 (ttm170) REVERT: C 199 ASP cc_start: 0.5619 (m-30) cc_final: 0.5278 (m-30) REVERT: C 200 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5465 (mmt) REVERT: D 11 PHE cc_start: 0.4930 (m-80) cc_final: 0.4729 (m-80) REVERT: D 22 ASN cc_start: 0.5265 (OUTLIER) cc_final: 0.4346 (m-40) REVERT: D 23 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6654 (mt-10) REVERT: D 27 ARG cc_start: 0.3673 (mmt-90) cc_final: 0.3293 (tpp-160) REVERT: D 129 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5467 (tt0) REVERT: D 167 ARG cc_start: 0.5149 (mtt90) cc_final: 0.4175 (mmt90) REVERT: D 191 LEU cc_start: 0.3248 (mp) cc_final: 0.2993 (tt) REVERT: E 6 ARG cc_start: 0.7557 (ttt90) cc_final: 0.7351 (tpp-160) REVERT: E 41 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7986 (mt-10) REVERT: E 42 ILE cc_start: 0.7391 (mm) cc_final: 0.7126 (mm) REVERT: E 80 MET cc_start: 0.6322 (mmp) cc_final: 0.6098 (mmp) REVERT: E 124 HIS cc_start: 0.7366 (t-170) cc_final: 0.7149 (t70) REVERT: E 153 GLU cc_start: 0.7362 (tt0) cc_final: 0.7065 (pt0) REVERT: E 158 PHE cc_start: 0.5437 (m-80) cc_final: 0.5172 (m-80) REVERT: E 177 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4553 (tt) REVERT: F 50 ASN cc_start: 0.7625 (m110) cc_final: 0.7327 (m-40) REVERT: F 73 ASP cc_start: 0.7902 (m-30) cc_final: 0.7637 (m-30) REVERT: F 87 MET cc_start: 0.6846 (tpp) cc_final: 0.6540 (tpp) REVERT: F 116 ASN cc_start: 0.8057 (m110) cc_final: 0.7608 (p0) REVERT: F 117 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: F 151 HIS cc_start: 0.6640 (t70) cc_final: 0.6052 (t-90) REVERT: F 153 ASP cc_start: 0.6746 (m-30) cc_final: 0.6529 (m-30) REVERT: F 156 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6578 (t) REVERT: F 161 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6857 (ttm-80) REVERT: F 168 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5646 (mtmm) REVERT: F 192 VAL cc_start: 0.6943 (t) cc_final: 0.6613 (t) REVERT: F 211 LYS cc_start: 0.7439 (ttpt) cc_final: 0.6798 (mmmm) REVERT: F 220 THR cc_start: 0.6293 (OUTLIER) cc_final: 0.5958 (m) REVERT: G 86 HIS cc_start: 0.6344 (m-70) cc_final: 0.6100 (m-70) REVERT: G 98 VAL cc_start: 0.4584 (OUTLIER) cc_final: 0.4364 (t) REVERT: H 31 ARG cc_start: 0.7023 (mtt90) cc_final: 0.6533 (mtp-110) REVERT: H 74 ARG cc_start: 0.6709 (mtt-85) cc_final: 0.6485 (mmm160) REVERT: H 85 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7531 (ttt180) REVERT: H 107 SER cc_start: 0.6185 (m) cc_final: 0.5879 (p) REVERT: H 137 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7648 (ttp-170) REVERT: H 143 LYS cc_start: 0.6972 (tmtt) cc_final: 0.6681 (tttt) REVERT: H 154 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6856 (mtp180) REVERT: H 170 PHE cc_start: 0.6054 (m-80) cc_final: 0.5678 (m-10) REVERT: H 171 ILE cc_start: 0.7943 (mt) cc_final: 0.7630 (pt) REVERT: H 196 LYS cc_start: 0.6523 (mttt) cc_final: 0.5899 (tttt) REVERT: H 199 LEU cc_start: 0.7376 (mt) cc_final: 0.7147 (tp) REVERT: H 206 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7789 (tppt) REVERT: I 35 LYS cc_start: 0.5402 (OUTLIER) cc_final: 0.4660 (mmtt) REVERT: I 109 LYS cc_start: 0.2915 (OUTLIER) cc_final: 0.1797 (tmtt) REVERT: I 134 PRO cc_start: 0.4803 (Cg_endo) cc_final: 0.4583 (Cg_exo) REVERT: I 147 THR cc_start: 0.4816 (p) cc_final: 0.4152 (p) REVERT: I 160 ILE cc_start: 0.4860 (tp) cc_final: 0.4079 (mm) REVERT: I 183 LYS cc_start: 0.3494 (ttmt) cc_final: 0.3158 (mtpt) REVERT: J 20 ILE cc_start: 0.6441 (mt) cc_final: 0.6019 (mt) REVERT: J 31 SER cc_start: 0.0828 (OUTLIER) cc_final: 0.0436 (t) REVERT: J 68 ILE cc_start: 0.7728 (mm) cc_final: 0.7464 (mm) REVERT: K 2 VAL cc_start: 0.4692 (OUTLIER) cc_final: 0.4332 (t) REVERT: K 80 ASP cc_start: 0.7487 (p0) cc_final: 0.7272 (p0) REVERT: K 89 ILE cc_start: 0.6271 (mm) cc_final: 0.5931 (mm) REVERT: K 115 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4684 (mm-30) REVERT: K 120 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6258 (m90) REVERT: K 125 VAL cc_start: 0.3834 (OUTLIER) cc_final: 0.3626 (p) REVERT: L 52 ASN cc_start: 0.7426 (m110) cc_final: 0.7189 (m110) REVERT: L 59 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6165 (mtmt) REVERT: L 92 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6302 (tpt170) REVERT: L 98 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7551 (tmtt) REVERT: L 167 ASN cc_start: 0.2942 (m110) cc_final: 0.2604 (t0) REVERT: L 177 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6811 (tttt) REVERT: L 180 ARG cc_start: 0.5535 (mtp180) cc_final: 0.4819 (mtt-85) REVERT: M 103 LYS cc_start: 0.5134 (ttpp) cc_final: 0.4435 (ptpt) REVERT: N 28 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5724 (tt) REVERT: N 66 LYS cc_start: 0.6436 (mttt) cc_final: 0.6112 (mttp) REVERT: N 99 GLN cc_start: 0.3905 (OUTLIER) cc_final: 0.3537 (mm110) REVERT: O 36 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5697 (tptp) REVERT: O 42 ARG cc_start: 0.4863 (OUTLIER) cc_final: 0.4155 (mtt180) REVERT: O 69 LYS cc_start: 0.4485 (OUTLIER) cc_final: 0.4141 (ptpp) REVERT: O 72 TRP cc_start: 0.3617 (OUTLIER) cc_final: 0.2491 (p-90) REVERT: O 73 LYS cc_start: 0.5438 (OUTLIER) cc_final: 0.4688 (mtmm) REVERT: P 75 MET cc_start: 0.5362 (ttp) cc_final: 0.4818 (mmm) REVERT: Q 84 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.5684 (p) REVERT: R 85 MET cc_start: 0.4060 (mmm) cc_final: 0.3850 (tpt) REVERT: S 41 ARG cc_start: 0.2656 (OUTLIER) cc_final: 0.1176 (tpt-90) REVERT: S 84 TRP cc_start: 0.4919 (p-90) cc_final: 0.3705 (p-90) REVERT: S 85 PHE cc_start: 0.5223 (t80) cc_final: 0.5022 (t80) REVERT: S 96 LYS cc_start: 0.5766 (mmtt) cc_final: 0.5452 (mtmt) REVERT: S 98 ILE cc_start: 0.1084 (OUTLIER) cc_final: 0.0285 (mm) REVERT: T 17 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.3977 (ptt-90) REVERT: T 35 ASN cc_start: 0.4659 (m-40) cc_final: 0.4143 (m-40) REVERT: T 43 GLU cc_start: 0.5569 (mt-10) cc_final: 0.5253 (mt-10) REVERT: U 72 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3813 (mm) REVERT: V 52 LYS cc_start: 0.6810 (mtpp) cc_final: 0.6285 (mtmm) REVERT: V 130 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6419 (tp40) REVERT: W 78 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.5026 (tpt170) REVERT: W 97 TYR cc_start: 0.4999 (m-80) cc_final: 0.4447 (t80) REVERT: X 38 LYS cc_start: 0.4958 (pttt) cc_final: 0.4686 (mttt) REVERT: X 43 ARG cc_start: 0.4938 (ttt-90) cc_final: 0.3680 (tmm-80) REVERT: X 46 GLN cc_start: 0.2723 (OUTLIER) cc_final: 0.2246 (tt0) REVERT: X 72 LYS cc_start: 0.1016 (OUTLIER) cc_final: 0.0768 (mtmt) REVERT: X 89 MET cc_start: 0.2611 (mtm) cc_final: 0.2396 (mtm) REVERT: X 108 LYS cc_start: 0.1417 (OUTLIER) cc_final: 0.1172 (mmtt) REVERT: Y 38 ILE cc_start: 0.4776 (mt) cc_final: 0.3529 (mt) REVERT: Y 135 TYR cc_start: 0.4700 (m-80) cc_final: 0.3907 (m-10) REVERT: Y 160 ARG cc_start: 0.0444 (OUTLIER) cc_final: 0.0215 (ttm110) REVERT: Z 12 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.4618 (p90) REVERT: Z 38 MET cc_start: 0.3221 (mmp) cc_final: 0.2553 (mmp) REVERT: Z 76 LYS cc_start: 0.3390 (OUTLIER) cc_final: 0.2944 (ptmt) REVERT: 1 4 GLN cc_start: 0.7408 (mm110) cc_final: 0.7116 (tm-30) REVERT: 1 19 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5676 (mpp80) REVERT: 1 27 ILE cc_start: 0.7678 (mp) cc_final: 0.7419 (mp) REVERT: 1 42 GLU cc_start: 0.7314 (tt0) cc_final: 0.6939 (pp20) REVERT: 1 61 PHE cc_start: 0.7379 (m-10) cc_final: 0.7071 (m-10) REVERT: 1 63 THR cc_start: 0.6968 (p) cc_final: 0.6613 (t) REVERT: 1 98 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6796 (pt) REVERT: 1 112 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6573 (mt) REVERT: 1 113 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7523 (tppt) REVERT: 3 64 LEU cc_start: 0.1700 (OUTLIER) cc_final: 0.1280 (mt) REVERT: 3 88 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6568 (p) REVERT: 6 27 LYS cc_start: 0.6113 (mttt) cc_final: 0.5828 (mtpt) outliers start: 556 outliers final: 109 residues processed: 1451 average time/residue: 0.7885 time to fit residues: 1821.9451 Evaluate side-chains 835 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 675 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 72 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 74 ARG Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 120 HIS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 130 PHE Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 177 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 35 CYS Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 73 LYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 89 ARG Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 3 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 74 ILE Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 130 GLN Chi-restraints excluded: chain V residue 141 ASN Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain V residue 147 LYS Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain X residue 46 GLN Chi-restraints excluded: chain X residue 72 LYS Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain Y residue 50 LYS Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 160 ARG Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 48 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain 1 residue 19 ARG Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 50 GLN Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 88 SER Chi-restraints excluded: chain 4 residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 473 optimal weight: 9.9990 chunk 425 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 439 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 chunk 327 optimal weight: 8.9990 chunk 509 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 13 ASN E 38 ASN E 110 GLN E 155 HIS F 13 ASN F 74 ASN F 116 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN G 65 HIS H 11 ASN I 101 GLN J 105 GLN K 39 GLN L 88 ASN M 75 GLN N 27 ASN R 87 GLN S 87 ASN ** T 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN T 33 ASN U 101 HIS V 14 GLN V 16 GLN V 109 ASN V 130 GLN ** V 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 ASN W 48 ASN W 62 GLN Y 48 HIS 1 52 ASN 2 81 HIS 3 14 ASN 4 7 ASN 4 49 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 73565 Z= 0.336 Angle : 0.956 13.758 107238 Z= 0.482 Chirality : 0.049 0.416 13434 Planarity : 0.008 0.148 7296 Dihedral : 23.729 178.858 30459 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 1.54 % Allowed : 8.42 % Favored : 90.03 % Rotamer: Outliers : 8.92 % Allowed : 20.37 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4014 helix: 1.22 (0.13), residues: 1419 sheet: -2.21 (0.19), residues: 552 loop : -2.88 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP S 129 HIS 0.012 0.002 HIS I 42 PHE 0.029 0.003 PHE V 21 TYR 0.026 0.003 TYR Y 76 ARG 0.013 0.001 ARG X 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 910 time to evaluate : 3.707 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: B 37 MET cc_start: 0.4421 (mpp) cc_final: 0.4120 (mpp) REVERT: B 59 ASP cc_start: 0.4523 (m-30) cc_final: 0.4252 (m-30) REVERT: B 135 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.5236 (mm) REVERT: B 168 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6545 (ptm) REVERT: C 34 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6676 (mtmt) REVERT: D 22 ASN cc_start: 0.6163 (t0) cc_final: 0.4713 (m-40) REVERT: D 27 ARG cc_start: 0.4547 (mmt-90) cc_final: 0.4094 (ptt90) REVERT: D 151 MET cc_start: 0.4372 (mtm) cc_final: 0.4045 (mtm) REVERT: D 167 ARG cc_start: 0.5173 (mtt90) cc_final: 0.3997 (mtt180) REVERT: E 6 ARG cc_start: 0.8397 (ttt90) cc_final: 0.8171 (tpp-160) REVERT: E 53 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7476 (mtm110) REVERT: E 58 TYR cc_start: 0.7243 (t80) cc_final: 0.6958 (t80) REVERT: E 80 MET cc_start: 0.7168 (mmp) cc_final: 0.6740 (mmp) REVERT: E 111 THR cc_start: 0.8441 (m) cc_final: 0.8152 (p) REVERT: E 120 LYS cc_start: 0.7442 (mttp) cc_final: 0.7176 (mtmm) REVERT: E 138 LYS cc_start: 0.6959 (mttp) cc_final: 0.6107 (tttp) REVERT: E 145 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8782 (m) REVERT: E 177 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4708 (tt) REVERT: F 23 MET cc_start: 0.7788 (mmp) cc_final: 0.7509 (mmp) REVERT: F 40 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7875 (mt-10) REVERT: F 54 TYR cc_start: 0.7961 (m-80) cc_final: 0.7577 (m-10) REVERT: F 98 TYR cc_start: 0.6938 (m-80) cc_final: 0.6711 (m-80) REVERT: F 151 HIS cc_start: 0.6733 (t70) cc_final: 0.6313 (t-170) REVERT: F 161 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6907 (ttm-80) REVERT: F 180 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7787 (tp) REVERT: F 211 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7756 (ttmm) REVERT: F 231 ASN cc_start: 0.5800 (OUTLIER) cc_final: 0.5399 (t0) REVERT: F 232 THR cc_start: 0.6683 (p) cc_final: 0.6260 (m) REVERT: F 247 ASP cc_start: 0.6587 (m-30) cc_final: 0.6290 (t70) REVERT: F 255 ARG cc_start: 0.7120 (tpt90) cc_final: 0.6667 (ttt180) REVERT: G 69 ILE cc_start: 0.7629 (pt) cc_final: 0.7322 (mp) REVERT: G 89 LYS cc_start: 0.7695 (tptt) cc_final: 0.7418 (ttmm) REVERT: G 95 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7191 (mm) REVERT: G 99 GLN cc_start: 0.7628 (mt0) cc_final: 0.7350 (mt0) REVERT: G 123 CYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7427 (t) REVERT: G 125 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7480 (tp) REVERT: G 142 ILE cc_start: 0.8350 (mt) cc_final: 0.8144 (mm) REVERT: G 147 SER cc_start: 0.7699 (t) cc_final: 0.7051 (p) REVERT: G 171 SER cc_start: 0.8153 (t) cc_final: 0.7753 (p) REVERT: G 199 MET cc_start: 0.6612 (mmp) cc_final: 0.5856 (tpt) REVERT: G 227 PHE cc_start: 0.7923 (t80) cc_final: 0.7315 (t80) REVERT: H 5 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7906 (mp) REVERT: H 57 ASP cc_start: 0.7586 (p0) cc_final: 0.6700 (t0) REVERT: H 83 CYS cc_start: 0.7557 (m) cc_final: 0.7227 (t) REVERT: H 85 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8039 (ttp-170) REVERT: H 106 LEU cc_start: 0.7327 (pp) cc_final: 0.6918 (pp) REVERT: H 143 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6569 (tttt) REVERT: H 154 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6402 (mtp180) REVERT: H 170 PHE cc_start: 0.5514 (m-80) cc_final: 0.5297 (m-10) REVERT: H 171 ILE cc_start: 0.8093 (mt) cc_final: 0.7799 (pt) REVERT: H 196 LYS cc_start: 0.6749 (mttt) cc_final: 0.6053 (ptmt) REVERT: H 197 ARG cc_start: 0.6748 (tpp-160) cc_final: 0.6144 (tpp80) REVERT: H 200 GLU cc_start: 0.7432 (tt0) cc_final: 0.7221 (pt0) REVERT: H 207 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8003 (mm-30) REVERT: I 35 LYS cc_start: 0.5122 (OUTLIER) cc_final: 0.4438 (mmtt) REVERT: I 49 LYS cc_start: 0.5215 (mttm) cc_final: 0.4501 (tttm) REVERT: I 66 SER cc_start: 0.7103 (t) cc_final: 0.6884 (p) REVERT: I 69 MET cc_start: 0.1035 (tpp) cc_final: 0.0806 (tpp) REVERT: I 70 HIS cc_start: 0.1136 (OUTLIER) cc_final: 0.0919 (t70) REVERT: J 6 LYS cc_start: 0.3013 (tmmt) cc_final: 0.2612 (pttp) REVERT: J 110 PHE cc_start: 0.4846 (m-80) cc_final: 0.4531 (m-10) REVERT: J 154 MET cc_start: 0.4793 (ppp) cc_final: 0.4469 (ptp) REVERT: K 106 THR cc_start: 0.8638 (m) cc_final: 0.8216 (p) REVERT: K 121 THR cc_start: 0.7719 (t) cc_final: 0.7511 (p) REVERT: L 52 ASN cc_start: 0.7502 (m110) cc_final: 0.7107 (m-40) REVERT: L 59 LYS cc_start: 0.6780 (mptm) cc_final: 0.6487 (mttt) REVERT: L 86 SER cc_start: 0.8230 (t) cc_final: 0.8002 (p) REVERT: L 92 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6327 (tpt170) REVERT: L 98 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7227 (tmtt) REVERT: L 101 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8200 (mp) REVERT: L 111 THR cc_start: 0.7400 (m) cc_final: 0.7119 (p) REVERT: L 167 ASN cc_start: 0.3399 (m110) cc_final: 0.3144 (t0) REVERT: L 168 ILE cc_start: 0.5449 (OUTLIER) cc_final: 0.5242 (mm) REVERT: L 180 ARG cc_start: 0.6275 (mtp180) cc_final: 0.5937 (mtt-85) REVERT: L 210 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.6662 (tpt90) REVERT: L 212 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6744 (mtm) REVERT: M 31 LYS cc_start: 0.2903 (mttt) cc_final: 0.1971 (tttt) REVERT: M 76 THR cc_start: 0.2219 (p) cc_final: 0.1702 (m) REVERT: M 103 LYS cc_start: 0.4675 (ttpp) cc_final: 0.4222 (ptpp) REVERT: N 31 ILE cc_start: 0.5208 (tt) cc_final: 0.4914 (tp) REVERT: N 39 MET cc_start: 0.4851 (ptp) cc_final: 0.4607 (ptm) REVERT: N 66 LYS cc_start: 0.7245 (mttt) cc_final: 0.6993 (mttp) REVERT: N 74 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6214 (m-40) REVERT: N 99 GLN cc_start: 0.4584 (OUTLIER) cc_final: 0.3963 (mm110) REVERT: N 112 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3864 (mp0) REVERT: O 42 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4128 (mtt180) REVERT: O 69 LYS cc_start: 0.4243 (OUTLIER) cc_final: 0.3051 (tppt) REVERT: P 75 MET cc_start: 0.5593 (ttp) cc_final: 0.5322 (tmm) REVERT: P 147 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6732 (ptt180) REVERT: Q 23 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7956 (mtm-85) REVERT: Q 33 HIS cc_start: 0.8208 (m170) cc_final: 0.7951 (m170) REVERT: Q 66 SER cc_start: 0.6288 (m) cc_final: 0.5581 (p) REVERT: Q 73 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7405 (ttm-80) REVERT: Q 75 GLN cc_start: 0.7603 (mt0) cc_final: 0.7180 (pt0) REVERT: Q 76 LEU cc_start: 0.8883 (mt) cc_final: 0.8675 (mp) REVERT: Q 81 LYS cc_start: 0.6087 (mmtp) cc_final: 0.5367 (tppt) REVERT: Q 82 LYS cc_start: 0.7168 (mttm) cc_final: 0.6671 (mmmt) REVERT: Q 99 ASN cc_start: 0.7586 (t0) cc_final: 0.6846 (m-40) REVERT: S 41 ARG cc_start: 0.3196 (OUTLIER) cc_final: 0.2443 (ptm160) REVERT: S 84 TRP cc_start: 0.4780 (p-90) cc_final: 0.3757 (p-90) REVERT: S 96 LYS cc_start: 0.6523 (mmtt) cc_final: 0.6006 (mtmt) REVERT: S 107 SER cc_start: 0.2600 (t) cc_final: 0.2223 (m) REVERT: S 116 MET cc_start: 0.3337 (mmp) cc_final: 0.3015 (mpp) REVERT: T 17 ARG cc_start: 0.2907 (OUTLIER) cc_final: 0.2585 (tpt90) REVERT: T 31 LYS cc_start: 0.4558 (ttpt) cc_final: 0.4285 (ttmt) REVERT: T 43 GLU cc_start: 0.5841 (mt-10) cc_final: 0.5189 (mt-10) REVERT: V 81 ASN cc_start: 0.6679 (OUTLIER) cc_final: 0.6401 (m110) REVERT: V 82 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7821 (mtpp) REVERT: V 87 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7103 (tt) REVERT: V 125 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8217 (mt) REVERT: V 139 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7093 (mmt-90) REVERT: V 157 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: W 19 LYS cc_start: 0.3456 (tttp) cc_final: 0.3227 (tmtt) REVERT: W 47 LYS cc_start: 0.7242 (tttt) cc_final: 0.7034 (ttpp) REVERT: W 78 ARG cc_start: 0.5409 (OUTLIER) cc_final: 0.4812 (tpt-90) REVERT: X 43 ARG cc_start: 0.4708 (ttt-90) cc_final: 0.3634 (tmt170) REVERT: X 72 LYS cc_start: 0.2018 (OUTLIER) cc_final: 0.1585 (mtmt) REVERT: X 80 LEU cc_start: 0.2531 (OUTLIER) cc_final: 0.2127 (mp) REVERT: Y 20 VAL cc_start: 0.2603 (m) cc_final: 0.1869 (m) REVERT: Y 38 ILE cc_start: 0.4952 (mt) cc_final: 0.4574 (mt) REVERT: Y 73 GLU cc_start: 0.6947 (tp30) cc_final: 0.6442 (tt0) REVERT: Y 85 ARG cc_start: 0.4870 (ttp80) cc_final: 0.4633 (ttp80) REVERT: Y 150 LYS cc_start: 0.3868 (OUTLIER) cc_final: 0.3502 (tppt) REVERT: Y 164 LYS cc_start: 0.4185 (mtpt) cc_final: 0.3851 (mttp) REVERT: Z 76 LYS cc_start: 0.4485 (OUTLIER) cc_final: 0.3606 (ptmt) REVERT: 1 12 TYR cc_start: 0.8058 (t80) cc_final: 0.7824 (t80) REVERT: 1 18 LEU cc_start: 0.8368 (mm) cc_final: 0.8140 (mm) REVERT: 1 21 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8117 (mmtp) REVERT: 1 46 LYS cc_start: 0.7568 (tttp) cc_final: 0.7271 (mttt) REVERT: 1 47 MET cc_start: 0.6894 (ttm) cc_final: 0.6259 (mtp) REVERT: 1 81 ASP cc_start: 0.7854 (m-30) cc_final: 0.7280 (t0) REVERT: 1 86 PHE cc_start: 0.7253 (p90) cc_final: 0.6535 (p90) REVERT: 1 113 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7532 (tppt) REVERT: 1 117 LYS cc_start: 0.5261 (OUTLIER) cc_final: 0.3840 (tppt) REVERT: 2 41 PHE cc_start: 0.0963 (OUTLIER) cc_final: -0.0342 (p90) REVERT: 3 6 ARG cc_start: 0.7390 (ptm160) cc_final: 0.6936 (ttt180) REVERT: 4 22 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7366 (tp) REVERT: 4 44 LEU cc_start: 0.4150 (OUTLIER) cc_final: 0.3553 (tp) REVERT: 6 20 LYS cc_start: 0.7751 (ttmt) cc_final: 0.6969 (tptp) REVERT: 6 27 LYS cc_start: 0.6462 (mttt) cc_final: 0.5722 (tptt) outliers start: 322 outliers final: 140 residues processed: 1110 average time/residue: 0.7506 time to fit residues: 1360.6422 Evaluate side-chains 870 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 689 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 70 HIS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 22 CYS Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 111 CYS Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 82 LYS Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 157 GLN Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 72 LYS Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 74 CYS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 44 LEU Chi-restraints excluded: chain 5 residue 23 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 283 optimal weight: 0.0030 chunk 158 optimal weight: 9.9990 chunk 424 optimal weight: 30.0000 chunk 346 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 510 optimal weight: 6.9990 chunk 551 optimal weight: 20.0000 chunk 454 optimal weight: 2.9990 chunk 506 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 409 optimal weight: 10.0000 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 110 GLN F 157 ASN F 254 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 HIS K 101 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 ASN M 75 GLN O 43 HIS O 75 GLN ** Q 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS X 82 ASN Y 114 HIS Y 128 GLN 2 81 HIS 3 71 GLN 4 58 ASN ** 5 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 73565 Z= 0.228 Angle : 0.698 11.696 107238 Z= 0.360 Chirality : 0.040 0.355 13434 Planarity : 0.006 0.148 7296 Dihedral : 23.374 179.835 30265 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 1.44 % Allowed : 8.57 % Favored : 89.99 % Rotamer: Outliers : 7.51 % Allowed : 23.28 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 4014 helix: 1.60 (0.14), residues: 1419 sheet: -1.71 (0.20), residues: 555 loop : -2.71 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 255 HIS 0.009 0.002 HIS P 43 PHE 0.022 0.002 PHE K 50 TYR 0.054 0.002 TYR M 80 ARG 0.012 0.001 ARG S 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 825 time to evaluate : 3.664 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: B 99 ASP cc_start: 0.4426 (t0) cc_final: 0.4005 (t0) REVERT: B 107 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.5360 (mtt180) REVERT: B 137 MET cc_start: 0.7204 (mmt) cc_final: 0.7001 (mmt) REVERT: B 168 MET cc_start: 0.6920 (tmm) cc_final: 0.6708 (ptm) REVERT: B 223 LEU cc_start: 0.3998 (OUTLIER) cc_final: 0.3096 (tp) REVERT: C 154 GLU cc_start: 0.7933 (mp0) cc_final: 0.7422 (pm20) REVERT: C 203 TRP cc_start: 0.3951 (t60) cc_final: 0.3608 (t60) REVERT: D 22 ASN cc_start: 0.6170 (t0) cc_final: 0.4946 (m-40) REVERT: D 151 MET cc_start: 0.4959 (mtm) cc_final: 0.4374 (ptt) REVERT: D 167 ARG cc_start: 0.5284 (mtt90) cc_final: 0.3992 (mmt90) REVERT: D 179 LYS cc_start: 0.4702 (tppt) cc_final: 0.4330 (ptpt) REVERT: E 53 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7519 (mtm110) REVERT: E 58 TYR cc_start: 0.7362 (t80) cc_final: 0.7149 (t80) REVERT: E 74 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: E 111 THR cc_start: 0.8525 (m) cc_final: 0.8226 (p) REVERT: E 112 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7339 (mmmt) REVERT: E 138 LYS cc_start: 0.6917 (mttp) cc_final: 0.6171 (tttp) REVERT: E 177 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4822 (tt) REVERT: F 26 GLN cc_start: 0.8778 (tp40) cc_final: 0.8196 (tp40) REVERT: F 121 TYR cc_start: 0.8060 (p90) cc_final: 0.7597 (p90) REVERT: F 151 HIS cc_start: 0.6853 (t70) cc_final: 0.6609 (t-170) REVERT: F 157 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8172 (t160) REVERT: F 161 ARG cc_start: 0.7179 (ttt90) cc_final: 0.6661 (ttp-170) REVERT: F 211 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7821 (ttmm) REVERT: F 232 THR cc_start: 0.6347 (p) cc_final: 0.6088 (m) REVERT: G 69 ILE cc_start: 0.7875 (pt) cc_final: 0.7591 (mp) REVERT: G 89 LYS cc_start: 0.7587 (tptt) cc_final: 0.7245 (ttmm) REVERT: G 99 GLN cc_start: 0.7956 (mt0) cc_final: 0.7354 (mt0) REVERT: G 107 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7287 (ptm-80) REVERT: G 123 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (t) REVERT: G 147 SER cc_start: 0.7763 (t) cc_final: 0.7141 (p) REVERT: G 171 SER cc_start: 0.8733 (t) cc_final: 0.8420 (p) REVERT: G 178 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7629 (ptp-170) REVERT: G 199 MET cc_start: 0.6926 (mmp) cc_final: 0.6207 (tpt) REVERT: G 236 TYR cc_start: 0.7949 (t80) cc_final: 0.7399 (t80) REVERT: H 29 GLU cc_start: 0.7175 (tt0) cc_final: 0.6858 (tm-30) REVERT: H 57 ASP cc_start: 0.7866 (p0) cc_final: 0.7033 (t0) REVERT: H 83 CYS cc_start: 0.7644 (m) cc_final: 0.7184 (t) REVERT: H 106 LEU cc_start: 0.6825 (pp) cc_final: 0.6605 (pp) REVERT: H 143 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6527 (tttt) REVERT: H 154 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6347 (mtp180) REVERT: H 170 PHE cc_start: 0.5464 (m-80) cc_final: 0.5257 (m-10) REVERT: H 171 ILE cc_start: 0.8093 (mt) cc_final: 0.7760 (pt) REVERT: I 35 LYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4409 (mmtt) REVERT: I 49 LYS cc_start: 0.5443 (mttm) cc_final: 0.4922 (ttpt) REVERT: I 59 ILE cc_start: 0.4463 (tt) cc_final: 0.4052 (pt) REVERT: I 144 LEU cc_start: 0.3001 (OUTLIER) cc_final: 0.2741 (mm) REVERT: J 6 LYS cc_start: 0.3350 (tmmt) cc_final: 0.2724 (pttp) REVERT: K 23 ARG cc_start: 0.6527 (mmt-90) cc_final: 0.6041 (mmm160) REVERT: K 89 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7343 (mm) REVERT: K 106 THR cc_start: 0.8727 (m) cc_final: 0.8355 (p) REVERT: K 112 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.5895 (p0) REVERT: K 115 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6223 (mp0) REVERT: K 120 HIS cc_start: 0.7703 (t70) cc_final: 0.7448 (t70) REVERT: L 28 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: L 59 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7098 (mttt) REVERT: L 86 SER cc_start: 0.8382 (t) cc_final: 0.8094 (p) REVERT: L 92 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.6262 (tpt170) REVERT: L 117 PHE cc_start: 0.5676 (m-80) cc_final: 0.5273 (m-80) REVERT: L 166 LYS cc_start: 0.4298 (OUTLIER) cc_final: 0.3548 (mmmt) REVERT: L 180 ARG cc_start: 0.6677 (mtp180) cc_final: 0.5965 (mtt90) REVERT: L 198 TYR cc_start: 0.8305 (p90) cc_final: 0.7599 (p90) REVERT: L 210 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6717 (tpt90) REVERT: L 212 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6928 (mtm) REVERT: M 31 LYS cc_start: 0.3845 (mttt) cc_final: 0.3108 (mttp) REVERT: M 103 LYS cc_start: 0.4844 (ttpp) cc_final: 0.4546 (ptpp) REVERT: M 136 ARG cc_start: 0.5769 (mtm-85) cc_final: 0.5438 (mtt-85) REVERT: N 39 MET cc_start: 0.4600 (ptp) cc_final: 0.4366 (ptm) REVERT: N 66 LYS cc_start: 0.7264 (mttt) cc_final: 0.7007 (mttp) REVERT: N 99 GLN cc_start: 0.4941 (OUTLIER) cc_final: 0.4379 (mm110) REVERT: O 21 LEU cc_start: 0.1851 (OUTLIER) cc_final: 0.1568 (pp) REVERT: O 42 ARG cc_start: 0.5295 (OUTLIER) cc_final: 0.4013 (mtm110) REVERT: P 75 MET cc_start: 0.6320 (ttp) cc_final: 0.5944 (tmm) REVERT: P 76 MET cc_start: 0.5535 (tpt) cc_final: 0.5157 (tpt) REVERT: P 143 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6798 (tttt) REVERT: P 147 ARG cc_start: 0.8103 (ptm-80) cc_final: 0.7667 (ptm160) REVERT: Q 7 SER cc_start: 0.7616 (p) cc_final: 0.7040 (p) REVERT: Q 23 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.8202 (mtm-85) REVERT: Q 26 ASP cc_start: 0.8152 (t0) cc_final: 0.7835 (t70) REVERT: Q 33 HIS cc_start: 0.8391 (m170) cc_final: 0.8071 (m170) REVERT: Q 63 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6567 (tp-100) REVERT: Q 66 SER cc_start: 0.6353 (m) cc_final: 0.5651 (p) REVERT: Q 75 GLN cc_start: 0.7632 (mt0) cc_final: 0.7225 (pt0) REVERT: Q 81 LYS cc_start: 0.6393 (mmtp) cc_final: 0.5933 (tttt) REVERT: Q 99 ASN cc_start: 0.7720 (t0) cc_final: 0.7018 (m-40) REVERT: S 41 ARG cc_start: 0.3072 (OUTLIER) cc_final: 0.2169 (ptm160) REVERT: S 96 LYS cc_start: 0.6348 (mmtt) cc_final: 0.5837 (ttmt) REVERT: S 98 ILE cc_start: 0.3467 (OUTLIER) cc_final: 0.2496 (mt) REVERT: T 17 ARG cc_start: 0.3984 (OUTLIER) cc_final: 0.2681 (tpt90) REVERT: T 35 ASN cc_start: 0.6528 (m-40) cc_final: 0.5512 (t0) REVERT: T 51 LYS cc_start: 0.6078 (mptt) cc_final: 0.5856 (mmtt) REVERT: V 9 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6515 (m-70) REVERT: V 139 ARG cc_start: 0.7248 (mmt90) cc_final: 0.7016 (mmt-90) REVERT: V 160 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6627 (tt) REVERT: W 78 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.4640 (tpt-90) REVERT: W 80 ARG cc_start: 0.5307 (ttp80) cc_final: 0.3951 (mmm160) REVERT: W 104 ARG cc_start: 0.7238 (ptm160) cc_final: 0.6738 (ptp-170) REVERT: X 65 LYS cc_start: 0.3658 (tmtt) cc_final: 0.3236 (ptmt) REVERT: X 80 LEU cc_start: 0.2682 (OUTLIER) cc_final: 0.2239 (mp) REVERT: Y 20 VAL cc_start: 0.2510 (m) cc_final: 0.2265 (m) REVERT: Y 73 GLU cc_start: 0.6759 (tp30) cc_final: 0.6545 (tt0) REVERT: Y 85 ARG cc_start: 0.5109 (ttp80) cc_final: 0.4807 (ttp80) REVERT: Y 108 ARG cc_start: 0.3254 (tpm170) cc_final: 0.2858 (mmt90) REVERT: Y 150 LYS cc_start: 0.3973 (OUTLIER) cc_final: 0.3480 (tppt) REVERT: Y 164 LYS cc_start: 0.4116 (mtpt) cc_final: 0.3871 (mttp) REVERT: Z 60 GLN cc_start: 0.7280 (tp40) cc_final: 0.7014 (tp40) REVERT: Z 61 ASN cc_start: 0.6390 (m-40) cc_final: 0.5864 (m-40) REVERT: Z 74 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7826 (mp0) REVERT: Z 80 PHE cc_start: 0.5341 (p90) cc_final: 0.5067 (p90) REVERT: 1 18 LEU cc_start: 0.8234 (mm) cc_final: 0.7946 (mm) REVERT: 1 42 GLU cc_start: 0.7484 (tt0) cc_final: 0.6981 (pp20) REVERT: 1 46 LYS cc_start: 0.7482 (tttp) cc_final: 0.7229 (mttt) REVERT: 1 81 ASP cc_start: 0.7904 (m-30) cc_final: 0.7237 (t0) REVERT: 1 86 PHE cc_start: 0.7505 (p90) cc_final: 0.6858 (p90) REVERT: 1 113 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7661 (tppt) REVERT: 1 117 LYS cc_start: 0.5042 (OUTLIER) cc_final: 0.4650 (tppt) REVERT: 2 41 PHE cc_start: 0.0742 (OUTLIER) cc_final: -0.0309 (p90) REVERT: 3 88 SER cc_start: 0.7569 (m) cc_final: 0.7135 (p) REVERT: 4 22 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7152 (tt) REVERT: 4 82 GLU cc_start: 0.3685 (OUTLIER) cc_final: 0.2713 (pm20) REVERT: 6 20 LYS cc_start: 0.7832 (ttmt) cc_final: 0.6963 (tptp) REVERT: 6 27 LYS cc_start: 0.6965 (mttt) cc_final: 0.6167 (tptt) outliers start: 271 outliers final: 137 residues processed: 1005 average time/residue: 0.7365 time to fit residues: 1216.9605 Evaluate side-chains 859 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 689 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 173 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 70 ASN Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 184 CYS Chi-restraints excluded: chain L residue 200 ILE Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 111 CYS Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 9 HIS Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 69 CYS Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 28 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 504 optimal weight: 5.9990 chunk 383 optimal weight: 0.1980 chunk 264 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 342 optimal weight: 4.9990 chunk 512 optimal weight: 20.0000 chunk 542 optimal weight: 20.0000 chunk 267 optimal weight: 3.9990 chunk 485 optimal weight: 0.2980 chunk 146 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 HIS L 52 ASN N 27 ASN ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS Q 112 HIS S 21 ASN V 9 HIS V 16 GLN V 66 ASN W 31 ASN 1 15 ASN 2 81 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 73565 Z= 0.216 Angle : 0.671 13.942 107238 Z= 0.344 Chirality : 0.039 0.383 13434 Planarity : 0.006 0.144 7296 Dihedral : 23.215 179.295 30226 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 1.37 % Allowed : 7.47 % Favored : 91.16 % Rotamer: Outliers : 6.93 % Allowed : 23.88 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4014 helix: 1.38 (0.14), residues: 1421 sheet: -1.57 (0.20), residues: 568 loop : -2.54 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 29 HIS 0.065 0.002 HIS W 56 PHE 0.019 0.002 PHE Z 80 TYR 0.033 0.002 TYR M 80 ARG 0.010 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 811 time to evaluate : 3.656 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: B 37 MET cc_start: 0.6034 (mpp) cc_final: 0.5599 (mpp) REVERT: B 84 ILE cc_start: 0.6694 (mt) cc_final: 0.6287 (mt) REVERT: B 104 SER cc_start: 0.8120 (m) cc_final: 0.7872 (m) REVERT: B 157 GLN cc_start: 0.6909 (mt0) cc_final: 0.6027 (mp10) REVERT: B 220 ARG cc_start: 0.6934 (ptp-110) cc_final: 0.6308 (ttt90) REVERT: B 223 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.3563 (tp) REVERT: C 115 PHE cc_start: 0.6486 (t80) cc_final: 0.6051 (t80) REVERT: C 150 ASP cc_start: 0.6899 (t0) cc_final: 0.6213 (m-30) REVERT: C 154 GLU cc_start: 0.8101 (mp0) cc_final: 0.7608 (pm20) REVERT: C 197 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6982 (mmm) REVERT: D 22 ASN cc_start: 0.6156 (OUTLIER) cc_final: 0.4888 (m-40) REVERT: D 151 MET cc_start: 0.5439 (mtm) cc_final: 0.4662 (ptt) REVERT: D 167 ARG cc_start: 0.5574 (mtt90) cc_final: 0.4604 (ttt180) REVERT: D 179 LYS cc_start: 0.4890 (tppt) cc_final: 0.4630 (ptpt) REVERT: D 190 MET cc_start: 0.6701 (mtp) cc_final: 0.6465 (mtp) REVERT: E 74 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: E 77 LEU cc_start: 0.7534 (mm) cc_final: 0.7218 (mm) REVERT: E 106 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7361 (mt-10) REVERT: E 111 THR cc_start: 0.8487 (m) cc_final: 0.8077 (p) REVERT: E 177 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5144 (tt) REVERT: F 79 ASP cc_start: 0.7110 (m-30) cc_final: 0.6848 (t0) REVERT: F 102 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7087 (mm) REVERT: F 121 TYR cc_start: 0.8131 (p90) cc_final: 0.7750 (p90) REVERT: F 161 ARG cc_start: 0.7123 (ttt90) cc_final: 0.6680 (ttp-170) REVERT: F 180 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7850 (tm) REVERT: F 206 ASP cc_start: 0.8389 (m-30) cc_final: 0.7989 (m-30) REVERT: F 211 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7870 (ttmm) REVERT: F 232 THR cc_start: 0.6608 (p) cc_final: 0.6402 (m) REVERT: G 69 ILE cc_start: 0.7933 (pt) cc_final: 0.7676 (mp) REVERT: G 89 LYS cc_start: 0.7665 (tptt) cc_final: 0.7283 (ttmm) REVERT: G 99 GLN cc_start: 0.8232 (mt0) cc_final: 0.7434 (mt0) REVERT: G 107 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7370 (ttp80) REVERT: G 171 SER cc_start: 0.8863 (t) cc_final: 0.8542 (p) REVERT: G 199 MET cc_start: 0.7495 (mmp) cc_final: 0.6903 (tpt) REVERT: G 236 TYR cc_start: 0.8114 (t80) cc_final: 0.7560 (t80) REVERT: H 57 ASP cc_start: 0.7878 (p0) cc_final: 0.6947 (t0) REVERT: H 89 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8152 (tptt) REVERT: H 106 LEU cc_start: 0.6659 (pp) cc_final: 0.6458 (pp) REVERT: H 143 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6774 (tttt) REVERT: H 154 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.6489 (mtp180) REVERT: H 171 ILE cc_start: 0.8083 (mt) cc_final: 0.7704 (pt) REVERT: H 197 ARG cc_start: 0.7131 (tpp-160) cc_final: 0.6837 (tpp-160) REVERT: H 206 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7130 (tptt) REVERT: I 35 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.4775 (mmtt) REVERT: I 49 LYS cc_start: 0.5240 (mttm) cc_final: 0.4836 (ttpt) REVERT: I 144 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2607 (mm) REVERT: J 6 LYS cc_start: 0.3660 (tmmt) cc_final: 0.3026 (pttp) REVERT: J 115 ARG cc_start: 0.7222 (mmt90) cc_final: 0.6714 (mmm-85) REVERT: J 154 MET cc_start: 0.6426 (ptt) cc_final: 0.6149 (mtm) REVERT: K 89 ILE cc_start: 0.7630 (mm) cc_final: 0.7329 (mm) REVERT: K 106 THR cc_start: 0.8739 (m) cc_final: 0.8509 (p) REVERT: K 112 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7375 (p0) REVERT: K 115 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6115 (mm-30) REVERT: K 120 HIS cc_start: 0.7813 (t70) cc_final: 0.7372 (t70) REVERT: L 28 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: L 44 HIS cc_start: 0.7767 (m-70) cc_final: 0.7442 (m-70) REVERT: L 59 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7079 (mttt) REVERT: L 86 SER cc_start: 0.8219 (t) cc_final: 0.8002 (p) REVERT: L 92 ARG cc_start: 0.7535 (ttm-80) cc_final: 0.6413 (tpt170) REVERT: L 105 ASP cc_start: 0.8084 (t70) cc_final: 0.7602 (p0) REVERT: L 166 LYS cc_start: 0.4018 (OUTLIER) cc_final: 0.3276 (mmmt) REVERT: L 180 ARG cc_start: 0.6846 (mtp180) cc_final: 0.6111 (mpt180) REVERT: L 198 TYR cc_start: 0.8389 (p90) cc_final: 0.7928 (p90) REVERT: L 210 ARG cc_start: 0.7131 (ttp-110) cc_final: 0.6611 (tpt170) REVERT: L 212 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7015 (mtm) REVERT: M 31 LYS cc_start: 0.3661 (mttt) cc_final: 0.2673 (mttt) REVERT: M 103 LYS cc_start: 0.4834 (ttpp) cc_final: 0.4600 (ptpp) REVERT: N 66 LYS cc_start: 0.7093 (mttt) cc_final: 0.6842 (mttp) REVERT: N 112 GLU cc_start: 0.4720 (OUTLIER) cc_final: 0.4431 (pm20) REVERT: O 21 LEU cc_start: 0.1848 (OUTLIER) cc_final: 0.1573 (pp) REVERT: O 42 ARG cc_start: 0.5187 (OUTLIER) cc_final: 0.3768 (mtm110) REVERT: O 72 TRP cc_start: 0.3489 (OUTLIER) cc_final: 0.3275 (p-90) REVERT: P 53 LEU cc_start: 0.7497 (mt) cc_final: 0.7237 (mp) REVERT: P 75 MET cc_start: 0.6629 (ttp) cc_final: 0.6288 (tmm) REVERT: P 76 MET cc_start: 0.5862 (tpt) cc_final: 0.5512 (tpt) REVERT: P 85 LEU cc_start: 0.2465 (OUTLIER) cc_final: 0.2180 (mp) REVERT: P 142 LYS cc_start: 0.8123 (tttm) cc_final: 0.7833 (ttmt) REVERT: P 143 LYS cc_start: 0.7496 (ttmt) cc_final: 0.7228 (ttmt) REVERT: Q 7 SER cc_start: 0.7315 (p) cc_final: 0.6715 (p) REVERT: Q 26 ASP cc_start: 0.8307 (t0) cc_final: 0.7959 (t70) REVERT: Q 33 HIS cc_start: 0.8688 (m170) cc_final: 0.8350 (m170) REVERT: Q 63 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6681 (tp-100) REVERT: Q 66 SER cc_start: 0.6763 (m) cc_final: 0.6047 (p) REVERT: Q 73 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8125 (ttp-110) REVERT: Q 75 GLN cc_start: 0.7703 (mt0) cc_final: 0.7132 (pt0) REVERT: Q 81 LYS cc_start: 0.6361 (mmtp) cc_final: 0.5937 (tppt) REVERT: Q 99 ASN cc_start: 0.7767 (t0) cc_final: 0.7090 (m-40) REVERT: R 95 HIS cc_start: 0.2510 (OUTLIER) cc_final: 0.2234 (m90) REVERT: S 81 ILE cc_start: 0.1744 (OUTLIER) cc_final: 0.1540 (tp) REVERT: S 96 LYS cc_start: 0.6255 (mmtt) cc_final: 0.5754 (ttmt) REVERT: T 12 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.4064 (t80) REVERT: T 17 ARG cc_start: 0.3999 (OUTLIER) cc_final: 0.2700 (tpt90) REVERT: T 24 ASN cc_start: 0.4315 (t0) cc_final: 0.3943 (t0) REVERT: T 35 ASN cc_start: 0.6336 (m-40) cc_final: 0.5320 (t0) REVERT: T 51 LYS cc_start: 0.5926 (mptt) cc_final: 0.5704 (mmtt) REVERT: U 73 ARG cc_start: 0.6585 (mmt180) cc_final: 0.6229 (mtt-85) REVERT: U 76 ARG cc_start: 0.6829 (mmt90) cc_final: 0.6145 (mmm-85) REVERT: U 78 GLN cc_start: 0.7464 (tm-30) cc_final: 0.6873 (mm-40) REVERT: V 9 HIS cc_start: 0.7068 (m170) cc_final: 0.6848 (m-70) REVERT: V 40 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7879 (ptmt) REVERT: V 50 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7643 (tm-30) REVERT: V 139 ARG cc_start: 0.7675 (mmt90) cc_final: 0.7353 (mmt-90) REVERT: W 78 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.4747 (tpt-90) REVERT: W 80 ARG cc_start: 0.4856 (ttp80) cc_final: 0.3565 (mmm160) REVERT: W 104 ARG cc_start: 0.7181 (ptm160) cc_final: 0.6587 (ptp-170) REVERT: X 65 LYS cc_start: 0.3570 (OUTLIER) cc_final: 0.3026 (ptmt) REVERT: Y 20 VAL cc_start: 0.2619 (m) cc_final: 0.2365 (m) REVERT: Y 73 GLU cc_start: 0.6790 (tp30) cc_final: 0.6548 (tt0) REVERT: Y 114 HIS cc_start: 0.5106 (m-70) cc_final: 0.4811 (m-70) REVERT: Y 132 ASN cc_start: 0.6647 (m110) cc_final: 0.6344 (t0) REVERT: Y 150 LYS cc_start: 0.4039 (OUTLIER) cc_final: 0.3572 (tppt) REVERT: Y 164 LYS cc_start: 0.4021 (mtpt) cc_final: 0.3784 (mttp) REVERT: Z 38 MET cc_start: 0.4724 (mmt) cc_final: 0.4521 (mmt) REVERT: Z 60 GLN cc_start: 0.7766 (tp40) cc_final: 0.7499 (mm-40) REVERT: Z 61 ASN cc_start: 0.6699 (m-40) cc_final: 0.6186 (m-40) REVERT: Z 73 TYR cc_start: 0.7637 (t80) cc_final: 0.7386 (t80) REVERT: Z 74 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7817 (mp0) REVERT: 1 4 GLN cc_start: 0.7299 (mm110) cc_final: 0.6922 (pm20) REVERT: 1 42 GLU cc_start: 0.7521 (tt0) cc_final: 0.7083 (pp20) REVERT: 1 46 LYS cc_start: 0.7578 (tttp) cc_final: 0.7327 (mttt) REVERT: 1 47 MET cc_start: 0.7355 (ttm) cc_final: 0.6771 (mtp) REVERT: 1 81 ASP cc_start: 0.7877 (m-30) cc_final: 0.7208 (t0) REVERT: 1 113 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7703 (tppt) REVERT: 1 119 VAL cc_start: 0.2157 (OUTLIER) cc_final: 0.1789 (t) REVERT: 2 41 PHE cc_start: 0.0953 (OUTLIER) cc_final: -0.0379 (p90) REVERT: 4 22 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7143 (tt) REVERT: 4 29 TYR cc_start: 0.7473 (p90) cc_final: 0.7251 (p90) REVERT: 4 59 ILE cc_start: 0.6890 (tp) cc_final: 0.6645 (pt) REVERT: 4 82 GLU cc_start: 0.3979 (OUTLIER) cc_final: 0.3199 (pm20) outliers start: 250 outliers final: 145 residues processed: 979 average time/residue: 0.7196 time to fit residues: 1164.7680 Evaluate side-chains 883 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 704 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 173 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 200 ILE Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 94 HIS Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 12 TYR Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 22 CYS Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 4 MET Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 43 ARG Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 69 CYS Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 28 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 451 optimal weight: 0.0270 chunk 307 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 403 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 462 optimal weight: 0.2980 chunk 374 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 486 optimal weight: 2.9990 chunk 136 optimal weight: 40.0000 overall best weight: 2.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 GLN L 21 HIS O 80 ASN ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS Q 112 HIS S 137 HIS U 101 HIS V 16 GLN W 56 HIS Y 72 ASN Y 132 ASN 1 15 ASN 2 81 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.9069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 73565 Z= 0.206 Angle : 0.644 10.676 107238 Z= 0.329 Chirality : 0.037 0.388 13434 Planarity : 0.006 0.141 7296 Dihedral : 23.141 179.892 30201 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 1.37 % Allowed : 7.77 % Favored : 90.86 % Rotamer: Outliers : 6.79 % Allowed : 24.61 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.33 (0.13), residues: 4014 helix: 1.30 (0.14), residues: 1417 sheet: -1.49 (0.20), residues: 610 loop : -2.42 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 72 HIS 0.016 0.002 HIS P 94 PHE 0.030 0.002 PHE D 168 TYR 0.023 0.002 TYR W 20 ARG 0.010 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 841 time to evaluate : 3.702 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: B 76 ASP cc_start: 0.3511 (p0) cc_final: 0.2855 (p0) REVERT: B 104 SER cc_start: 0.8369 (m) cc_final: 0.8143 (m) REVERT: B 108 ASP cc_start: 0.7207 (m-30) cc_final: 0.6191 (p0) REVERT: B 132 ASN cc_start: 0.6116 (t0) cc_final: 0.5915 (t0) REVERT: B 220 ARG cc_start: 0.7007 (ptp-110) cc_final: 0.6195 (ptm160) REVERT: C 46 HIS cc_start: 0.6803 (m90) cc_final: 0.6340 (m90) REVERT: C 110 GLN cc_start: 0.8203 (pm20) cc_final: 0.7968 (pm20) REVERT: C 136 SER cc_start: 0.8049 (m) cc_final: 0.7842 (p) REVERT: C 150 ASP cc_start: 0.6741 (t0) cc_final: 0.6461 (t0) REVERT: C 154 GLU cc_start: 0.8189 (mp0) cc_final: 0.7601 (pm20) REVERT: C 198 VAL cc_start: 0.6393 (t) cc_final: 0.6086 (t) REVERT: C 201 PHE cc_start: 0.7976 (m-80) cc_final: 0.7641 (m-80) REVERT: D 22 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.5032 (m-40) REVERT: D 151 MET cc_start: 0.5432 (mtm) cc_final: 0.4823 (ptt) REVERT: D 167 ARG cc_start: 0.5371 (mtt90) cc_final: 0.4093 (ttt180) REVERT: D 188 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4727 (mtmt) REVERT: D 190 MET cc_start: 0.6599 (mtp) cc_final: 0.6380 (mtt) REVERT: E 17 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7455 (ptp-170) REVERT: E 47 TYR cc_start: 0.8618 (t80) cc_final: 0.8353 (t80) REVERT: E 74 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: E 106 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7394 (mt-10) REVERT: E 177 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5209 (tt) REVERT: F 60 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8277 (mt-10) REVERT: F 79 ASP cc_start: 0.7131 (m-30) cc_final: 0.6843 (t0) REVERT: F 118 GLU cc_start: 0.7812 (pm20) cc_final: 0.7572 (pm20) REVERT: F 143 ASP cc_start: 0.7762 (t70) cc_final: 0.7508 (t70) REVERT: F 180 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7870 (tm) REVERT: F 206 ASP cc_start: 0.8163 (m-30) cc_final: 0.7671 (m-30) REVERT: F 232 THR cc_start: 0.6917 (p) cc_final: 0.6676 (m) REVERT: F 255 ARG cc_start: 0.7130 (tpt90) cc_final: 0.6439 (ttt180) REVERT: G 60 GLU cc_start: 0.7322 (mp0) cc_final: 0.7058 (pp20) REVERT: G 69 ILE cc_start: 0.7933 (pt) cc_final: 0.7586 (mp) REVERT: G 70 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7161 (mmmt) REVERT: G 82 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6150 (p0) REVERT: G 89 LYS cc_start: 0.7698 (tptt) cc_final: 0.7318 (ttmm) REVERT: G 99 GLN cc_start: 0.8272 (mt0) cc_final: 0.7932 (mt0) REVERT: G 168 MET cc_start: 0.8643 (pmm) cc_final: 0.8407 (pmm) REVERT: G 171 SER cc_start: 0.8923 (t) cc_final: 0.8719 (p) REVERT: G 180 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7536 (mtp85) REVERT: G 199 MET cc_start: 0.7451 (mmp) cc_final: 0.6824 (tpt) REVERT: G 232 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7958 (ttmt) REVERT: G 248 ASP cc_start: 0.5978 (m-30) cc_final: 0.5557 (t0) REVERT: H 16 ILE cc_start: 0.5359 (tt) cc_final: 0.5001 (tp) REVERT: H 57 ASP cc_start: 0.7916 (p0) cc_final: 0.7049 (t0) REVERT: H 89 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8189 (tptt) REVERT: H 106 LEU cc_start: 0.6969 (pp) cc_final: 0.6731 (pp) REVERT: H 143 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6695 (tttt) REVERT: H 154 ARG cc_start: 0.6836 (mtm-85) cc_final: 0.6495 (mtp180) REVERT: H 171 ILE cc_start: 0.8054 (mt) cc_final: 0.7629 (pt) REVERT: H 197 ARG cc_start: 0.7219 (tpp-160) cc_final: 0.6501 (tpp-160) REVERT: H 203 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8147 (tm-30) REVERT: H 207 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8024 (mm-30) REVERT: I 35 LYS cc_start: 0.5417 (OUTLIER) cc_final: 0.4919 (mmtt) REVERT: I 49 LYS cc_start: 0.5120 (mttm) cc_final: 0.4738 (ttpt) REVERT: I 144 LEU cc_start: 0.2839 (OUTLIER) cc_final: 0.2554 (mm) REVERT: J 6 LYS cc_start: 0.3031 (tmmt) cc_final: 0.2784 (pttp) REVERT: J 83 GLU cc_start: 0.6031 (mm-30) cc_final: 0.5230 (tm-30) REVERT: J 128 GLU cc_start: 0.7354 (tp30) cc_final: 0.7138 (mm-30) REVERT: K 89 ILE cc_start: 0.7777 (mm) cc_final: 0.7525 (mm) REVERT: K 112 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7822 (p0) REVERT: K 120 HIS cc_start: 0.7943 (t70) cc_final: 0.7574 (t70) REVERT: L 28 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: L 44 HIS cc_start: 0.7684 (m-70) cc_final: 0.7329 (m-70) REVERT: L 59 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7039 (mttt) REVERT: L 92 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.6450 (tpt170) REVERT: L 101 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8012 (mp) REVERT: L 105 ASP cc_start: 0.8129 (t70) cc_final: 0.7681 (p0) REVERT: L 166 LYS cc_start: 0.4083 (OUTLIER) cc_final: 0.3608 (mmmt) REVERT: L 180 ARG cc_start: 0.7045 (mtp180) cc_final: 0.6492 (mmt180) REVERT: L 198 TYR cc_start: 0.8519 (p90) cc_final: 0.8278 (p90) REVERT: L 210 ARG cc_start: 0.7203 (ttp-110) cc_final: 0.6613 (tpt170) REVERT: L 212 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6893 (mtm) REVERT: M 31 LYS cc_start: 0.3249 (mttt) cc_final: 0.2510 (tttt) REVERT: M 103 LYS cc_start: 0.4622 (ttpp) cc_final: 0.4355 (ptpp) REVERT: M 112 ARG cc_start: 0.3629 (ptm-80) cc_final: 0.3362 (ptm160) REVERT: M 133 LYS cc_start: 0.6867 (mtmm) cc_final: 0.5445 (tmtt) REVERT: N 66 LYS cc_start: 0.7251 (mttt) cc_final: 0.6941 (mttp) REVERT: N 99 GLN cc_start: 0.4119 (OUTLIER) cc_final: 0.3770 (mm110) REVERT: N 112 GLU cc_start: 0.5148 (OUTLIER) cc_final: 0.4747 (pm20) REVERT: O 21 LEU cc_start: 0.1672 (OUTLIER) cc_final: 0.1407 (pp) REVERT: O 42 ARG cc_start: 0.5049 (OUTLIER) cc_final: 0.3543 (mtm110) REVERT: O 72 TRP cc_start: 0.3749 (OUTLIER) cc_final: 0.3526 (p-90) REVERT: P 53 LEU cc_start: 0.7674 (mt) cc_final: 0.7391 (mp) REVERT: P 63 LYS cc_start: 0.4215 (tptt) cc_final: 0.3911 (tppt) REVERT: P 76 MET cc_start: 0.6321 (tpt) cc_final: 0.5826 (tpt) REVERT: P 85 LEU cc_start: 0.3427 (OUTLIER) cc_final: 0.3129 (mp) REVERT: P 93 ILE cc_start: 0.6936 (mt) cc_final: 0.6654 (pt) REVERT: P 126 ILE cc_start: 0.7485 (mm) cc_final: 0.7284 (mm) REVERT: P 142 LYS cc_start: 0.8143 (tttm) cc_final: 0.7812 (ttmt) REVERT: P 143 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7565 (tttt) REVERT: Q 7 SER cc_start: 0.7426 (p) cc_final: 0.6809 (p) REVERT: Q 26 ASP cc_start: 0.8355 (t0) cc_final: 0.8061 (t70) REVERT: Q 33 HIS cc_start: 0.8578 (m170) cc_final: 0.8273 (m170) REVERT: Q 37 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7506 (tmm-80) REVERT: Q 46 SER cc_start: 0.9070 (m) cc_final: 0.8841 (p) REVERT: Q 63 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6712 (tp-100) REVERT: Q 66 SER cc_start: 0.6527 (m) cc_final: 0.6215 (m) REVERT: Q 72 VAL cc_start: 0.8784 (t) cc_final: 0.8298 (m) REVERT: Q 75 GLN cc_start: 0.7741 (mt0) cc_final: 0.7105 (pt0) REVERT: Q 81 LYS cc_start: 0.6438 (mmtp) cc_final: 0.5976 (tppt) REVERT: Q 99 ASN cc_start: 0.7796 (t0) cc_final: 0.7082 (m-40) REVERT: Q 144 ARG cc_start: 0.8317 (ttt180) cc_final: 0.7835 (mmt90) REVERT: R 85 MET cc_start: 0.3605 (tpp) cc_final: 0.3402 (tpt) REVERT: R 95 HIS cc_start: 0.2608 (OUTLIER) cc_final: 0.2184 (m90) REVERT: S 41 ARG cc_start: 0.3253 (OUTLIER) cc_final: 0.2688 (ptm160) REVERT: S 81 ILE cc_start: 0.1853 (OUTLIER) cc_final: 0.1652 (tp) REVERT: S 96 LYS cc_start: 0.6163 (mmtt) cc_final: 0.5712 (ttmt) REVERT: T 12 TYR cc_start: 0.4712 (OUTLIER) cc_final: 0.4485 (t80) REVERT: T 17 ARG cc_start: 0.4990 (OUTLIER) cc_final: 0.3450 (tpt90) REVERT: T 35 ASN cc_start: 0.6414 (m-40) cc_final: 0.5470 (t0) REVERT: T 54 ARG cc_start: 0.4757 (ttp-110) cc_final: 0.4349 (ttp-110) REVERT: U 54 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7726 (mp) REVERT: U 78 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7172 (mm-40) REVERT: U 125 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8359 (mp) REVERT: V 9 HIS cc_start: 0.7130 (m170) cc_final: 0.6900 (m-70) REVERT: V 17 GLU cc_start: 0.7886 (tt0) cc_final: 0.7364 (tt0) REVERT: V 50 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7441 (tm-30) REVERT: V 124 ASP cc_start: 0.8738 (m-30) cc_final: 0.8410 (m-30) REVERT: V 139 ARG cc_start: 0.7769 (mmt90) cc_final: 0.7515 (mmt-90) REVERT: V 159 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.6952 (m) REVERT: W 47 LYS cc_start: 0.7224 (tttt) cc_final: 0.6950 (mtpt) REVERT: W 78 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.4697 (tpt-90) REVERT: W 80 ARG cc_start: 0.4616 (ttp80) cc_final: 0.3554 (mmm160) REVERT: W 104 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6664 (ptp-170) REVERT: X 22 LEU cc_start: 0.2411 (OUTLIER) cc_final: 0.1804 (mt) REVERT: X 43 ARG cc_start: 0.4261 (ttt-90) cc_final: 0.3092 (tmt170) REVERT: X 65 LYS cc_start: 0.3166 (OUTLIER) cc_final: 0.2550 (ptmt) REVERT: X 80 LEU cc_start: 0.2689 (OUTLIER) cc_final: 0.2096 (mp) REVERT: Y 20 VAL cc_start: 0.2716 (m) cc_final: 0.2497 (m) REVERT: Y 132 ASN cc_start: 0.6790 (m-40) cc_final: 0.6522 (t0) REVERT: Y 150 LYS cc_start: 0.3963 (OUTLIER) cc_final: 0.3549 (tppt) REVERT: Y 158 PHE cc_start: 0.2794 (t80) cc_final: 0.2538 (t80) REVERT: Y 164 LYS cc_start: 0.4041 (mtpt) cc_final: 0.3801 (mttp) REVERT: Z 55 SER cc_start: 0.7870 (p) cc_final: 0.7644 (t) REVERT: Z 59 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8215 (mtp85) REVERT: Z 60 GLN cc_start: 0.7584 (tp40) cc_final: 0.7329 (mt0) REVERT: Z 61 ASN cc_start: 0.6242 (m-40) cc_final: 0.5773 (m-40) REVERT: 1 4 GLN cc_start: 0.7261 (mm110) cc_final: 0.6850 (pm20) REVERT: 1 42 GLU cc_start: 0.7532 (tt0) cc_final: 0.7112 (pp20) REVERT: 1 46 LYS cc_start: 0.7751 (tttp) cc_final: 0.7505 (mttt) REVERT: 1 47 MET cc_start: 0.7469 (ttm) cc_final: 0.7049 (mtp) REVERT: 1 50 LEU cc_start: 0.7671 (mt) cc_final: 0.7453 (mt) REVERT: 1 81 ASP cc_start: 0.7779 (m-30) cc_final: 0.7080 (t0) REVERT: 1 99 ASP cc_start: 0.6850 (t0) cc_final: 0.6575 (t0) REVERT: 1 113 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7671 (tppt) REVERT: 2 41 PHE cc_start: 0.0724 (OUTLIER) cc_final: -0.0234 (p90) REVERT: 3 63 GLN cc_start: 0.6397 (tp40) cc_final: 0.6169 (mm-40) REVERT: 3 82 ARG cc_start: 0.7635 (mmt90) cc_final: 0.7213 (mmt90) REVERT: 4 22 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7062 (tt) REVERT: 4 23 ILE cc_start: 0.8457 (mt) cc_final: 0.8128 (tp) REVERT: 4 59 ILE cc_start: 0.6955 (tp) cc_final: 0.6628 (pt) REVERT: 4 78 ARG cc_start: 0.6231 (ptt-90) cc_final: 0.5996 (ptt90) REVERT: 4 82 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.3770 (pm20) REVERT: 5 28 GLN cc_start: 0.4760 (OUTLIER) cc_final: 0.4349 (mm-40) REVERT: 5 64 ARG cc_start: 0.2803 (mtt180) cc_final: 0.1781 (ptt-90) outliers start: 245 outliers final: 136 residues processed: 1004 average time/residue: 0.7336 time to fit residues: 1227.7456 Evaluate side-chains 915 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 738 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 200 ILE Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 12 TYR Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 11 VAL Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 28 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 182 optimal weight: 5.9990 chunk 488 optimal weight: 1.9990 chunk 107 optimal weight: 40.0000 chunk 318 optimal weight: 9.9990 chunk 133 optimal weight: 40.0000 chunk 542 optimal weight: 5.9990 chunk 450 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN B 232 HIS ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS F 112 HIS ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 70 HIS I 74 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 HIS L 88 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN Y 128 GLN 2 81 HIS 3 13 HIS 4 40 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 1.0341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 73565 Z= 0.299 Angle : 0.746 11.858 107238 Z= 0.379 Chirality : 0.041 0.377 13434 Planarity : 0.006 0.143 7296 Dihedral : 23.305 179.844 30201 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 1.40 % Allowed : 8.20 % Favored : 90.41 % Rotamer: Outliers : 7.51 % Allowed : 25.77 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 4014 helix: 0.78 (0.13), residues: 1422 sheet: -1.56 (0.19), residues: 591 loop : -2.46 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 129 HIS 0.012 0.002 HIS K 101 PHE 0.029 0.002 PHE Z 80 TYR 0.033 0.002 TYR J 91 ARG 0.013 0.001 ARG I 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 847 time to evaluate : 3.666 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: B 50 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6578 (mmtp) REVERT: B 100 PHE cc_start: 0.8124 (t80) cc_final: 0.7904 (t80) REVERT: B 106 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7469 (p) REVERT: B 132 ASN cc_start: 0.7086 (t0) cc_final: 0.6755 (m-40) REVERT: B 134 HIS cc_start: 0.7243 (m90) cc_final: 0.7029 (m-70) REVERT: B 161 ILE cc_start: 0.8003 (pt) cc_final: 0.7433 (mt) REVERT: B 220 ARG cc_start: 0.7198 (ptp-110) cc_final: 0.6645 (ttm-80) REVERT: B 223 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5921 (pp) REVERT: B 233 THR cc_start: 0.2308 (OUTLIER) cc_final: 0.2090 (m) REVERT: C 114 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6251 (mmtt) REVERT: C 150 ASP cc_start: 0.7140 (t0) cc_final: 0.6913 (t0) REVERT: C 154 GLU cc_start: 0.8528 (mp0) cc_final: 0.7664 (pm20) REVERT: C 197 MET cc_start: 0.7839 (mtp) cc_final: 0.6823 (tmm) REVERT: C 198 VAL cc_start: 0.6480 (t) cc_final: 0.5809 (t) REVERT: C 199 ASP cc_start: 0.7485 (m-30) cc_final: 0.7267 (m-30) REVERT: D 34 TYR cc_start: 0.3378 (t80) cc_final: 0.3140 (t80) REVERT: D 151 MET cc_start: 0.5483 (mtm) cc_final: 0.4942 (ptt) REVERT: E 17 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7593 (ptp-170) REVERT: E 74 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: E 106 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7241 (tm-30) REVERT: E 114 PHE cc_start: 0.7529 (t80) cc_final: 0.7277 (t80) REVERT: E 177 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5532 (tt) REVERT: F 6 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7127 (mtpp) REVERT: F 26 GLN cc_start: 0.8729 (tp40) cc_final: 0.8301 (tp40) REVERT: F 60 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8242 (mt-10) REVERT: F 79 ASP cc_start: 0.7204 (m-30) cc_final: 0.6895 (t0) REVERT: F 102 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7507 (mm) REVERT: F 143 ASP cc_start: 0.7854 (t70) cc_final: 0.7578 (t70) REVERT: F 161 ARG cc_start: 0.7267 (ttt90) cc_final: 0.6812 (ttp-170) REVERT: F 206 ASP cc_start: 0.8270 (m-30) cc_final: 0.7746 (m-30) REVERT: F 255 ARG cc_start: 0.7076 (tpt90) cc_final: 0.6287 (ttt180) REVERT: G 53 GLU cc_start: 0.7380 (mp0) cc_final: 0.7093 (mm-30) REVERT: G 70 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7640 (mmtt) REVERT: G 77 TYR cc_start: 0.7522 (t80) cc_final: 0.7292 (t80) REVERT: G 82 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6263 (p0) REVERT: G 89 LYS cc_start: 0.7808 (tptt) cc_final: 0.7410 (ttmm) REVERT: G 168 MET cc_start: 0.8745 (pmm) cc_final: 0.8291 (pmm) REVERT: G 171 SER cc_start: 0.9063 (t) cc_final: 0.8519 (m) REVERT: G 176 SER cc_start: 0.8933 (p) cc_final: 0.8630 (p) REVERT: G 180 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7168 (ttm170) REVERT: G 199 MET cc_start: 0.7737 (mmp) cc_final: 0.6938 (tpt) REVERT: G 254 GLU cc_start: 0.7876 (tt0) cc_final: 0.7602 (tt0) REVERT: H 57 ASP cc_start: 0.8007 (p0) cc_final: 0.7332 (t0) REVERT: H 59 GLN cc_start: 0.8267 (mp10) cc_final: 0.8003 (mp10) REVERT: H 89 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8024 (tptt) REVERT: H 106 LEU cc_start: 0.7086 (pp) cc_final: 0.6885 (pp) REVERT: H 143 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6734 (tttt) REVERT: H 154 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6544 (mtp180) REVERT: H 171 ILE cc_start: 0.8118 (mt) cc_final: 0.7654 (pt) REVERT: H 203 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8011 (tp-100) REVERT: H 206 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7022 (tptt) REVERT: H 207 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7301 (pt0) REVERT: I 35 LYS cc_start: 0.5478 (OUTLIER) cc_final: 0.4989 (mmtt) REVERT: I 49 LYS cc_start: 0.5333 (mttm) cc_final: 0.5010 (tttm) REVERT: J 77 GLN cc_start: 0.7424 (pm20) cc_final: 0.6605 (tp40) REVERT: J 115 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7028 (mmm-85) REVERT: J 123 TYR cc_start: 0.7713 (m-10) cc_final: 0.7307 (m-10) REVERT: J 128 GLU cc_start: 0.7399 (tp30) cc_final: 0.7082 (mm-30) REVERT: J 141 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8565 (mp) REVERT: K 43 LYS cc_start: 0.7271 (mmmt) cc_final: 0.7061 (ttpp) REVERT: K 85 GLU cc_start: 0.7781 (mp0) cc_final: 0.7411 (mp0) REVERT: K 86 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7751 (mt) REVERT: K 89 ILE cc_start: 0.7603 (mm) cc_final: 0.7347 (mm) REVERT: K 111 MET cc_start: 0.8451 (pmm) cc_final: 0.8241 (pmm) REVERT: K 112 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (p0) REVERT: K 115 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7001 (mm-30) REVERT: K 120 HIS cc_start: 0.7903 (t70) cc_final: 0.7504 (t-170) REVERT: L 28 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: L 44 HIS cc_start: 0.8123 (m-70) cc_final: 0.7648 (m-70) REVERT: L 59 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6967 (mttt) REVERT: L 92 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.6284 (tpt170) REVERT: L 101 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7744 (mm) REVERT: L 105 ASP cc_start: 0.8224 (t70) cc_final: 0.7341 (p0) REVERT: L 166 LYS cc_start: 0.4041 (OUTLIER) cc_final: 0.3566 (mmmt) REVERT: L 180 ARG cc_start: 0.7407 (mtp180) cc_final: 0.6715 (mpt180) REVERT: L 210 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.6787 (tpt170) REVERT: L 212 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6934 (mtm) REVERT: M 31 LYS cc_start: 0.3872 (mttt) cc_final: 0.3012 (tttt) REVERT: M 71 LYS cc_start: 0.3731 (tttt) cc_final: 0.3438 (ttpp) REVERT: M 133 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6241 (tmtt) REVERT: N 61 ARG cc_start: 0.5941 (ptp-110) cc_final: 0.5732 (ptp-110) REVERT: N 62 ILE cc_start: 0.6522 (tp) cc_final: 0.6194 (tt) REVERT: N 83 ILE cc_start: 0.3784 (pt) cc_final: 0.3479 (tt) REVERT: N 99 GLN cc_start: 0.4469 (OUTLIER) cc_final: 0.4133 (mp10) REVERT: N 112 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.4635 (pm20) REVERT: O 21 LEU cc_start: 0.2087 (OUTLIER) cc_final: 0.1823 (pp) REVERT: O 42 ARG cc_start: 0.5399 (OUTLIER) cc_final: 0.3704 (mtm110) REVERT: O 72 TRP cc_start: 0.3728 (OUTLIER) cc_final: 0.3516 (p-90) REVERT: P 40 THR cc_start: 0.8130 (m) cc_final: 0.7784 (p) REVERT: P 63 LYS cc_start: 0.4982 (tptt) cc_final: 0.4284 (ptpp) REVERT: P 75 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7005 (ppp) REVERT: P 76 MET cc_start: 0.7414 (tpt) cc_final: 0.6767 (tpp) REVERT: P 114 SER cc_start: 0.7633 (m) cc_final: 0.7428 (t) REVERT: P 143 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7654 (ttmt) REVERT: Q 33 HIS cc_start: 0.8759 (m170) cc_final: 0.8170 (m170) REVERT: Q 37 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7461 (tmm-80) REVERT: Q 66 SER cc_start: 0.7542 (m) cc_final: 0.6741 (p) REVERT: Q 72 VAL cc_start: 0.8746 (t) cc_final: 0.8369 (m) REVERT: Q 75 GLN cc_start: 0.7598 (mt0) cc_final: 0.6956 (pt0) REVERT: Q 99 ASN cc_start: 0.7809 (t0) cc_final: 0.7247 (m-40) REVERT: Q 144 ARG cc_start: 0.8399 (ttt180) cc_final: 0.7880 (mmt90) REVERT: R 95 HIS cc_start: 0.3322 (OUTLIER) cc_final: 0.2904 (m90) REVERT: S 41 ARG cc_start: 0.3685 (OUTLIER) cc_final: 0.3112 (ptm160) REVERT: S 79 PHE cc_start: 0.4988 (m-80) cc_final: 0.4689 (m-80) REVERT: S 81 ILE cc_start: 0.2308 (OUTLIER) cc_final: 0.1899 (tp) REVERT: S 96 LYS cc_start: 0.6361 (mmtt) cc_final: 0.5930 (ttpt) REVERT: S 121 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5429 (tt) REVERT: T 17 ARG cc_start: 0.5273 (OUTLIER) cc_final: 0.4077 (tpt90) REVERT: T 26 HIS cc_start: 0.4032 (m-70) cc_final: 0.3587 (m170) REVERT: T 35 ASN cc_start: 0.7469 (m-40) cc_final: 0.6572 (t0) REVERT: T 54 ARG cc_start: 0.4466 (ttp-110) cc_final: 0.4084 (ttp-110) REVERT: U 20 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.7037 (mtm-85) REVERT: U 76 ARG cc_start: 0.6985 (mmm-85) cc_final: 0.6042 (mmm-85) REVERT: U 78 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7372 (mm-40) REVERT: U 102 LEU cc_start: 0.7876 (mt) cc_final: 0.7618 (mt) REVERT: V 50 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7283 (tm-30) REVERT: V 124 ASP cc_start: 0.8655 (m-30) cc_final: 0.8331 (m-30) REVERT: W 11 ARG cc_start: 0.5880 (OUTLIER) cc_final: 0.4575 (ttp80) REVERT: W 45 ARG cc_start: 0.6349 (ttp80) cc_final: 0.5794 (ttp-170) REVERT: W 46 MET cc_start: 0.7210 (tpt) cc_final: 0.6816 (mmp) REVERT: W 78 ARG cc_start: 0.5368 (OUTLIER) cc_final: 0.4750 (tpt-90) REVERT: W 80 ARG cc_start: 0.4685 (ttp80) cc_final: 0.3547 (mmm160) REVERT: W 101 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.6038 (p0) REVERT: X 43 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.3340 (tmt170) REVERT: X 65 LYS cc_start: 0.3322 (OUTLIER) cc_final: 0.2620 (ptmt) REVERT: X 80 LEU cc_start: 0.2902 (OUTLIER) cc_final: 0.2480 (mt) REVERT: Y 31 ASP cc_start: 0.3438 (OUTLIER) cc_final: 0.2734 (t0) REVERT: Z 18 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7195 (p) REVERT: Z 20 THR cc_start: 0.7530 (p) cc_final: 0.6980 (t) REVERT: Z 60 GLN cc_start: 0.7647 (tp40) cc_final: 0.7310 (mm-40) REVERT: Z 61 ASN cc_start: 0.6923 (m-40) cc_final: 0.6568 (m110) REVERT: 1 4 GLN cc_start: 0.6993 (mm110) cc_final: 0.6686 (pm20) REVERT: 1 47 MET cc_start: 0.7576 (ttm) cc_final: 0.7191 (mtp) REVERT: 1 90 TYR cc_start: 0.7930 (p90) cc_final: 0.7469 (p90) REVERT: 1 97 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7310 (mp) REVERT: 1 113 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7699 (tppt) REVERT: 2 41 PHE cc_start: 0.0134 (OUTLIER) cc_final: -0.0500 (p90) REVERT: 3 10 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7002 (ptm160) REVERT: 3 11 SER cc_start: 0.8183 (m) cc_final: 0.7933 (p) REVERT: 3 42 ARG cc_start: 0.6795 (ptm-80) cc_final: 0.6593 (ttm-80) REVERT: 3 43 ASN cc_start: 0.8017 (m-40) cc_final: 0.6910 (t0) REVERT: 3 63 GLN cc_start: 0.7060 (tp40) cc_final: 0.6777 (mm-40) REVERT: 3 66 LYS cc_start: 0.6114 (mmmt) cc_final: 0.5595 (mttt) REVERT: 4 22 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7072 (tp) REVERT: 4 23 ILE cc_start: 0.8426 (mt) cc_final: 0.8175 (mm) REVERT: 4 59 ILE cc_start: 0.7428 (tp) cc_final: 0.7146 (pt) REVERT: 4 63 GLN cc_start: 0.6812 (tp40) cc_final: 0.6169 (mt0) REVERT: 4 70 LYS cc_start: 0.5980 (ptpt) cc_final: 0.5752 (ptmt) REVERT: 4 78 ARG cc_start: 0.6835 (ptt-90) cc_final: 0.6495 (ptt90) REVERT: 4 82 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4536 (pm20) REVERT: 5 64 ARG cc_start: 0.2530 (OUTLIER) cc_final: 0.1672 (ptt-90) REVERT: 6 27 LYS cc_start: 0.6910 (mtmm) cc_final: 0.6051 (mmmt) outliers start: 271 outliers final: 144 residues processed: 1024 average time/residue: 0.7237 time to fit residues: 1226.1480 Evaluate side-chains 954 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 763 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 200 ILE Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 75 MET Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 74 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 43 ARG Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 11 VAL Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 53 LEU Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 64 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 523 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 396 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 456 optimal weight: 0.9980 chunk 303 optimal weight: 20.0000 chunk 540 optimal weight: 4.9990 chunk 338 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN C 96 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN G 164 HIS ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 ASN O 75 GLN ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS 2 81 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 1.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 73565 Z= 0.230 Angle : 0.667 10.341 107238 Z= 0.338 Chirality : 0.039 0.380 13434 Planarity : 0.006 0.141 7296 Dihedral : 23.184 179.447 30186 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 1.32 % Allowed : 7.50 % Favored : 91.18 % Rotamer: Outliers : 6.76 % Allowed : 26.60 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.59 (0.13), residues: 4014 helix: 0.89 (0.13), residues: 1418 sheet: -1.64 (0.19), residues: 587 loop : -2.41 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 175 HIS 0.013 0.002 HIS I 42 PHE 0.022 0.002 PHE Z 80 TYR 0.029 0.002 TYR W 21 ARG 0.011 0.001 ARG N 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 813 time to evaluate : 3.726 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: B 36 LYS cc_start: 0.7319 (mmtt) cc_final: 0.7067 (ptpt) REVERT: B 100 PHE cc_start: 0.8008 (t80) cc_final: 0.7708 (t80) REVERT: B 104 SER cc_start: 0.8065 (m) cc_final: 0.7338 (p) REVERT: B 132 ASN cc_start: 0.7286 (t0) cc_final: 0.7009 (m-40) REVERT: B 161 ILE cc_start: 0.7927 (pt) cc_final: 0.7536 (mt) REVERT: B 220 ARG cc_start: 0.7219 (ptp-110) cc_final: 0.6777 (mtp180) REVERT: C 114 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.6087 (mmtt) REVERT: C 150 ASP cc_start: 0.6988 (t0) cc_final: 0.6763 (t70) REVERT: C 197 MET cc_start: 0.7061 (mtp) cc_final: 0.6252 (tmm) REVERT: C 199 ASP cc_start: 0.7305 (m-30) cc_final: 0.7091 (m-30) REVERT: D 23 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6447 (tp30) REVERT: D 151 MET cc_start: 0.5424 (mtm) cc_final: 0.4853 (ptt) REVERT: D 182 VAL cc_start: 0.5312 (m) cc_final: 0.4860 (t) REVERT: E 17 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7610 (ptp-170) REVERT: E 74 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: E 106 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7671 (tm-30) REVERT: E 114 PHE cc_start: 0.7471 (t80) cc_final: 0.7235 (t80) REVERT: E 135 ARG cc_start: 0.7079 (ptt180) cc_final: 0.6152 (ptp-110) REVERT: E 177 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5574 (tt) REVERT: F 6 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7092 (mtpp) REVERT: F 26 GLN cc_start: 0.8701 (tp40) cc_final: 0.8363 (tp40) REVERT: F 60 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 79 ASP cc_start: 0.7231 (m-30) cc_final: 0.6906 (t0) REVERT: F 102 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7394 (mm) REVERT: F 143 ASP cc_start: 0.7753 (t70) cc_final: 0.7519 (t70) REVERT: F 206 ASP cc_start: 0.8298 (m-30) cc_final: 0.7751 (m-30) REVERT: F 255 ARG cc_start: 0.6954 (tpt90) cc_final: 0.6238 (ttt180) REVERT: G 53 GLU cc_start: 0.7388 (mp0) cc_final: 0.7082 (mm-30) REVERT: G 60 GLU cc_start: 0.7825 (mp0) cc_final: 0.7563 (pt0) REVERT: G 70 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7215 (mmtt) REVERT: G 77 TYR cc_start: 0.7540 (t80) cc_final: 0.7222 (t80) REVERT: G 89 LYS cc_start: 0.7589 (tptt) cc_final: 0.7175 (ttmm) REVERT: G 93 VAL cc_start: 0.8784 (p) cc_final: 0.8436 (m) REVERT: G 99 GLN cc_start: 0.8386 (mt0) cc_final: 0.7768 (mt0) REVERT: G 116 ILE cc_start: 0.9217 (tt) cc_final: 0.8989 (tp) REVERT: G 168 MET cc_start: 0.8621 (pmm) cc_final: 0.7959 (pmm) REVERT: G 171 SER cc_start: 0.9052 (t) cc_final: 0.8497 (m) REVERT: G 180 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7092 (mtt180) REVERT: G 199 MET cc_start: 0.7780 (mmp) cc_final: 0.7048 (tpt) REVERT: G 252 TYR cc_start: 0.8349 (m-10) cc_final: 0.8093 (m-10) REVERT: G 254 GLU cc_start: 0.7798 (tt0) cc_final: 0.7502 (tt0) REVERT: H 27 PHE cc_start: 0.6270 (m-10) cc_final: 0.5923 (m-80) REVERT: H 57 ASP cc_start: 0.7867 (p0) cc_final: 0.7172 (t0) REVERT: H 89 LYS cc_start: 0.8527 (mmmt) cc_final: 0.7982 (tptt) REVERT: H 143 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6734 (tttt) REVERT: H 154 ARG cc_start: 0.6901 (mtm-85) cc_final: 0.6526 (mtp180) REVERT: H 206 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.6983 (tptt) REVERT: H 207 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7703 (tp30) REVERT: I 35 LYS cc_start: 0.5123 (OUTLIER) cc_final: 0.4886 (mmtt) REVERT: I 49 LYS cc_start: 0.5332 (mttm) cc_final: 0.5028 (tttm) REVERT: J 68 ILE cc_start: 0.7359 (mm) cc_final: 0.7088 (mt) REVERT: K 86 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7856 (mt) REVERT: K 89 ILE cc_start: 0.7829 (mm) cc_final: 0.7462 (mm) REVERT: K 112 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8126 (p0) REVERT: K 120 HIS cc_start: 0.7844 (t70) cc_final: 0.7260 (t-170) REVERT: L 28 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: L 44 HIS cc_start: 0.7952 (m-70) cc_final: 0.7543 (m-70) REVERT: L 59 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6997 (mtpt) REVERT: L 92 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.6364 (tpt170) REVERT: L 101 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7913 (mp) REVERT: L 105 ASP cc_start: 0.8119 (t70) cc_final: 0.7526 (p0) REVERT: L 166 LYS cc_start: 0.4243 (OUTLIER) cc_final: 0.4016 (mmmt) REVERT: L 180 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6703 (mmt180) REVERT: L 210 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.6805 (tpt170) REVERT: L 212 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6928 (mtm) REVERT: M 31 LYS cc_start: 0.3818 (mttt) cc_final: 0.3146 (tttt) REVERT: M 71 LYS cc_start: 0.4068 (tttt) cc_final: 0.3751 (ttpp) REVERT: M 133 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6479 (tmtt) REVERT: M 141 LYS cc_start: 0.6450 (mtmt) cc_final: 0.5999 (ptmt) REVERT: N 61 ARG cc_start: 0.5471 (ptp-110) cc_final: 0.5260 (ptp-110) REVERT: N 62 ILE cc_start: 0.6357 (tp) cc_final: 0.6006 (tt) REVERT: N 83 ILE cc_start: 0.3289 (pt) cc_final: 0.3064 (tt) REVERT: N 112 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.4708 (pm20) REVERT: O 21 LEU cc_start: 0.1115 (OUTLIER) cc_final: 0.0909 (pp) REVERT: O 42 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.3623 (mtm110) REVERT: O 72 TRP cc_start: 0.4786 (OUTLIER) cc_final: 0.4447 (p-90) REVERT: O 78 ILE cc_start: 0.4394 (OUTLIER) cc_final: 0.3977 (mp) REVERT: P 40 THR cc_start: 0.8174 (m) cc_final: 0.7866 (p) REVERT: P 63 LYS cc_start: 0.5124 (tptt) cc_final: 0.4417 (ptpp) REVERT: P 75 MET cc_start: 0.7248 (tmm) cc_final: 0.6623 (ppp) REVERT: P 76 MET cc_start: 0.6985 (tpt) cc_final: 0.6039 (mmp) REVERT: P 107 THR cc_start: 0.8194 (m) cc_final: 0.7965 (p) REVERT: P 142 LYS cc_start: 0.8397 (tttm) cc_final: 0.8172 (ttmt) REVERT: P 143 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7033 (ttpt) REVERT: Q 26 ASP cc_start: 0.8577 (t0) cc_final: 0.8177 (t70) REVERT: Q 33 HIS cc_start: 0.8702 (m170) cc_final: 0.8322 (m170) REVERT: Q 37 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7400 (tmm-80) REVERT: Q 63 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6602 (tp-100) REVERT: Q 66 SER cc_start: 0.7690 (m) cc_final: 0.6839 (p) REVERT: Q 72 VAL cc_start: 0.8777 (t) cc_final: 0.8394 (m) REVERT: Q 75 GLN cc_start: 0.7669 (mt0) cc_final: 0.7107 (pt0) REVERT: Q 99 ASN cc_start: 0.7872 (t0) cc_final: 0.7264 (m-40) REVERT: Q 144 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7840 (mmt90) REVERT: R 40 ILE cc_start: 0.3923 (mt) cc_final: 0.3541 (tt) REVERT: R 95 HIS cc_start: 0.2597 (OUTLIER) cc_final: 0.2224 (m90) REVERT: S 79 PHE cc_start: 0.4872 (m-80) cc_final: 0.4531 (m-80) REVERT: S 81 ILE cc_start: 0.1909 (OUTLIER) cc_final: 0.1513 (tp) REVERT: S 123 ARG cc_start: 0.4371 (tmm-80) cc_final: 0.4132 (tmm-80) REVERT: T 17 ARG cc_start: 0.5603 (OUTLIER) cc_final: 0.4648 (tpt90) REVERT: T 26 HIS cc_start: 0.4217 (m-70) cc_final: 0.3840 (m170) REVERT: T 35 ASN cc_start: 0.7593 (m-40) cc_final: 0.6647 (t0) REVERT: U 69 ASN cc_start: 0.7408 (p0) cc_final: 0.7142 (p0) REVERT: U 76 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6280 (mmm-85) REVERT: U 78 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7486 (mm-40) REVERT: V 50 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7285 (tm-30) REVERT: V 58 ASP cc_start: 0.9270 (t0) cc_final: 0.9049 (t0) REVERT: V 124 ASP cc_start: 0.8727 (m-30) cc_final: 0.8496 (m-30) REVERT: V 135 SER cc_start: 0.9295 (m) cc_final: 0.9046 (t) REVERT: W 3 ARG cc_start: 0.4965 (ttt180) cc_final: 0.2669 (ttp80) REVERT: W 23 LYS cc_start: 0.5443 (tptt) cc_final: 0.4851 (mttp) REVERT: W 45 ARG cc_start: 0.6480 (ttp80) cc_final: 0.6050 (tmm-80) REVERT: W 58 MET cc_start: 0.4793 (mmm) cc_final: 0.4461 (mmt) REVERT: W 78 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.4713 (tpt-90) REVERT: X 22 LEU cc_start: 0.2530 (OUTLIER) cc_final: 0.2038 (mp) REVERT: X 43 ARG cc_start: 0.4560 (ttt-90) cc_final: 0.3270 (tmt170) REVERT: X 65 LYS cc_start: 0.3422 (OUTLIER) cc_final: 0.2610 (ptmt) REVERT: X 80 LEU cc_start: 0.2957 (OUTLIER) cc_final: 0.2132 (mt) REVERT: Y 61 LYS cc_start: 0.5132 (pptt) cc_final: 0.4797 (ptpt) REVERT: Y 164 LYS cc_start: 0.4306 (mtpt) cc_final: 0.3999 (mttp) REVERT: Z 20 THR cc_start: 0.7616 (p) cc_final: 0.6960 (t) REVERT: Z 60 GLN cc_start: 0.7700 (tp40) cc_final: 0.7426 (mm-40) REVERT: Z 61 ASN cc_start: 0.6611 (m-40) cc_final: 0.6221 (m110) REVERT: 1 47 MET cc_start: 0.7565 (ttm) cc_final: 0.7195 (mtp) REVERT: 1 90 TYR cc_start: 0.7948 (p90) cc_final: 0.7482 (p90) REVERT: 1 97 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7191 (mp) REVERT: 1 113 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7655 (tppt) REVERT: 2 41 PHE cc_start: -0.0136 (OUTLIER) cc_final: -0.0669 (p90) REVERT: 3 10 ARG cc_start: 0.7457 (ptm160) cc_final: 0.6837 (ptm160) REVERT: 3 11 SER cc_start: 0.8109 (m) cc_final: 0.7886 (p) REVERT: 3 42 ARG cc_start: 0.6845 (ptm-80) cc_final: 0.6602 (ttm-80) REVERT: 3 43 ASN cc_start: 0.7799 (m-40) cc_final: 0.6491 (t0) REVERT: 3 50 GLN cc_start: 0.5209 (mm-40) cc_final: 0.4824 (mt0) REVERT: 3 63 GLN cc_start: 0.7139 (tp40) cc_final: 0.6842 (mm-40) REVERT: 3 66 LYS cc_start: 0.6152 (mmmt) cc_final: 0.5668 (mttt) REVERT: 4 22 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6862 (tt) REVERT: 4 23 ILE cc_start: 0.8442 (mt) cc_final: 0.8230 (mm) REVERT: 4 40 GLN cc_start: 0.5059 (pt0) cc_final: 0.4569 (pt0) REVERT: 4 49 GLN cc_start: 0.7976 (mt0) cc_final: 0.7707 (mt0) REVERT: 4 63 GLN cc_start: 0.6922 (tp40) cc_final: 0.6378 (mt0) REVERT: 4 70 LYS cc_start: 0.6314 (ptpt) cc_final: 0.6100 (ptmt) REVERT: 4 78 ARG cc_start: 0.6570 (ptt-90) cc_final: 0.6263 (ptt90) REVERT: 4 82 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4719 (pm20) REVERT: 5 64 ARG cc_start: 0.2935 (OUTLIER) cc_final: 0.2065 (ptt-90) REVERT: 6 27 LYS cc_start: 0.6909 (mtmm) cc_final: 0.6018 (mmmt) outliers start: 244 outliers final: 138 residues processed: 979 average time/residue: 0.7548 time to fit residues: 1219.0142 Evaluate side-chains 933 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 759 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 146 CYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 63 TYR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 11 VAL Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 53 LEU Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 64 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 334 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 106 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 368 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 425 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN M 75 GLN P 38 ASN ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 ASN 2 81 HIS 3 71 GLN ** 4 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 1.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 73565 Z= 0.349 Angle : 0.774 11.730 107238 Z= 0.390 Chirality : 0.043 0.366 13434 Planarity : 0.006 0.144 7296 Dihedral : 23.329 179.765 30182 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 1.30 % Allowed : 8.82 % Favored : 89.89 % Rotamer: Outliers : 6.59 % Allowed : 26.82 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 4014 helix: 0.48 (0.13), residues: 1431 sheet: -1.76 (0.19), residues: 589 loop : -2.51 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 29 HIS 0.016 0.002 HIS K 101 PHE 0.033 0.002 PHE G 258 TYR 0.030 0.002 TYR G 155 ARG 0.010 0.001 ARG N 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 797 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 PHE cc_start: 0.6854 (m-80) cc_final: 0.5517 (t80) REVERT: B 36 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7264 (ptpt) REVERT: B 69 ASN cc_start: 0.7941 (t0) cc_final: 0.7142 (t0) REVERT: B 100 PHE cc_start: 0.8105 (t80) cc_final: 0.7746 (t80) REVERT: B 132 ASN cc_start: 0.7528 (t0) cc_final: 0.7253 (m-40) REVERT: B 148 ASN cc_start: 0.6147 (m-40) cc_final: 0.5421 (t0) REVERT: B 149 GLN cc_start: 0.5609 (pt0) cc_final: 0.5384 (pt0) REVERT: B 161 ILE cc_start: 0.7998 (pt) cc_final: 0.7504 (mt) REVERT: B 220 ARG cc_start: 0.7382 (ptp-110) cc_final: 0.6823 (mtp180) REVERT: C 84 ARG cc_start: 0.5634 (mmm-85) cc_final: 0.5430 (mmm-85) REVERT: C 108 THR cc_start: 0.8422 (p) cc_final: 0.8100 (p) REVERT: C 114 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6236 (mmtt) REVERT: C 197 MET cc_start: 0.7444 (mtp) cc_final: 0.6481 (tmm) REVERT: C 199 ASP cc_start: 0.7522 (m-30) cc_final: 0.7283 (m-30) REVERT: D 23 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6551 (tp30) REVERT: D 34 TYR cc_start: 0.4146 (t80) cc_final: 0.3933 (t80) REVERT: D 151 MET cc_start: 0.5420 (mtm) cc_final: 0.4744 (ptt) REVERT: E 17 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7557 (ptp-170) REVERT: E 20 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8079 (mm-30) REVERT: E 77 LEU cc_start: 0.8279 (mm) cc_final: 0.8032 (mt) REVERT: E 106 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7604 (mt-10) REVERT: E 114 PHE cc_start: 0.7483 (t80) cc_final: 0.7276 (t80) REVERT: E 116 LEU cc_start: 0.8437 (mp) cc_final: 0.8214 (pp) REVERT: E 177 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5452 (tt) REVERT: F 6 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7248 (mtpp) REVERT: F 26 GLN cc_start: 0.8757 (tp40) cc_final: 0.8453 (tp40) REVERT: F 60 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8186 (mt-10) REVERT: F 79 ASP cc_start: 0.6989 (m-30) cc_final: 0.6734 (t0) REVERT: F 143 ASP cc_start: 0.7772 (t70) cc_final: 0.7498 (t70) REVERT: F 206 ASP cc_start: 0.8298 (m-30) cc_final: 0.7811 (m-30) REVERT: G 49 ARG cc_start: 0.5948 (mtp85) cc_final: 0.5320 (mtm-85) REVERT: G 70 LYS cc_start: 0.7596 (mmtt) cc_final: 0.7227 (mmtt) REVERT: G 77 TYR cc_start: 0.7827 (t80) cc_final: 0.7540 (t80) REVERT: G 82 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.6284 (p0) REVERT: G 89 LYS cc_start: 0.7702 (tptt) cc_final: 0.7311 (ttmm) REVERT: G 93 VAL cc_start: 0.8858 (p) cc_final: 0.8522 (m) REVERT: G 99 GLN cc_start: 0.8342 (mt0) cc_final: 0.7964 (mt0) REVERT: G 116 ILE cc_start: 0.9219 (tt) cc_final: 0.8961 (tp) REVERT: G 168 MET cc_start: 0.8716 (pmm) cc_final: 0.8177 (pmm) REVERT: G 171 SER cc_start: 0.9047 (t) cc_final: 0.8554 (m) REVERT: G 176 SER cc_start: 0.8996 (p) cc_final: 0.8652 (p) REVERT: G 180 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7230 (ttm170) REVERT: G 199 MET cc_start: 0.7638 (mmp) cc_final: 0.7020 (tpt) REVERT: G 254 GLU cc_start: 0.8114 (tt0) cc_final: 0.7714 (tp30) REVERT: H 27 PHE cc_start: 0.6046 (m-10) cc_final: 0.5696 (m-80) REVERT: H 57 ASP cc_start: 0.8050 (p0) cc_final: 0.7426 (t0) REVERT: H 59 GLN cc_start: 0.8126 (mp10) cc_final: 0.7910 (mp10) REVERT: H 89 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7987 (tptt) REVERT: H 143 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6515 (tttt) REVERT: H 154 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.6595 (mtp180) REVERT: H 174 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7048 (mttm) REVERT: H 206 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.6994 (tptt) REVERT: H 207 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8028 (mm-30) REVERT: I 35 LYS cc_start: 0.5462 (OUTLIER) cc_final: 0.5045 (mmtt) REVERT: I 49 LYS cc_start: 0.5536 (mttm) cc_final: 0.5202 (tttm) REVERT: J 104 LYS cc_start: 0.6582 (mmtt) cc_final: 0.6305 (pttp) REVERT: J 123 TYR cc_start: 0.7721 (m-10) cc_final: 0.7335 (m-10) REVERT: J 183 ASP cc_start: 0.6915 (t70) cc_final: 0.6256 (m-30) REVERT: K 89 ILE cc_start: 0.7752 (mm) cc_final: 0.7426 (mm) REVERT: K 112 ASP cc_start: 0.8579 (p0) cc_final: 0.8211 (p0) REVERT: K 115 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6966 (mm-30) REVERT: K 120 HIS cc_start: 0.7772 (t70) cc_final: 0.7215 (t-170) REVERT: L 8 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.5099 (pmt170) REVERT: L 28 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: L 44 HIS cc_start: 0.8130 (m-70) cc_final: 0.7669 (m-70) REVERT: L 59 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6896 (mtpt) REVERT: L 92 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.6476 (tpt170) REVERT: L 101 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7638 (mp) REVERT: L 105 ASP cc_start: 0.8100 (t70) cc_final: 0.7451 (p0) REVERT: L 110 THR cc_start: 0.7625 (m) cc_final: 0.7266 (p) REVERT: L 180 ARG cc_start: 0.7092 (mtp180) cc_final: 0.6580 (mmt-90) REVERT: L 210 ARG cc_start: 0.7498 (ttp-110) cc_final: 0.6811 (tpt170) REVERT: L 212 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7008 (mtm) REVERT: M 51 GLU cc_start: 0.4924 (OUTLIER) cc_final: 0.4032 (tt0) REVERT: M 133 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7502 (ptmt) REVERT: M 141 LYS cc_start: 0.6197 (mtmt) cc_final: 0.5645 (ptmt) REVERT: N 100 MET cc_start: 0.1570 (tmm) cc_final: 0.0648 (mmt) REVERT: N 112 GLU cc_start: 0.5545 (OUTLIER) cc_final: 0.4792 (pm20) REVERT: O 21 LEU cc_start: 0.1133 (OUTLIER) cc_final: 0.0925 (pp) REVERT: O 42 ARG cc_start: 0.5343 (OUTLIER) cc_final: 0.3423 (mtm110) REVERT: O 78 ILE cc_start: 0.4815 (OUTLIER) cc_final: 0.4490 (mp) REVERT: P 37 PHE cc_start: 0.7444 (m-80) cc_final: 0.7048 (m-80) REVERT: P 39 ASP cc_start: 0.7840 (t70) cc_final: 0.7047 (t0) REVERT: P 40 THR cc_start: 0.7987 (m) cc_final: 0.7553 (p) REVERT: P 75 MET cc_start: 0.7323 (tmm) cc_final: 0.6852 (ppp) REVERT: P 76 MET cc_start: 0.6993 (tpt) cc_final: 0.6302 (mmp) REVERT: P 143 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7145 (ttpt) REVERT: Q 26 ASP cc_start: 0.8871 (t0) cc_final: 0.8575 (t70) REVERT: Q 33 HIS cc_start: 0.8816 (m170) cc_final: 0.8252 (m170) REVERT: Q 37 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7425 (tmm-80) REVERT: Q 63 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6652 (tp-100) REVERT: Q 72 VAL cc_start: 0.8702 (t) cc_final: 0.8283 (m) REVERT: Q 75 GLN cc_start: 0.7754 (mt0) cc_final: 0.7187 (pt0) REVERT: Q 81 LYS cc_start: 0.6621 (tttt) cc_final: 0.6178 (ttmm) REVERT: Q 99 ASN cc_start: 0.7866 (t0) cc_final: 0.7378 (m-40) REVERT: Q 144 ARG cc_start: 0.8152 (ttt180) cc_final: 0.7738 (mmt90) REVERT: R 95 HIS cc_start: 0.2487 (OUTLIER) cc_final: 0.2115 (m90) REVERT: S 79 PHE cc_start: 0.5103 (m-80) cc_final: 0.4734 (m-80) REVERT: S 81 ILE cc_start: 0.2750 (OUTLIER) cc_final: 0.2450 (tp) REVERT: T 17 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.5032 (tpt90) REVERT: T 26 HIS cc_start: 0.4247 (m-70) cc_final: 0.3856 (m170) REVERT: U 20 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6672 (mtm-85) REVERT: U 76 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.6437 (mmm-85) REVERT: U 97 SER cc_start: 0.7929 (t) cc_final: 0.7462 (m) REVERT: U 125 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8451 (mp) REVERT: V 50 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7460 (tm-30) REVERT: W 23 LYS cc_start: 0.5679 (tptt) cc_final: 0.5090 (mttp) REVERT: W 45 ARG cc_start: 0.6535 (ttp80) cc_final: 0.6118 (tmm-80) REVERT: W 58 MET cc_start: 0.4878 (mmm) cc_final: 0.4561 (mmt) REVERT: W 78 ARG cc_start: 0.5502 (OUTLIER) cc_final: 0.5016 (tpt-90) REVERT: X 43 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4020 (tmt170) REVERT: X 80 LEU cc_start: 0.3080 (OUTLIER) cc_final: 0.2489 (mt) REVERT: Y 31 ASP cc_start: 0.3243 (OUTLIER) cc_final: 0.3016 (t0) REVERT: Y 53 TYR cc_start: 0.7111 (t80) cc_final: 0.6881 (t80) REVERT: Y 106 GLN cc_start: 0.6235 (tm-30) cc_final: 0.5866 (tm-30) REVERT: Z 18 SER cc_start: 0.8286 (t) cc_final: 0.8012 (m) REVERT: Z 60 GLN cc_start: 0.7569 (tp40) cc_final: 0.7331 (mm-40) REVERT: Z 61 ASN cc_start: 0.6937 (m-40) cc_final: 0.6533 (m110) REVERT: 1 47 MET cc_start: 0.7557 (ttm) cc_final: 0.7243 (mtp) REVERT: 1 90 TYR cc_start: 0.7983 (p90) cc_final: 0.7520 (p90) REVERT: 1 97 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7405 (mp) REVERT: 1 113 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7702 (tppt) REVERT: 2 41 PHE cc_start: -0.0349 (OUTLIER) cc_final: -0.0936 (p90) REVERT: 3 10 ARG cc_start: 0.7679 (ptm160) cc_final: 0.7293 (ptm160) REVERT: 3 11 SER cc_start: 0.8241 (m) cc_final: 0.7897 (p) REVERT: 3 42 ARG cc_start: 0.7114 (ptm-80) cc_final: 0.6795 (ttm-80) REVERT: 3 43 ASN cc_start: 0.7990 (m-40) cc_final: 0.6926 (t0) REVERT: 3 63 GLN cc_start: 0.7158 (tp40) cc_final: 0.6901 (mm-40) REVERT: 3 66 LYS cc_start: 0.6728 (mmmt) cc_final: 0.6307 (mptt) REVERT: 4 22 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7195 (tp) REVERT: 4 63 GLN cc_start: 0.6891 (tp40) cc_final: 0.6382 (mt0) REVERT: 4 70 LYS cc_start: 0.6068 (ptpt) cc_final: 0.5627 (ptmt) REVERT: 4 82 GLU cc_start: 0.5166 (OUTLIER) cc_final: 0.4902 (pm20) REVERT: 5 64 ARG cc_start: 0.3374 (OUTLIER) cc_final: 0.2242 (pmt170) REVERT: 6 27 LYS cc_start: 0.7042 (mtmm) cc_final: 0.6287 (mmmt) outliers start: 238 outliers final: 154 residues processed: 954 average time/residue: 0.7531 time to fit residues: 1200.3213 Evaluate side-chains 921 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 731 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 16 TYR Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 63 TYR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 43 ARG Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 31 ASP Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 70 ARG Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 44 ILE Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 79 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 11 VAL Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 53 LEU Chi-restraints excluded: chain 4 residue 59 ILE Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 64 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 491 optimal weight: 40.0000 chunk 518 optimal weight: 5.9990 chunk 472 optimal weight: 6.9990 chunk 503 optimal weight: 3.9990 chunk 517 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 395 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 476 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN M 84 GLN O 43 HIS O 50 ASN ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS Y 157 ASN 2 81 HIS 4 40 GLN 4 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 1.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 73565 Z= 0.215 Angle : 0.674 13.581 107238 Z= 0.341 Chirality : 0.038 0.373 13434 Planarity : 0.006 0.142 7296 Dihedral : 23.189 179.441 30180 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 1.27 % Allowed : 7.67 % Favored : 91.06 % Rotamer: Outliers : 5.46 % Allowed : 28.29 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.74 (0.13), residues: 4014 helix: 0.66 (0.13), residues: 1447 sheet: -1.61 (0.20), residues: 575 loop : -2.48 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 29 HIS 0.015 0.001 HIS S 137 PHE 0.022 0.002 PHE G 258 TYR 0.029 0.002 TYR 3 59 ARG 0.013 0.001 ARG I 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 772 time to evaluate : 3.693 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: B 24 PHE cc_start: 0.6955 (m-80) cc_final: 0.5514 (t80) REVERT: B 36 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7318 (ptpt) REVERT: B 69 ASN cc_start: 0.7963 (t0) cc_final: 0.7616 (t0) REVERT: B 82 LYS cc_start: 0.7593 (mmtp) cc_final: 0.7370 (mttp) REVERT: B 84 ILE cc_start: 0.8183 (mt) cc_final: 0.7826 (mt) REVERT: B 100 PHE cc_start: 0.8108 (t80) cc_final: 0.7799 (t80) REVERT: B 137 MET cc_start: 0.8401 (mmt) cc_final: 0.8179 (mmm) REVERT: B 148 ASN cc_start: 0.6139 (m-40) cc_final: 0.5381 (t0) REVERT: B 149 GLN cc_start: 0.5630 (pt0) cc_final: 0.5413 (pt0) REVERT: B 161 ILE cc_start: 0.7988 (pt) cc_final: 0.7547 (mt) REVERT: B 184 LEU cc_start: 0.6949 (tp) cc_final: 0.6699 (tp) REVERT: B 220 ARG cc_start: 0.7316 (ptp-110) cc_final: 0.6977 (mtp180) REVERT: C 46 HIS cc_start: 0.6875 (m90) cc_final: 0.6236 (m90) REVERT: C 108 THR cc_start: 0.8088 (p) cc_final: 0.7767 (p) REVERT: C 109 ASN cc_start: 0.7983 (t0) cc_final: 0.7633 (t0) REVERT: C 114 LYS cc_start: 0.6329 (OUTLIER) cc_final: 0.6122 (mmtt) REVERT: C 197 MET cc_start: 0.7350 (mtp) cc_final: 0.6337 (tmm) REVERT: D 23 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6378 (tp30) REVERT: D 151 MET cc_start: 0.5794 (mtm) cc_final: 0.4745 (ptt) REVERT: D 182 VAL cc_start: 0.5218 (OUTLIER) cc_final: 0.4748 (t) REVERT: E 17 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7694 (ptp-170) REVERT: E 106 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7480 (tm-30) REVERT: E 116 LEU cc_start: 0.8540 (mp) cc_final: 0.8336 (pp) REVERT: E 135 ARG cc_start: 0.7006 (ptt180) cc_final: 0.6125 (ptp-110) REVERT: E 177 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5394 (tt) REVERT: F 6 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7246 (mtpp) REVERT: F 26 GLN cc_start: 0.8733 (tp40) cc_final: 0.8434 (tp40) REVERT: F 60 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8222 (mt-10) REVERT: F 79 ASP cc_start: 0.7267 (m-30) cc_final: 0.6917 (t0) REVERT: F 143 ASP cc_start: 0.7794 (t70) cc_final: 0.7573 (t70) REVERT: F 200 LYS cc_start: 0.6389 (mmtp) cc_final: 0.6155 (mmmm) REVERT: F 206 ASP cc_start: 0.8356 (m-30) cc_final: 0.7774 (m-30) REVERT: G 60 GLU cc_start: 0.7026 (pt0) cc_final: 0.6681 (pp20) REVERT: G 70 LYS cc_start: 0.7500 (mmtt) cc_final: 0.6962 (mmtt) REVERT: G 77 TYR cc_start: 0.7774 (t80) cc_final: 0.7472 (t80) REVERT: G 89 LYS cc_start: 0.7761 (tptt) cc_final: 0.7343 (ttmm) REVERT: G 93 VAL cc_start: 0.8811 (p) cc_final: 0.8508 (m) REVERT: G 99 GLN cc_start: 0.8317 (mt0) cc_final: 0.8018 (mt0) REVERT: G 116 ILE cc_start: 0.9133 (tt) cc_final: 0.8883 (tp) REVERT: G 120 ASN cc_start: 0.7614 (t0) cc_final: 0.7216 (p0) REVERT: G 171 SER cc_start: 0.9062 (t) cc_final: 0.8562 (m) REVERT: G 176 SER cc_start: 0.8862 (p) cc_final: 0.8505 (p) REVERT: G 180 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7179 (mtt180) REVERT: G 199 MET cc_start: 0.7772 (mmp) cc_final: 0.7039 (tpt) REVERT: G 254 GLU cc_start: 0.7959 (tt0) cc_final: 0.7712 (tp30) REVERT: H 27 PHE cc_start: 0.6140 (m-10) cc_final: 0.5797 (m-80) REVERT: H 57 ASP cc_start: 0.8045 (p0) cc_final: 0.7401 (t0) REVERT: H 59 GLN cc_start: 0.8003 (mp10) cc_final: 0.7760 (mp10) REVERT: H 89 LYS cc_start: 0.8531 (mmmt) cc_final: 0.7971 (tptt) REVERT: H 143 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6764 (tttt) REVERT: H 154 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6613 (mtp180) REVERT: H 206 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.6958 (tptt) REVERT: H 207 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7818 (mm-30) REVERT: I 49 LYS cc_start: 0.5565 (mttm) cc_final: 0.5213 (tttm) REVERT: I 109 LYS cc_start: 0.2140 (OUTLIER) cc_final: 0.1750 (ttpp) REVERT: I 128 GLN cc_start: 0.3412 (pt0) cc_final: 0.3204 (pt0) REVERT: J 104 LYS cc_start: 0.6751 (mmtt) cc_final: 0.6350 (pttp) REVERT: J 123 TYR cc_start: 0.7651 (m-10) cc_final: 0.7400 (m-10) REVERT: J 144 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7634 (mtmt) REVERT: K 89 ILE cc_start: 0.7746 (mm) cc_final: 0.7385 (mm) REVERT: K 111 MET cc_start: 0.8323 (pmm) cc_final: 0.8031 (pmm) REVERT: K 112 ASP cc_start: 0.8534 (p0) cc_final: 0.8189 (p0) REVERT: K 115 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: K 120 HIS cc_start: 0.7836 (t70) cc_final: 0.7292 (t-170) REVERT: L 28 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: L 44 HIS cc_start: 0.8021 (m-70) cc_final: 0.7618 (m-70) REVERT: L 59 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6899 (mtpt) REVERT: L 92 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.6404 (tpt170) REVERT: L 101 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7795 (mp) REVERT: L 105 ASP cc_start: 0.7745 (t70) cc_final: 0.7406 (p0) REVERT: L 110 THR cc_start: 0.7547 (m) cc_final: 0.7149 (p) REVERT: L 180 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6562 (mmt-90) REVERT: L 210 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.6793 (tpt170) REVERT: L 212 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7163 (mtm) REVERT: M 71 LYS cc_start: 0.4881 (tttt) cc_final: 0.4416 (ttpp) REVERT: M 133 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7051 (tmtt) REVERT: M 141 LYS cc_start: 0.5700 (mtmt) cc_final: 0.5227 (ptmt) REVERT: N 100 MET cc_start: 0.0856 (tmm) cc_final: -0.0108 (mmt) REVERT: N 112 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.4863 (pm20) REVERT: O 21 LEU cc_start: 0.1969 (OUTLIER) cc_final: 0.1666 (pp) REVERT: O 42 ARG cc_start: 0.5157 (OUTLIER) cc_final: 0.3494 (mtm110) REVERT: O 78 ILE cc_start: 0.4493 (OUTLIER) cc_final: 0.4117 (mp) REVERT: P 37 PHE cc_start: 0.7652 (m-80) cc_final: 0.7328 (m-80) REVERT: P 40 THR cc_start: 0.8022 (m) cc_final: 0.7683 (p) REVERT: P 75 MET cc_start: 0.7348 (tmm) cc_final: 0.6861 (ppp) REVERT: P 76 MET cc_start: 0.6966 (tpt) cc_final: 0.6277 (mmp) REVERT: P 128 ARG cc_start: 0.7837 (ptp-110) cc_final: 0.7614 (ptp-110) REVERT: P 142 LYS cc_start: 0.8403 (tttm) cc_final: 0.8178 (ttmt) REVERT: P 143 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7161 (ttpt) REVERT: Q 26 ASP cc_start: 0.8582 (t0) cc_final: 0.8179 (t70) REVERT: Q 33 HIS cc_start: 0.8766 (m170) cc_final: 0.8308 (m170) REVERT: Q 37 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7384 (tmm-80) REVERT: Q 63 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6610 (tp-100) REVERT: Q 72 VAL cc_start: 0.8741 (t) cc_final: 0.8330 (m) REVERT: Q 75 GLN cc_start: 0.7686 (mt0) cc_final: 0.7099 (pt0) REVERT: Q 99 ASN cc_start: 0.7894 (t0) cc_final: 0.7344 (m-40) REVERT: Q 144 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7689 (mmt90) REVERT: R 95 HIS cc_start: 0.2600 (OUTLIER) cc_final: 0.2011 (m90) REVERT: S 81 ILE cc_start: 0.2451 (OUTLIER) cc_final: 0.2170 (tp) REVERT: T 17 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5285 (tpp80) REVERT: T 26 HIS cc_start: 0.4203 (m-70) cc_final: 0.3905 (m170) REVERT: T 54 ARG cc_start: 0.5300 (ttp-110) cc_final: 0.4903 (ttp-110) REVERT: U 20 ARG cc_start: 0.7187 (ttp-170) cc_final: 0.6689 (mtm-85) REVERT: U 76 ARG cc_start: 0.7199 (mmm-85) cc_final: 0.6351 (mmm-85) REVERT: U 125 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8430 (mp) REVERT: V 50 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7373 (tm-30) REVERT: V 135 SER cc_start: 0.9289 (m) cc_final: 0.9045 (t) REVERT: W 23 LYS cc_start: 0.5634 (tptt) cc_final: 0.5160 (mttp) REVERT: W 58 MET cc_start: 0.5061 (mmm) cc_final: 0.4654 (mmt) REVERT: W 60 ARG cc_start: 0.5459 (mmp80) cc_final: 0.4246 (ttm110) REVERT: W 78 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.5012 (tpt-90) REVERT: X 22 LEU cc_start: 0.2596 (OUTLIER) cc_final: 0.2152 (mp) REVERT: X 43 ARG cc_start: 0.5008 (ttt-90) cc_final: 0.4080 (tmt170) REVERT: X 65 LYS cc_start: 0.3202 (OUTLIER) cc_final: 0.2537 (ptmt) REVERT: X 80 LEU cc_start: 0.2953 (OUTLIER) cc_final: 0.2506 (mt) REVERT: Y 61 LYS cc_start: 0.5846 (pptt) cc_final: 0.5282 (ptpt) REVERT: Y 105 LYS cc_start: 0.6203 (ptmt) cc_final: 0.5964 (ttpt) REVERT: Y 106 GLN cc_start: 0.5833 (tm-30) cc_final: 0.5465 (tm-30) REVERT: Z 60 GLN cc_start: 0.7838 (tp40) cc_final: 0.7584 (mm-40) REVERT: Z 61 ASN cc_start: 0.6830 (m-40) cc_final: 0.6485 (m110) REVERT: 1 47 MET cc_start: 0.7631 (ttm) cc_final: 0.7162 (mtp) REVERT: 1 90 TYR cc_start: 0.7883 (p90) cc_final: 0.7268 (p90) REVERT: 1 97 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7178 (mp) REVERT: 1 113 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7709 (tppt) REVERT: 3 10 ARG cc_start: 0.7461 (ptm160) cc_final: 0.6883 (ptm160) REVERT: 3 11 SER cc_start: 0.8238 (m) cc_final: 0.7964 (p) REVERT: 3 42 ARG cc_start: 0.7139 (ptm-80) cc_final: 0.6796 (ttm-80) REVERT: 3 43 ASN cc_start: 0.7969 (m-40) cc_final: 0.6694 (t0) REVERT: 3 50 GLN cc_start: 0.6381 (mm-40) cc_final: 0.5978 (mt0) REVERT: 3 63 GLN cc_start: 0.7214 (tp40) cc_final: 0.6957 (mm-40) REVERT: 3 66 LYS cc_start: 0.6876 (mmmt) cc_final: 0.6404 (mttt) REVERT: 4 22 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7736 (tp) REVERT: 4 63 GLN cc_start: 0.7135 (tp40) cc_final: 0.6674 (mt0) REVERT: 4 70 LYS cc_start: 0.5868 (ptpt) cc_final: 0.5349 (ptmt) REVERT: 4 82 GLU cc_start: 0.5242 (OUTLIER) cc_final: 0.4933 (pm20) REVERT: 5 64 ARG cc_start: 0.3569 (OUTLIER) cc_final: 0.2400 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7010 (mtmm) cc_final: 0.6150 (mmmt) outliers start: 197 outliers final: 131 residues processed: 904 average time/residue: 0.7802 time to fit residues: 1177.4057 Evaluate side-chains 892 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 729 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 44 ILE Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 6 residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 502 optimal weight: 8.9990 chunk 330 optimal weight: 0.0980 chunk 532 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 370 optimal weight: 0.4980 chunk 558 optimal weight: 40.0000 chunk 514 optimal weight: 0.9980 chunk 445 optimal weight: 0.3980 chunk 46 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN F 112 HIS F 254 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN M 84 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS 2 81 HIS 4 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 1.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 73565 Z= 0.165 Angle : 0.635 11.868 107238 Z= 0.321 Chirality : 0.036 0.385 13434 Planarity : 0.005 0.140 7296 Dihedral : 23.027 179.782 30174 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.80 % Favored : 91.03 % Rotamer: Outliers : 4.10 % Allowed : 29.51 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.51 (0.13), residues: 4014 helix: 0.88 (0.14), residues: 1439 sheet: -1.43 (0.20), residues: 569 loop : -2.38 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 18 HIS 0.012 0.001 HIS D 126 PHE 0.017 0.001 PHE Z 80 TYR 0.043 0.001 TYR 3 59 ARG 0.012 0.001 ARG S 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 792 time to evaluate : 3.704 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: B 24 PHE cc_start: 0.7005 (m-80) cc_final: 0.5405 (t80) REVERT: B 36 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7315 (ptpt) REVERT: B 69 ASN cc_start: 0.7880 (t0) cc_final: 0.7592 (t0) REVERT: B 137 MET cc_start: 0.8390 (mmt) cc_final: 0.8185 (mmm) REVERT: B 148 ASN cc_start: 0.6255 (m-40) cc_final: 0.5491 (t0) REVERT: B 149 GLN cc_start: 0.5639 (pt0) cc_final: 0.5422 (pt0) REVERT: B 161 ILE cc_start: 0.7913 (pt) cc_final: 0.7551 (mt) REVERT: C 46 HIS cc_start: 0.6553 (m90) cc_final: 0.6160 (m90) REVERT: C 106 MET cc_start: 0.7624 (mtp) cc_final: 0.7212 (mtp) REVERT: C 197 MET cc_start: 0.7370 (mtp) cc_final: 0.6413 (tmm) REVERT: D 23 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6249 (tp30) REVERT: D 151 MET cc_start: 0.5351 (mtm) cc_final: 0.4869 (ptt) REVERT: E 17 ARG cc_start: 0.8066 (ttm110) cc_final: 0.7692 (ptp-170) REVERT: E 106 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7418 (tm-30) REVERT: E 111 THR cc_start: 0.8496 (m) cc_final: 0.8137 (p) REVERT: E 120 LYS cc_start: 0.7291 (mttp) cc_final: 0.7047 (mtmm) REVERT: E 177 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5452 (tt) REVERT: F 60 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8187 (mt-10) REVERT: F 79 ASP cc_start: 0.7268 (m-30) cc_final: 0.6859 (t0) REVERT: F 172 HIS cc_start: 0.7363 (p-80) cc_final: 0.6800 (p-80) REVERT: F 200 LYS cc_start: 0.6342 (mmtp) cc_final: 0.6042 (mmmm) REVERT: F 206 ASP cc_start: 0.8314 (m-30) cc_final: 0.7656 (m-30) REVERT: F 255 ARG cc_start: 0.7049 (tpt90) cc_final: 0.6337 (ttt180) REVERT: G 53 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7613 (pm20) REVERT: G 60 GLU cc_start: 0.7097 (pt0) cc_final: 0.6745 (pp20) REVERT: G 70 LYS cc_start: 0.7522 (mmtt) cc_final: 0.7236 (mmtt) REVERT: G 77 TYR cc_start: 0.7542 (t80) cc_final: 0.7210 (t80) REVERT: G 89 LYS cc_start: 0.7735 (tptt) cc_final: 0.7325 (ttmm) REVERT: G 93 VAL cc_start: 0.8692 (p) cc_final: 0.8435 (m) REVERT: G 99 GLN cc_start: 0.8181 (mt0) cc_final: 0.7977 (mt0) REVERT: G 107 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7438 (mtp-110) REVERT: G 116 ILE cc_start: 0.9160 (tt) cc_final: 0.8944 (tp) REVERT: G 120 ASN cc_start: 0.7525 (t0) cc_final: 0.6998 (p0) REVERT: G 159 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7371 (mppt) REVERT: G 168 MET cc_start: 0.8498 (pmm) cc_final: 0.7663 (ptp) REVERT: G 171 SER cc_start: 0.9037 (t) cc_final: 0.8538 (m) REVERT: G 180 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7134 (mtt180) REVERT: G 199 MET cc_start: 0.7746 (mmp) cc_final: 0.6964 (tpt) REVERT: H 27 PHE cc_start: 0.6251 (m-10) cc_final: 0.5916 (m-80) REVERT: H 57 ASP cc_start: 0.8105 (p0) cc_final: 0.7421 (t0) REVERT: H 89 LYS cc_start: 0.8512 (mmmt) cc_final: 0.7946 (tptt) REVERT: H 142 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7484 (mtt180) REVERT: H 143 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6960 (ttmm) REVERT: H 154 ARG cc_start: 0.7031 (mtm-85) cc_final: 0.6616 (mtp180) REVERT: H 207 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7851 (mm-30) REVERT: I 49 LYS cc_start: 0.5457 (mttm) cc_final: 0.5118 (tttm) REVERT: I 107 VAL cc_start: 0.4894 (p) cc_final: 0.4692 (p) REVERT: J 43 LYS cc_start: 0.6228 (mttt) cc_final: 0.5497 (mptt) REVERT: J 83 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5996 (pp20) REVERT: J 90 LYS cc_start: 0.5936 (mtmt) cc_final: 0.5521 (ptpp) REVERT: J 104 LYS cc_start: 0.6615 (mmtt) cc_final: 0.6320 (pttp) REVERT: J 144 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7679 (mtmt) REVERT: K 20 ARG cc_start: 0.6847 (mmm160) cc_final: 0.6148 (ttm-80) REVERT: K 62 VAL cc_start: 0.8213 (m) cc_final: 0.7787 (p) REVERT: K 64 ASN cc_start: 0.7846 (m-40) cc_final: 0.7639 (m-40) REVERT: K 89 ILE cc_start: 0.7775 (mm) cc_final: 0.7370 (mm) REVERT: K 111 MET cc_start: 0.8121 (pmm) cc_final: 0.7910 (pmm) REVERT: K 112 ASP cc_start: 0.8401 (p0) cc_final: 0.8017 (p0) REVERT: K 115 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: K 120 HIS cc_start: 0.7822 (t70) cc_final: 0.7276 (t-170) REVERT: L 28 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: L 55 TYR cc_start: 0.7243 (m-80) cc_final: 0.6040 (m-80) REVERT: L 59 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6809 (mtpt) REVERT: L 101 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7960 (mp) REVERT: L 110 THR cc_start: 0.7470 (m) cc_final: 0.7069 (p) REVERT: L 180 ARG cc_start: 0.7292 (mtp180) cc_final: 0.6894 (mmt180) REVERT: L 210 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.6807 (mmt180) REVERT: L 211 LYS cc_start: 0.7621 (mptt) cc_final: 0.7162 (mmmt) REVERT: L 212 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6798 (mtm) REVERT: M 105 GLU cc_start: 0.5099 (tp30) cc_final: 0.4464 (mt-10) REVERT: M 126 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6461 (mm-30) REVERT: M 141 LYS cc_start: 0.5531 (mtmt) cc_final: 0.4997 (ptmt) REVERT: N 55 LEU cc_start: 0.6240 (tt) cc_final: 0.5924 (tp) REVERT: N 62 ILE cc_start: 0.6769 (tp) cc_final: 0.6294 (tt) REVERT: N 77 ASP cc_start: 0.7396 (p0) cc_final: 0.7175 (p0) REVERT: N 100 MET cc_start: 0.1006 (tmm) cc_final: 0.0103 (mmt) REVERT: N 112 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4514 (pt0) REVERT: O 21 LEU cc_start: 0.2027 (OUTLIER) cc_final: 0.1707 (pp) REVERT: O 42 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.3446 (mtm110) REVERT: O 51 LEU cc_start: 0.5801 (tp) cc_final: 0.4856 (mm) REVERT: O 78 ILE cc_start: 0.4501 (OUTLIER) cc_final: 0.4129 (mp) REVERT: P 37 PHE cc_start: 0.7832 (m-80) cc_final: 0.7476 (m-80) REVERT: P 40 THR cc_start: 0.7972 (m) cc_final: 0.7631 (p) REVERT: P 75 MET cc_start: 0.7305 (tmm) cc_final: 0.6837 (ppp) REVERT: P 76 MET cc_start: 0.6940 (tpt) cc_final: 0.6245 (mmp) REVERT: P 130 GLU cc_start: 0.7867 (tt0) cc_final: 0.6964 (tp30) REVERT: P 142 LYS cc_start: 0.8423 (tttm) cc_final: 0.8217 (ttmt) REVERT: P 143 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7203 (ttpt) REVERT: Q 26 ASP cc_start: 0.8757 (t0) cc_final: 0.8448 (t0) REVERT: Q 31 LYS cc_start: 0.8674 (tptm) cc_final: 0.8287 (ttpp) REVERT: Q 33 HIS cc_start: 0.8623 (m170) cc_final: 0.8415 (m170) REVERT: Q 37 ARG cc_start: 0.7844 (ttt180) cc_final: 0.7404 (tmm-80) REVERT: Q 52 ILE cc_start: 0.8314 (pt) cc_final: 0.8015 (pt) REVERT: Q 62 LYS cc_start: 0.6023 (mmtm) cc_final: 0.5399 (tppt) REVERT: Q 66 SER cc_start: 0.7631 (m) cc_final: 0.6782 (p) REVERT: Q 75 GLN cc_start: 0.7803 (mt0) cc_final: 0.7271 (pt0) REVERT: Q 81 LYS cc_start: 0.7028 (tttt) cc_final: 0.6640 (ttmt) REVERT: Q 99 ASN cc_start: 0.7940 (t0) cc_final: 0.7387 (m-40) REVERT: Q 136 PHE cc_start: 0.8198 (t80) cc_final: 0.7652 (t80) REVERT: Q 144 ARG cc_start: 0.7909 (ttt180) cc_final: 0.7655 (mmt90) REVERT: R 40 ILE cc_start: 0.2790 (mt) cc_final: 0.2532 (tt) REVERT: R 95 HIS cc_start: 0.2588 (OUTLIER) cc_final: 0.1943 (m90) REVERT: S 79 PHE cc_start: 0.4576 (m-80) cc_final: 0.4162 (m-80) REVERT: S 81 ILE cc_start: 0.2736 (OUTLIER) cc_final: 0.2392 (tp) REVERT: S 121 LEU cc_start: 0.6728 (mt) cc_final: 0.6159 (tt) REVERT: T 17 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.5221 (tpp80) REVERT: T 26 HIS cc_start: 0.4150 (m-70) cc_final: 0.3847 (m170) REVERT: T 31 LYS cc_start: 0.5576 (mmmm) cc_final: 0.5312 (ttmt) REVERT: T 42 ARG cc_start: 0.6627 (mtp85) cc_final: 0.5763 (mmm-85) REVERT: U 20 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6821 (mtm-85) REVERT: U 76 ARG cc_start: 0.6976 (mmm-85) cc_final: 0.5866 (mmm-85) REVERT: V 50 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7385 (tm-30) REVERT: V 124 ASP cc_start: 0.8256 (m-30) cc_final: 0.7835 (m-30) REVERT: V 135 SER cc_start: 0.9271 (m) cc_final: 0.9038 (t) REVERT: W 3 ARG cc_start: 0.4145 (ttt180) cc_final: 0.2540 (ttp80) REVERT: W 23 LYS cc_start: 0.5298 (tptt) cc_final: 0.5014 (pttt) REVERT: W 45 ARG cc_start: 0.6085 (ttp80) cc_final: 0.5879 (tmm-80) REVERT: W 60 ARG cc_start: 0.5451 (mmp80) cc_final: 0.4501 (ttm110) REVERT: W 78 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.5010 (tpt-90) REVERT: X 22 LEU cc_start: 0.2521 (OUTLIER) cc_final: 0.2073 (mp) REVERT: X 43 ARG cc_start: 0.4981 (ttt-90) cc_final: 0.4055 (tmt170) REVERT: X 65 LYS cc_start: 0.3304 (OUTLIER) cc_final: 0.2539 (ptmt) REVERT: X 80 LEU cc_start: 0.3539 (OUTLIER) cc_final: 0.2803 (mt) REVERT: Y 49 ASN cc_start: 0.4439 (t0) cc_final: 0.3500 (t0) REVERT: Y 61 LYS cc_start: 0.5626 (pptt) cc_final: 0.5043 (ptpt) REVERT: 1 47 MET cc_start: 0.7695 (ttm) cc_final: 0.7329 (mtp) REVERT: 1 90 TYR cc_start: 0.7836 (p90) cc_final: 0.7264 (p90) REVERT: 1 113 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7710 (tppt) REVERT: 3 10 ARG cc_start: 0.7224 (ptm160) cc_final: 0.6917 (ptm160) REVERT: 3 11 SER cc_start: 0.8227 (m) cc_final: 0.7940 (p) REVERT: 3 33 ASP cc_start: 0.7608 (p0) cc_final: 0.6931 (p0) REVERT: 3 42 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6865 (ttm-80) REVERT: 3 43 ASN cc_start: 0.7945 (m-40) cc_final: 0.6902 (t0) REVERT: 3 63 GLN cc_start: 0.7230 (tp40) cc_final: 0.6968 (mm-40) REVERT: 3 66 LYS cc_start: 0.6890 (mmmt) cc_final: 0.6438 (mttt) REVERT: 4 22 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7762 (tp) REVERT: 4 63 GLN cc_start: 0.7264 (tp40) cc_final: 0.6831 (mt0) REVERT: 4 70 LYS cc_start: 0.5872 (ptpt) cc_final: 0.5383 (ptmt) REVERT: 4 82 GLU cc_start: 0.4846 (OUTLIER) cc_final: 0.4479 (pm20) REVERT: 5 22 VAL cc_start: 0.4522 (OUTLIER) cc_final: 0.4084 (p) REVERT: 5 64 ARG cc_start: 0.3533 (mtt180) cc_final: 0.2549 (mtm110) REVERT: 6 27 LYS cc_start: 0.6803 (mtmm) cc_final: 0.5912 (mmmt) outliers start: 148 outliers final: 109 residues processed: 893 average time/residue: 0.7261 time to fit residues: 1069.0505 Evaluate side-chains 859 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 727 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 85 ILE Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 52 VAL Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 6 residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 272 optimal weight: 2.9990 chunk 353 optimal weight: 10.0000 chunk 474 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 chunk 410 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 445 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 457 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN U 45 GLN W 56 HIS ** Y 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 4 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.179150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150603 restraints weight = 123114.822| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.46 r_work: 0.3689 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 1.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.457 73565 Z= 0.346 Angle : 0.726 59.176 107238 Z= 0.385 Chirality : 0.040 1.101 13434 Planarity : 0.006 0.155 7296 Dihedral : 23.022 179.866 30169 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.75 % Favored : 91.13 % Rotamer: Outliers : 4.54 % Allowed : 29.81 % Favored : 65.64 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 4014 helix: 0.85 (0.13), residues: 1439 sheet: -1.43 (0.20), residues: 569 loop : -2.38 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 129 HIS 0.010 0.001 HIS D 126 PHE 0.039 0.002 PHE E 114 TYR 0.041 0.002 TYR 3 59 ARG 0.018 0.001 ARG D 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18967.59 seconds wall clock time: 328 minutes 40.85 seconds (19720.85 seconds total)