Starting phenix.real_space_refine on Sun Mar 24 01:21:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5an9_3145/03_2024/5an9_3145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5an9_3145/03_2024/5an9_3145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5an9_3145/03_2024/5an9_3145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5an9_3145/03_2024/5an9_3145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5an9_3145/03_2024/5an9_3145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5an9_3145/03_2024/5an9_3145.pdb" } resolution = 3.3 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= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1158 5.49 5 S 85 5.16 5 C 20518 2.51 5 N 7140 2.21 5 O 10792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39693 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3176 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1491 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 184} Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1571 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1245 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 151} Chain: "E" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1017 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 125} Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "G" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "H" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 427 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "I" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1686 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "J" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "N" Number of atoms: 24758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 24758 Inner-chain residues flagged as termini: ['pdbres=" C N1356 "', 'pdbres=" A N2392 "', 'pdbres=" A N2925 "'] Classifications: {'RNA': 1162} Modifications used: {'5*END': 4, 'rna2p_pur': 108, 'rna2p_pyr': 58, 'rna3p_pur': 516, 'rna3p_pyr': 480} Link IDs: {'rna2p': 166, 'rna3p': 995} Time building chain proxies: 20.63, per 1000 atoms: 0.52 Number of scatterers: 39693 At special positions: 0 Unit cell: (180.88, 192.85, 207.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 1158 15.00 O 10792 8.00 N 7140 7.00 C 20518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 19.68 Conformation dependent library (CDL) restraints added in 3.0 seconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3530 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 29 sheets defined 25.6% alpha, 18.3% beta 331 base pairs and 574 stacking pairs defined. Time for finding SS restraints: 17.80 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.622A pdb=" N PHE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'B' and resid 61 through 84 removed outlier: 3.648A pdb=" N ILE B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.006A pdb=" N PHE C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.635A pdb=" N LYS C 41 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 49 removed outlier: 3.766A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.707A pdb=" N LEU C 67 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 68 " --> pdb=" O ARG C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 68' Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.845A pdb=" N GLN C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.694A pdb=" N LEU C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 39 through 51 removed outlier: 3.691A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 removed outlier: 3.896A pdb=" N VAL D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.519A pdb=" N CYS D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'F' and resid 5 through 10 removed outlier: 3.704A pdb=" N ARG F 10 " --> pdb=" O ARG F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 74 Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.551A pdb=" N TYR F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.513A pdb=" N LYS F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.521A pdb=" N GLU G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 Processing helix chain 'H' and resid 1 through 14 removed outlier: 3.626A pdb=" N LEU H 5 " --> pdb=" O ILE H 1 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 12 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 41 removed outlier: 3.500A pdb=" N LEU I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS I 36 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 88 Processing helix chain 'I' and resid 122 through 134 Processing helix chain 'I' and resid 166 through 178 Processing helix chain 'I' and resid 192 through 196 removed outlier: 4.302A pdb=" N GLY I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 192 through 196' Processing helix chain 'I' and resid 211 through 223 Processing helix chain 'J' and resid 34 through 42 Processing helix chain 'J' and resid 45 through 51 removed outlier: 4.000A pdb=" N GLU J 49 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 51' Processing helix chain 'J' and resid 67 through 76 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 96 through 116 removed outlier: 3.820A pdb=" N PHE J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 141 removed outlier: 3.649A pdb=" N ILE J 133 " --> pdb=" O THR J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 165 Processing helix chain 'J' and resid 182 through 194 removed outlier: 4.453A pdb=" N LEU J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Proline residue: J 192 - end of helix Processing helix chain 'J' and resid 217 through 230 removed outlier: 3.628A pdb=" N LYS J 225 " --> pdb=" O ASP J 221 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 228 " --> pdb=" O ILE J 224 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 277 through 283 removed outlier: 5.700A pdb=" N VAL A 279 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY A 222 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG A 281 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 220 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 223 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 343 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS A 55 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 367 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 57 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 277 through 283 removed outlier: 5.700A pdb=" N VAL A 279 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY A 222 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG A 281 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 220 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 223 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 343 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS A 50 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLU A 80 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 52 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 364 through 367 removed outlier: 6.525A pdb=" N VAL A 57 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 367 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS A 55 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 101 through 106 removed outlier: 3.512A pdb=" N LYS A 103 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.831A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 87 " --> pdb=" O TRP A 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TRP A 106 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 89 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 104 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY A 91 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.831A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.508A pdb=" N GLY A 228 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'B' and resid 8 through 11 Processing sheet with id= BB, first strand: chain 'B' and resid 17 through 20 Processing sheet with id= BC, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.685A pdb=" N VAL B 143 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 89 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.826A pdb=" N VAL B 110 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'C' and resid 50 through 52 removed outlier: 6.979A pdb=" N MET C 26 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE C 191 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 28 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 187 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.617A pdb=" N TYR C 184 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'C' and resid 145 through 146 Processing sheet with id= DA, first strand: chain 'D' and resid 15 through 16 removed outlier: 4.187A pdb=" N ARG D 16 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS D 61 " --> pdb=" O ARG D 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= DA Processing sheet with id= EA, first strand: chain 'E' and resid 17 through 18 Processing sheet with id= EB, first strand: chain 'E' and resid 22 through 24 removed outlier: 5.237A pdb=" N VAL E 36 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 61 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA E 99 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain 'E' and resid 85 through 86 Processing sheet with id= FA, first strand: chain 'F' and resid 133 through 140 removed outlier: 6.444A pdb=" N ILE F 134 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER F 54 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 166 " --> pdb=" O HIS F 51 " (cutoff:3.500A) Processing sheet with id= FB, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.135A pdb=" N ILE F 99 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY F 124 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 4 through 5 Processing sheet with id= IA, first strand: chain 'I' and resid 2 through 4 removed outlier: 3.522A pdb=" N VAL I 198 " --> pdb=" O ILE I 205 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 17 through 19 Processing sheet with id= IC, first strand: chain 'I' and resid 64 through 65 removed outlier: 3.566A pdb=" N ALA I 64 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 72 " --> pdb=" O GLN I 95 " (cutoff:3.500A) Processing sheet with id= ID, first strand: chain 'I' and resid 109 through 110 removed outlier: 3.516A pdb=" N ALA I 109 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id= IE, first strand: chain 'I' and resid 152 through 154 removed outlier: 3.549A pdb=" N ALA I 153 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing sheet with id= JA, first strand: chain 'J' and resid 26 through 31 removed outlier: 3.838A pdb=" N VAL J 17 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing sheet with id= JB, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.746A pdb=" N GLN J 64 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= JC, first strand: chain 'J' and resid 195 through 200 removed outlier: 6.298A pdb=" N VAL J 196 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE J 212 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU J 198 " --> pdb=" O CYS J 210 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS J 210 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL J 209 " --> pdb=" O PHE J 176 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 174 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N HIS J 171 " --> pdb=" O LYS J 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS J 240 " --> pdb=" O HIS J 171 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG J 173 " --> pdb=" O ASN J 238 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 177 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU J 234 " --> pdb=" O ILE J 177 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 804 hydrogen bonds 1350 hydrogen bond angles 0 basepair planarities 331 basepair parallelities 574 stacking parallelities Total time for adding SS restraints: 35.49 Time building geometry restraints manager: 20.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4421 1.32 - 1.45: 17831 1.45 - 1.57: 18180 1.57 - 1.69: 2310 1.69 - 1.81: 129 Bond restraints: 42871 Sorted by residual: bond pdb=" N HIS A 321 " pdb=" CA HIS A 321 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.16e+01 bond pdb=" O3' C N3131 " pdb=" P A N3132 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.50e-02 4.44e+03 1.06e+01 bond pdb=" CA ALA A 8 " pdb=" C ALA A 8 " ideal model delta sigma weight residual 1.524 1.565 -0.041 1.26e-02 6.30e+03 1.05e+01 bond pdb=" C TYR G 55 " pdb=" O TYR G 55 " ideal model delta sigma weight residual 1.236 1.273 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" CA PRO D 88 " pdb=" C PRO D 88 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.56e+00 ... (remaining 42866 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.56: 5780 105.56 - 112.68: 23240 112.68 - 119.81: 16700 119.81 - 126.94: 14893 126.94 - 134.06: 2935 Bond angle restraints: 63548 Sorted by residual: angle pdb=" O3' G N2995 " pdb=" C3' G N2995 " pdb=" C2' G N2995 " ideal model delta sigma weight residual 113.70 128.95 -15.25 1.50e+00 4.44e-01 1.03e+02 angle pdb=" O3' G N1542 " pdb=" C3' G N1542 " pdb=" C2' G N1542 " ideal model delta sigma weight residual 109.50 123.01 -13.51 1.50e+00 4.44e-01 8.11e+01 angle pdb=" C4' G N1565 " pdb=" C3' G N1565 " pdb=" O3' G N1565 " ideal model delta sigma weight residual 113.00 125.88 -12.88 1.50e+00 4.44e-01 7.37e+01 angle pdb=" O3' A N1582 " pdb=" C3' A N1582 " pdb=" C2' A N1582 " ideal model delta sigma weight residual 113.70 126.41 -12.71 1.50e+00 4.44e-01 7.18e+01 angle pdb=" O3' U N1550 " pdb=" C3' U N1550 " pdb=" C2' U N1550 " ideal model delta sigma weight residual 109.50 121.26 -11.76 1.50e+00 4.44e-01 6.15e+01 ... (remaining 63543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 24296 35.97 - 71.93: 2530 71.93 - 107.90: 284 107.90 - 143.87: 11 143.87 - 179.83: 33 Dihedral angle restraints: 27154 sinusoidal: 21679 harmonic: 5475 Sorted by residual: dihedral pdb=" CA ASN E 10 " pdb=" C ASN E 10 " pdb=" N TYR E 11 " pdb=" CA TYR E 11 " ideal model delta harmonic sigma weight residual 180.00 51.32 128.68 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" O4' C N3169 " pdb=" C1' C N3169 " pdb=" N1 C N3169 " pdb=" C2 C N3169 " ideal model delta sinusoidal sigma weight residual -160.00 19.83 -179.83 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U N1240 " pdb=" C1' U N1240 " pdb=" N1 U N1240 " pdb=" C2 U N1240 " ideal model delta sinusoidal sigma weight residual -160.00 16.38 -176.38 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 27151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 7025 0.157 - 0.314: 1071 0.314 - 0.471: 20 0.471 - 0.628: 5 0.628 - 0.785: 2 Chirality restraints: 8123 Sorted by residual: chirality pdb=" C3' G N1457 " pdb=" C4' G N1457 " pdb=" O3' G N1457 " pdb=" C2' G N1457 " both_signs ideal model delta sigma weight residual False -2.74 -1.96 -0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3' U N1476 " pdb=" C4' U N1476 " pdb=" O3' U N1476 " pdb=" C2' U N1476 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C3' U N1550 " pdb=" C4' U N1550 " pdb=" O3' U N1550 " pdb=" C2' U N1550 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.71e+00 ... (remaining 8120 not shown) Planarity restraints: 3754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N1393 " 0.025 2.00e-02 2.50e+03 4.70e-02 4.97e+01 pdb=" N1 C N1393 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C N1393 " -0.023 2.00e-02 2.50e+03 pdb=" O2 C N1393 " 0.064 2.00e-02 2.50e+03 pdb=" N3 C N1393 " -0.103 2.00e-02 2.50e+03 pdb=" C4 C N1393 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C N1393 " 0.054 2.00e-02 2.50e+03 pdb=" C5 C N1393 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C N1393 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G N1385 " 0.003 2.00e-02 2.50e+03 3.65e-02 3.99e+01 pdb=" N9 G N1385 " -0.019 2.00e-02 2.50e+03 pdb=" C8 G N1385 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G N1385 " 0.011 2.00e-02 2.50e+03 pdb=" C5 G N1385 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G N1385 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G N1385 " -0.063 2.00e-02 2.50e+03 pdb=" N1 G N1385 " 0.095 2.00e-02 2.50e+03 pdb=" C2 G N1385 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G N1385 " -0.048 2.00e-02 2.50e+03 pdb=" N3 G N1385 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G N1385 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C N3462 " 0.031 2.00e-02 2.50e+03 4.08e-02 3.75e+01 pdb=" N1 C N3462 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C N3462 " 0.013 2.00e-02 2.50e+03 pdb=" O2 C N3462 " -0.066 2.00e-02 2.50e+03 pdb=" N3 C N3462 " 0.091 2.00e-02 2.50e+03 pdb=" C4 C N3462 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C N3462 " -0.024 2.00e-02 2.50e+03 pdb=" C5 C N3462 " -0.013 2.00e-02 2.50e+03 pdb=" C6 C N3462 " -0.009 2.00e-02 2.50e+03 ... (remaining 3751 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 3 1.93 - 2.67: 1954 2.67 - 3.42: 50654 3.42 - 4.16: 126798 4.16 - 4.90: 175671 Nonbonded interactions: 355080 Sorted by model distance: nonbonded pdb=" N1 A N2425 " pdb=" O4 U N2442 " model vdw 1.192 2.496 nonbonded pdb=" O4 U N2676 " pdb=" N1 A N3134 " model vdw 1.537 2.496 nonbonded pdb=" C2 A N2425 " pdb=" O4 U N2442 " model vdw 1.931 3.340 nonbonded pdb=" O6 G N1541 " pdb=" O2' A N2632 " model vdw 2.142 2.440 nonbonded pdb=" O TYR A 134 " pdb=" OH TYR A 138 " model vdw 2.181 2.440 ... (remaining 355075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.740 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: 7.870 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 131.110 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 42871 Z= 0.418 Angle : 1.218 15.255 63548 Z= 0.819 Chirality : 0.098 0.785 8123 Planarity : 0.007 0.140 3754 Dihedral : 23.203 179.833 23624 Min Nonbonded Distance : 1.192 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 2.86 % Allowed : 9.12 % Favored : 88.01 % Rotamer: Outliers : 2.32 % Allowed : 6.54 % Favored : 91.13 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 1.47 % Twisted General : 0.16 % 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: -3.68 (0.15), residues: 1885 helix: -0.93 (0.21), residues: 430 sheet: -2.89 (0.26), residues: 271 loop : -3.10 (0.14), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 258 HIS 0.012 0.002 HIS A 276 PHE 0.024 0.003 PHE B 115 TYR 0.028 0.003 TYR A 134 ARG 0.009 0.001 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 441 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5400 (mtt) cc_final: 0.5089 (mtt) REVERT: A 61 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6753 (tp30) REVERT: A 71 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 79 ILE cc_start: 0.9086 (pt) cc_final: 0.8681 (mt) REVERT: A 99 LEU cc_start: 0.7343 (mp) cc_final: 0.6930 (mp) REVERT: A 100 LYS cc_start: 0.5734 (tptp) cc_final: 0.5125 (mmmt) REVERT: A 156 LYS cc_start: 0.7971 (ttpp) cc_final: 0.7756 (ttmt) REVERT: A 171 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7824 (mmtm) REVERT: A 178 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.6204 (mppt) REVERT: A 193 GLU cc_start: 0.7958 (tt0) cc_final: 0.7724 (tt0) REVERT: A 224 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 261 SER cc_start: 0.7701 (m) cc_final: 0.7098 (p) REVERT: A 262 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6695 (mtm-85) REVERT: A 273 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 282 ASN cc_start: 0.8586 (m-40) cc_final: 0.8300 (m110) REVERT: A 347 ARG cc_start: 0.7990 (mtt90) cc_final: 0.5955 (ttp-170) REVERT: A 348 LYS cc_start: 0.8486 (mttt) cc_final: 0.8191 (mttt) REVERT: A 366 PHE cc_start: 0.7241 (m-80) cc_final: 0.7014 (m-80) REVERT: B 20 VAL cc_start: 0.8716 (p) cc_final: 0.8410 (t) REVERT: B 21 LYS cc_start: 0.7652 (tttp) cc_final: 0.6768 (tppt) REVERT: B 26 LYS cc_start: 0.8164 (mttm) cc_final: 0.7589 (ttmm) REVERT: B 34 LEU cc_start: 0.8233 (mt) cc_final: 0.8006 (mt) REVERT: B 52 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6631 (mm-30) REVERT: B 70 THR cc_start: 0.8265 (m) cc_final: 0.7942 (p) REVERT: B 109 VAL cc_start: 0.8420 (p) cc_final: 0.7615 (m) REVERT: B 125 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6764 (mm-30) REVERT: B 167 TYR cc_start: 0.6935 (m-80) cc_final: 0.6427 (m-80) REVERT: C 25 LYS cc_start: 0.3914 (mmtt) cc_final: 0.3491 (mmmt) REVERT: C 56 LYS cc_start: 0.1393 (mptt) cc_final: 0.0960 (mtmm) REVERT: D 25 MET cc_start: 0.1007 (mtt) cc_final: 0.0670 (ttp) REVERT: D 99 LYS cc_start: 0.4708 (pttm) cc_final: 0.4351 (pttm) REVERT: D 116 MET cc_start: 0.1968 (ttm) cc_final: 0.1606 (tpt) REVERT: E 33 ASN cc_start: 0.8390 (m110) cc_final: 0.8081 (m-40) REVERT: E 51 SER cc_start: 0.9071 (m) cc_final: 0.8785 (m) REVERT: E 83 LYS cc_start: 0.8715 (tptp) cc_final: 0.6110 (mptt) REVERT: E 106 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7322 (mmtt) REVERT: E 112 ASN cc_start: 0.7325 (p0) cc_final: 0.6928 (p0) REVERT: E 125 TRP cc_start: 0.8470 (m100) cc_final: 0.8251 (m100) REVERT: E 127 LYS cc_start: 0.7965 (tptm) cc_final: 0.7738 (tppt) REVERT: F 22 TYR cc_start: 0.8551 (m-80) cc_final: 0.8330 (m-80) REVERT: F 78 LYS cc_start: 0.6066 (mttt) cc_final: 0.5850 (mptt) REVERT: F 123 MET cc_start: 0.7171 (ttt) cc_final: 0.6952 (ttt) REVERT: F 143 ASN cc_start: 0.7299 (m110) cc_final: 0.7085 (m-40) REVERT: F 144 MET cc_start: 0.7226 (mtt) cc_final: 0.6973 (mtm) REVERT: F 153 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7545 (ttt-90) REVERT: G 50 ARG cc_start: 0.5850 (ptm-80) cc_final: 0.3257 (mtt90) REVERT: H 17 MET cc_start: 0.7938 (mmt) cc_final: 0.7246 (mmt) REVERT: I 1 MET cc_start: 0.3776 (mmm) cc_final: 0.2179 (tmm) REVERT: I 24 CYS cc_start: 0.6645 (t) cc_final: 0.6378 (t) REVERT: I 62 LEU cc_start: 0.5396 (tp) cc_final: 0.5130 (tt) REVERT: I 80 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5541 (mt-10) REVERT: I 86 ASN cc_start: 0.6255 (m-40) cc_final: 0.6048 (m-40) REVERT: I 111 ASN cc_start: 0.7391 (p0) cc_final: 0.6794 (p0) REVERT: I 136 GLU cc_start: 0.4001 (tt0) cc_final: 0.3739 (tp30) REVERT: I 155 THR cc_start: 0.6098 (p) cc_final: 0.5885 (p) REVERT: I 164 MET cc_start: 0.5094 (mmt) cc_final: 0.4681 (mtm) REVERT: J 21 LYS cc_start: 0.6838 (tttp) cc_final: 0.6557 (ttpt) REVERT: J 35 LYS cc_start: 0.4609 (mttm) cc_final: 0.4247 (mtmm) REVERT: J 145 LYS cc_start: 0.6652 (mmtm) cc_final: 0.6108 (ttmt) REVERT: J 188 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5943 (tt0) REVERT: J 200 GLU cc_start: 0.3202 (mt-10) cc_final: 0.2789 (mt-10) REVERT: J 209 VAL cc_start: 0.3732 (m) cc_final: 0.3342 (p) outliers start: 38 outliers final: 13 residues processed: 470 average time/residue: 0.6161 time to fit residues: 441.3988 Evaluate side-chains 335 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 317 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain J residue 128 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 40.0000 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 166 HIS A 168 GLN A 170 HIS A 176 GLN A 180 HIS A 276 HIS ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS B 40 HIS B 114 ASN B 135 ASN B 147 ASN C 93 ASN C 133 GLN C 164 GLN D 103 ASN D 137 HIS F 59 GLN F 177 ASN G 30 HIS G 33 ASN H 43 ASN I 40 ASN I 118 HIS J 14 ASN J 121 ASN J 147 ASN J 181 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 42871 Z= 0.386 Angle : 0.826 14.178 63548 Z= 0.421 Chirality : 0.046 0.273 8123 Planarity : 0.006 0.150 3754 Dihedral : 23.576 179.783 19879 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.81 % Favored : 89.44 % Rotamer: Outliers : 4.71 % Allowed : 13.64 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.97 (0.17), residues: 1885 helix: 0.02 (0.24), residues: 445 sheet: -2.24 (0.29), residues: 239 loop : -2.90 (0.14), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 122 HIS 0.009 0.002 HIS A 55 PHE 0.022 0.003 PHE A 202 TYR 0.026 0.003 TYR F 17 ARG 0.009 0.001 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 326 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5404 (mtt) cc_final: 0.4999 (mtt) REVERT: A 61 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: A 68 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5890 (m-70) REVERT: A 71 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 100 LYS cc_start: 0.5211 (tptp) cc_final: 0.4840 (mmmt) REVERT: A 132 THR cc_start: 0.6841 (m) cc_final: 0.6567 (m) REVERT: A 156 LYS cc_start: 0.7707 (ttpp) cc_final: 0.7490 (ttpt) REVERT: A 157 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6745 (mtp180) REVERT: A 171 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8071 (mmtm) REVERT: A 178 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.5969 (mptp) REVERT: A 224 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8056 (p) REVERT: A 261 SER cc_start: 0.7132 (m) cc_final: 0.6830 (p) REVERT: A 347 ARG cc_start: 0.8149 (mtt90) cc_final: 0.6385 (ttp-170) REVERT: A 348 LYS cc_start: 0.8592 (mttt) cc_final: 0.8356 (mttp) REVERT: A 388 PHE cc_start: 0.6162 (m-10) cc_final: 0.5952 (m-10) REVERT: A 393 SER cc_start: 0.3951 (OUTLIER) cc_final: 0.3288 (m) REVERT: A 395 SER cc_start: 0.4123 (OUTLIER) cc_final: 0.2633 (m) REVERT: B 21 LYS cc_start: 0.7512 (tttp) cc_final: 0.6821 (tmtt) REVERT: B 26 LYS cc_start: 0.8224 (mttm) cc_final: 0.7421 (tttt) REVERT: B 52 GLU cc_start: 0.8158 (mt-10) cc_final: 0.6925 (mm-30) REVERT: B 75 ILE cc_start: 0.8531 (pt) cc_final: 0.8237 (mt) REVERT: B 82 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8403 (t) REVERT: B 91 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7353 (mtp-110) REVERT: B 125 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7533 (pm20) REVERT: B 167 TYR cc_start: 0.7015 (m-80) cc_final: 0.6060 (m-80) REVERT: C 1 MET cc_start: 0.0310 (ptt) cc_final: -0.0165 (tpp) REVERT: C 98 LYS cc_start: 0.1998 (mttt) cc_final: 0.1532 (mmtm) REVERT: D 25 MET cc_start: 0.1345 (mtt) cc_final: 0.0930 (ttp) REVERT: D 56 MET cc_start: 0.3360 (mtt) cc_final: 0.2366 (mmt) REVERT: E 106 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7703 (ptpp) REVERT: E 112 ASN cc_start: 0.7265 (p0) cc_final: 0.6945 (p0) REVERT: F 24 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5665 (pmm150) REVERT: F 33 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7283 (mm) REVERT: F 59 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: F 61 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7727 (p) REVERT: F 102 MET cc_start: 0.7581 (mmt) cc_final: 0.7324 (mmt) REVERT: F 144 MET cc_start: 0.7239 (mtt) cc_final: 0.6923 (mtm) REVERT: F 147 ASN cc_start: 0.8238 (m-40) cc_final: 0.7897 (m110) REVERT: F 153 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7477 (ttt-90) REVERT: G 43 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7952 (mttt) REVERT: G 50 ARG cc_start: 0.6262 (ptm-80) cc_final: 0.3702 (mtt90) REVERT: H 17 MET cc_start: 0.7610 (mmt) cc_final: 0.7045 (mmt) REVERT: H 44 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8428 (mm) REVERT: I 1 MET cc_start: 0.3681 (mmm) cc_final: 0.2150 (tmm) REVERT: I 19 LEU cc_start: 0.7717 (mt) cc_final: 0.7499 (tp) REVERT: I 50 GLU cc_start: 0.5503 (mt-10) cc_final: 0.5121 (mt-10) REVERT: I 111 ASN cc_start: 0.6084 (p0) cc_final: 0.5523 (p0) REVERT: J 35 LYS cc_start: 0.4168 (mttm) cc_final: 0.3945 (mtpp) REVERT: J 145 LYS cc_start: 0.6665 (mmtm) cc_final: 0.6427 (ttmt) REVERT: J 151 LYS cc_start: 0.3753 (tptt) cc_final: 0.3363 (mmtm) REVERT: J 165 MET cc_start: 0.1683 (mtm) cc_final: 0.0938 (tpp) REVERT: J 201 ASP cc_start: 0.6655 (t0) cc_final: 0.6379 (t0) REVERT: J 241 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6655 (t70) outliers start: 77 outliers final: 40 residues processed: 376 average time/residue: 0.5847 time to fit residues: 345.9621 Evaluate side-chains 330 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 277 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 241 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 186 optimal weight: 40.0000 chunk 75 optimal weight: 0.0030 chunk 273 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN E 33 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN I 86 ASN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN J 80 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 42871 Z= 0.387 Angle : 0.793 13.645 63548 Z= 0.404 Chirality : 0.046 0.284 8123 Planarity : 0.006 0.151 3754 Dihedral : 23.563 178.978 19870 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.71 % Favored : 89.71 % Rotamer: Outliers : 5.81 % Allowed : 15.60 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.88 (0.17), residues: 1885 helix: 0.07 (0.24), residues: 433 sheet: -2.13 (0.28), residues: 255 loop : -2.81 (0.15), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 125 HIS 0.013 0.002 HIS A 276 PHE 0.020 0.002 PHE B 115 TYR 0.029 0.003 TYR B 133 ARG 0.011 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 294 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5148 (mtt) cc_final: 0.4938 (mtt) REVERT: A 61 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6483 (tp30) REVERT: A 89 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 92 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.5942 (t80) REVERT: A 100 LYS cc_start: 0.4994 (tptp) cc_final: 0.4637 (mmmt) REVERT: A 117 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5098 (mtt-85) REVERT: A 171 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7871 (mmtm) REVERT: A 347 ARG cc_start: 0.8047 (mtt90) cc_final: 0.6266 (ttp-170) REVERT: A 348 LYS cc_start: 0.8525 (mttt) cc_final: 0.8273 (mttt) REVERT: A 388 PHE cc_start: 0.6382 (m-10) cc_final: 0.6023 (m-10) REVERT: A 393 SER cc_start: 0.3253 (OUTLIER) cc_final: 0.2345 (m) REVERT: A 395 SER cc_start: 0.3615 (OUTLIER) cc_final: 0.2169 (m) REVERT: B 21 LYS cc_start: 0.7579 (tttp) cc_final: 0.6877 (tmtt) REVERT: B 26 LYS cc_start: 0.7783 (mttm) cc_final: 0.7154 (tttt) REVERT: B 75 ILE cc_start: 0.8540 (pt) cc_final: 0.8320 (mt) REVERT: B 118 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 125 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7617 (pm20) REVERT: B 181 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7649 (tp30) REVERT: C 1 MET cc_start: 0.0016 (ptt) cc_final: -0.0339 (tpt) REVERT: C 61 ARG cc_start: 0.4722 (mmm160) cc_final: 0.4235 (mtp85) REVERT: C 73 GLU cc_start: 0.3316 (OUTLIER) cc_final: 0.2920 (pm20) REVERT: C 98 LYS cc_start: 0.2393 (mttt) cc_final: 0.1843 (mmtm) REVERT: D 25 MET cc_start: 0.1032 (mtt) cc_final: 0.0742 (ttp) REVERT: D 56 MET cc_start: 0.3549 (mtt) cc_final: 0.2763 (mmt) REVERT: E 1 MET cc_start: 0.5218 (tpp) cc_final: 0.4912 (tpp) REVERT: E 106 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7807 (ptpp) REVERT: E 112 ASN cc_start: 0.7424 (p0) cc_final: 0.6918 (p0) REVERT: E 125 TRP cc_start: 0.8709 (m100) cc_final: 0.8411 (m100) REVERT: F 21 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7646 (ptt-90) REVERT: F 24 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5632 (pmm150) REVERT: F 33 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7231 (mm) REVERT: F 102 MET cc_start: 0.7645 (mmt) cc_final: 0.7372 (mmt) REVERT: F 144 MET cc_start: 0.7256 (mtt) cc_final: 0.6927 (mtm) REVERT: F 153 ARG cc_start: 0.8019 (ttt90) cc_final: 0.7495 (ttt-90) REVERT: F 171 TRP cc_start: 0.7276 (m100) cc_final: 0.6941 (m100) REVERT: F 183 LYS cc_start: 0.8156 (tttt) cc_final: 0.7858 (tttp) REVERT: F 191 MET cc_start: 0.7269 (ttt) cc_final: 0.7062 (ttt) REVERT: G 43 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8033 (mttt) REVERT: G 50 ARG cc_start: 0.6734 (ptm-80) cc_final: 0.4091 (mtm180) REVERT: G 53 MET cc_start: 0.8156 (tpp) cc_final: 0.7898 (tpt) REVERT: I 1 MET cc_start: 0.2975 (mmm) cc_final: 0.1771 (tmm) REVERT: I 19 LEU cc_start: 0.7886 (mt) cc_final: 0.7628 (mt) REVERT: I 80 GLU cc_start: 0.5423 (mt-10) cc_final: 0.5033 (mt-10) REVERT: J 145 LYS cc_start: 0.7014 (mmtm) cc_final: 0.6785 (ttmt) REVERT: J 165 MET cc_start: 0.1824 (mtm) cc_final: 0.0832 (tpp) REVERT: J 208 ILE cc_start: 0.1723 (mm) cc_final: 0.1219 (tt) REVERT: J 241 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.5836 (t70) outliers start: 95 outliers final: 58 residues processed: 363 average time/residue: 0.5529 time to fit residues: 317.1698 Evaluate side-chains 340 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 271 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 241 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 10.0000 chunk 205 optimal weight: 30.0000 chunk 142 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 78 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN E 33 ASN E 47 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN I 21 ASN I 162 HIS I 170 GLN J 8 ASN J 238 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 42871 Z= 0.461 Angle : 0.869 14.748 63548 Z= 0.437 Chirality : 0.049 0.301 8123 Planarity : 0.007 0.154 3754 Dihedral : 23.631 179.990 19869 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.77 % Favored : 88.70 % Rotamer: Outliers : 7.09 % Allowed : 17.74 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.16 % 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: -3.13 (0.17), residues: 1885 helix: -0.65 (0.23), residues: 461 sheet: -2.10 (0.29), residues: 245 loop : -2.84 (0.15), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP F 171 HIS 0.014 0.002 HIS A 276 PHE 0.033 0.003 PHE B 115 TYR 0.027 0.003 TYR B 133 ARG 0.009 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 298 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6455 (tp30) REVERT: A 68 HIS cc_start: 0.5885 (OUTLIER) cc_final: 0.5612 (m170) REVERT: A 70 LYS cc_start: 0.7482 (mtpt) cc_final: 0.7224 (mtpp) REVERT: A 89 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8869 (tp) REVERT: A 92 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.5826 (t80) REVERT: A 100 LYS cc_start: 0.5108 (tptp) cc_final: 0.4725 (mmmt) REVERT: A 117 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5198 (mtt-85) REVERT: A 137 GLN cc_start: 0.4249 (OUTLIER) cc_final: 0.3992 (tm-30) REVERT: A 233 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8636 (mm) REVERT: A 331 MET cc_start: 0.8485 (ttm) cc_final: 0.8192 (ttm) REVERT: A 347 ARG cc_start: 0.8191 (mtt90) cc_final: 0.6353 (ttp-170) REVERT: A 366 PHE cc_start: 0.7749 (m-80) cc_final: 0.7547 (m-80) REVERT: A 388 PHE cc_start: 0.6422 (m-10) cc_final: 0.6199 (m-80) REVERT: A 395 SER cc_start: 0.3979 (OUTLIER) cc_final: 0.3128 (m) REVERT: B 21 LYS cc_start: 0.7786 (tttp) cc_final: 0.7041 (tmtt) REVERT: B 26 LYS cc_start: 0.7826 (mttm) cc_final: 0.7185 (tttt) REVERT: B 35 SER cc_start: 0.8119 (m) cc_final: 0.7497 (p) REVERT: B 75 ILE cc_start: 0.8486 (pt) cc_final: 0.8185 (mt) REVERT: B 120 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7228 (tp) REVERT: B 125 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7566 (pm20) REVERT: B 181 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7747 (tp30) REVERT: C 1 MET cc_start: 0.0794 (ptt) cc_final: 0.0387 (mmt) REVERT: C 73 GLU cc_start: 0.3318 (OUTLIER) cc_final: 0.2868 (pm20) REVERT: D 25 MET cc_start: 0.2012 (mtt) cc_final: 0.1596 (ptt) REVERT: D 56 MET cc_start: 0.3843 (mtt) cc_final: 0.3352 (mmt) REVERT: D 83 LYS cc_start: 0.2820 (tptp) cc_final: 0.2348 (ptpt) REVERT: E 106 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7889 (ptpp) REVERT: E 112 ASN cc_start: 0.7281 (p0) cc_final: 0.6668 (p0) REVERT: F 21 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7687 (ptt-90) REVERT: F 24 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5697 (pmm150) REVERT: F 33 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.6956 (mm) REVERT: F 102 MET cc_start: 0.7673 (mmt) cc_final: 0.7388 (mmt) REVERT: F 136 PHE cc_start: 0.8478 (m-80) cc_final: 0.8182 (m-80) REVERT: F 144 MET cc_start: 0.7209 (mtt) cc_final: 0.6915 (mtm) REVERT: F 153 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7526 (ttt-90) REVERT: G 12 LYS cc_start: 0.8305 (mttm) cc_final: 0.8061 (mttm) REVERT: G 43 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8183 (mttt) REVERT: I 62 LEU cc_start: 0.5648 (tp) cc_final: 0.5389 (tt) REVERT: I 111 ASN cc_start: 0.6138 (p0) cc_final: 0.5707 (p0) REVERT: I 164 MET cc_start: 0.5840 (mtm) cc_final: 0.5481 (mtt) REVERT: I 191 GLU cc_start: 0.6816 (tt0) cc_final: 0.6511 (tt0) REVERT: J 68 LYS cc_start: 0.2670 (OUTLIER) cc_final: 0.2362 (ttmt) REVERT: J 145 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6818 (ttmt) REVERT: J 165 MET cc_start: 0.1729 (mtm) cc_final: 0.0905 (tpt) outliers start: 116 outliers final: 79 residues processed: 380 average time/residue: 0.5584 time to fit residues: 336.3182 Evaluate side-chains 369 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 276 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 241 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 201 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 148 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 73 optimal weight: 50.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 98 ASN ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN H 32 ASN J 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 42871 Z= 0.369 Angle : 0.772 13.982 63548 Z= 0.391 Chirality : 0.045 0.281 8123 Planarity : 0.006 0.152 3754 Dihedral : 23.515 178.724 19868 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.13 % Favored : 89.34 % Rotamer: Outliers : 7.34 % Allowed : 19.94 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.97 (0.17), residues: 1885 helix: -0.45 (0.24), residues: 458 sheet: -1.90 (0.30), residues: 236 loop : -2.78 (0.15), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 125 HIS 0.010 0.002 HIS A 276 PHE 0.019 0.002 PHE A 131 TYR 0.036 0.003 TYR A 286 ARG 0.011 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 277 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.5620 (t0) cc_final: 0.5379 (t0) REVERT: A 59 ASP cc_start: 0.7923 (p0) cc_final: 0.7365 (p0) REVERT: A 70 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7562 (mtpp) REVERT: A 89 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8847 (tp) REVERT: A 100 LYS cc_start: 0.5065 (tptp) cc_final: 0.4719 (mmmt) REVERT: A 117 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5080 (mtt-85) REVERT: A 137 GLN cc_start: 0.4236 (OUTLIER) cc_final: 0.3149 (tm-30) REVERT: A 157 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6633 (mtp180) REVERT: A 233 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8592 (mm) REVERT: A 341 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7581 (pttt) REVERT: A 347 ARG cc_start: 0.8136 (mtt90) cc_final: 0.6323 (ttp-170) REVERT: A 395 SER cc_start: 0.3534 (OUTLIER) cc_final: 0.2730 (m) REVERT: B 14 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6777 (pm20) REVERT: B 21 LYS cc_start: 0.7733 (tttp) cc_final: 0.7031 (tmtt) REVERT: B 26 LYS cc_start: 0.7834 (mttm) cc_final: 0.7204 (tttt) REVERT: B 35 SER cc_start: 0.8103 (m) cc_final: 0.7474 (p) REVERT: B 70 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 120 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7061 (tp) REVERT: B 125 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7608 (pm20) REVERT: B 181 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7748 (tp30) REVERT: C 1 MET cc_start: 0.0958 (ptt) cc_final: 0.0632 (mmm) REVERT: D 25 MET cc_start: 0.2507 (mtt) cc_final: 0.1817 (ptt) REVERT: D 56 MET cc_start: 0.3827 (mtt) cc_final: 0.3073 (mmt) REVERT: D 99 LYS cc_start: 0.3767 (OUTLIER) cc_final: 0.3560 (ptmm) REVERT: E 1 MET cc_start: 0.5316 (tpp) cc_final: 0.4802 (tpp) REVERT: E 106 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7901 (ptpp) REVERT: E 112 ASN cc_start: 0.7279 (p0) cc_final: 0.6645 (p0) REVERT: F 21 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7631 (ptt-90) REVERT: F 24 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5763 (pmm150) REVERT: F 33 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7372 (mm) REVERT: F 102 MET cc_start: 0.7544 (mmt) cc_final: 0.7290 (mmt) REVERT: F 144 MET cc_start: 0.7296 (mtt) cc_final: 0.7011 (mtm) REVERT: F 147 ASN cc_start: 0.8035 (m-40) cc_final: 0.7689 (m110) REVERT: F 153 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7551 (ttt-90) REVERT: F 171 TRP cc_start: 0.7435 (m100) cc_final: 0.7061 (t-100) REVERT: G 44 ILE cc_start: 0.7877 (mm) cc_final: 0.7566 (tt) REVERT: G 53 MET cc_start: 0.8218 (tpp) cc_final: 0.8008 (tpt) REVERT: I 32 LYS cc_start: 0.4832 (OUTLIER) cc_final: 0.3973 (mmmt) REVERT: I 111 ASN cc_start: 0.6182 (p0) cc_final: 0.5977 (p0) REVERT: J 145 LYS cc_start: 0.6702 (mmtm) cc_final: 0.6484 (ttmt) REVERT: J 165 MET cc_start: 0.1746 (mtm) cc_final: 0.0848 (tpp) outliers start: 120 outliers final: 77 residues processed: 360 average time/residue: 0.5739 time to fit residues: 326.3210 Evaluate side-chains 355 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 265 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 97 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 chunk 57 optimal weight: 40.0000 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 98 ASN F 14 ASN ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42871 Z= 0.252 Angle : 0.669 13.344 63548 Z= 0.342 Chirality : 0.040 0.267 8123 Planarity : 0.005 0.152 3754 Dihedral : 23.397 179.177 19865 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.18 % Favored : 90.29 % Rotamer: Outliers : 6.06 % Allowed : 21.47 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.59 (0.17), residues: 1885 helix: 0.06 (0.25), residues: 443 sheet: -1.71 (0.31), residues: 230 loop : -2.58 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 125 HIS 0.006 0.001 HIS F 95 PHE 0.015 0.002 PHE J 57 TYR 0.021 0.002 TYR B 133 ARG 0.012 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 286 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.5489 (t0) cc_final: 0.5275 (t0) REVERT: A 59 ASP cc_start: 0.7741 (p0) cc_final: 0.7183 (p0) REVERT: A 70 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7558 (mtpp) REVERT: A 100 LYS cc_start: 0.4904 (tptp) cc_final: 0.4566 (mmmt) REVERT: A 117 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5439 (mtt-85) REVERT: A 137 GLN cc_start: 0.4217 (OUTLIER) cc_final: 0.3961 (tm-30) REVERT: A 157 ARG cc_start: 0.6853 (mtp180) cc_final: 0.6594 (mtp180) REVERT: A 341 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7603 (pttt) REVERT: A 347 ARG cc_start: 0.8073 (mtt90) cc_final: 0.6318 (ttp-170) REVERT: A 353 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6588 (mm-40) REVERT: A 388 PHE cc_start: 0.6178 (m-10) cc_final: 0.5895 (m-80) REVERT: A 395 SER cc_start: 0.3564 (OUTLIER) cc_final: 0.2817 (m) REVERT: B 14 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6779 (pm20) REVERT: B 21 LYS cc_start: 0.7658 (tttp) cc_final: 0.6973 (tmtt) REVERT: B 26 LYS cc_start: 0.7782 (mttm) cc_final: 0.7387 (tttt) REVERT: B 54 THR cc_start: 0.7567 (t) cc_final: 0.7031 (p) REVERT: B 70 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 120 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.6843 (tp) REVERT: B 125 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7485 (pm20) REVERT: C 1 MET cc_start: 0.0960 (ptt) cc_final: 0.0668 (mmm) REVERT: D 25 MET cc_start: 0.1830 (mtt) cc_final: 0.1353 (ptt) REVERT: D 56 MET cc_start: 0.3858 (mtt) cc_final: 0.3171 (mmt) REVERT: D 99 LYS cc_start: 0.3814 (OUTLIER) cc_final: 0.3535 (ptmm) REVERT: E 1 MET cc_start: 0.5381 (tpp) cc_final: 0.4892 (tpp) REVERT: E 33 ASN cc_start: 0.7953 (m110) cc_final: 0.7651 (m-40) REVERT: E 106 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7939 (ptpp) REVERT: E 112 ASN cc_start: 0.7318 (p0) cc_final: 0.6683 (p0) REVERT: E 119 LYS cc_start: 0.7784 (tmtt) cc_final: 0.7401 (tmtt) REVERT: E 123 ASP cc_start: 0.7687 (m-30) cc_final: 0.7349 (m-30) REVERT: F 24 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5814 (pmm150) REVERT: F 87 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6517 (ptm) REVERT: F 102 MET cc_start: 0.7502 (mmt) cc_final: 0.7281 (mmt) REVERT: F 147 ASN cc_start: 0.7926 (m-40) cc_final: 0.7628 (m110) REVERT: F 153 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7570 (ttt-90) REVERT: F 171 TRP cc_start: 0.7346 (m100) cc_final: 0.7065 (t-100) REVERT: G 43 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8063 (mttt) REVERT: G 44 ILE cc_start: 0.7907 (mm) cc_final: 0.7572 (tt) REVERT: G 47 ARG cc_start: 0.6418 (mtt90) cc_final: 0.6047 (mtp85) REVERT: G 53 MET cc_start: 0.8229 (tpp) cc_final: 0.7936 (tpt) REVERT: H 34 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7447 (ptt90) REVERT: I 32 LYS cc_start: 0.4716 (OUTLIER) cc_final: 0.3867 (mmmt) REVERT: I 111 ASN cc_start: 0.6167 (p0) cc_final: 0.5771 (p0) REVERT: J 48 ASP cc_start: 0.5061 (OUTLIER) cc_final: 0.4782 (m-30) REVERT: J 68 LYS cc_start: 0.3177 (OUTLIER) cc_final: 0.2964 (ttmt) REVERT: J 165 MET cc_start: 0.1975 (mtm) cc_final: 0.1151 (tpt) outliers start: 99 outliers final: 66 residues processed: 350 average time/residue: 0.5993 time to fit residues: 335.8017 Evaluate side-chains 351 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 271 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 ASN Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 280 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 314 ASN A 353 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN I 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 42871 Z= 0.276 Angle : 0.686 13.274 63548 Z= 0.350 Chirality : 0.040 0.256 8123 Planarity : 0.005 0.152 3754 Dihedral : 23.411 179.417 19865 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.39 % Favored : 90.08 % Rotamer: Outliers : 6.91 % Allowed : 21.65 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.51 (0.18), residues: 1885 helix: 0.14 (0.25), residues: 444 sheet: -1.66 (0.30), residues: 239 loop : -2.54 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 125 HIS 0.007 0.001 HIS A 276 PHE 0.017 0.002 PHE J 57 TYR 0.025 0.002 TYR A 286 ARG 0.013 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 269 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8515 (t0) cc_final: 0.8043 (t0) REVERT: A 35 ASP cc_start: 0.5363 (t0) cc_final: 0.5140 (t0) REVERT: A 59 ASP cc_start: 0.7853 (p0) cc_final: 0.7282 (p0) REVERT: A 70 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7479 (mtpp) REVERT: A 89 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8879 (tp) REVERT: A 100 LYS cc_start: 0.4976 (tptp) cc_final: 0.4645 (mmmt) REVERT: A 117 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.4958 (mtt-85) REVERT: A 137 GLN cc_start: 0.4200 (OUTLIER) cc_final: 0.3937 (tm-30) REVERT: A 233 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 341 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7586 (pttt) REVERT: A 347 ARG cc_start: 0.8120 (mtt90) cc_final: 0.6395 (ttp-170) REVERT: A 353 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6540 (mm110) REVERT: A 388 PHE cc_start: 0.5904 (m-10) cc_final: 0.5505 (m-80) REVERT: A 395 SER cc_start: 0.3396 (OUTLIER) cc_final: 0.2573 (m) REVERT: B 14 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6709 (pm20) REVERT: B 21 LYS cc_start: 0.7701 (tttp) cc_final: 0.6942 (tmtt) REVERT: B 26 LYS cc_start: 0.7754 (mttm) cc_final: 0.7352 (tttt) REVERT: B 54 THR cc_start: 0.7478 (t) cc_final: 0.6961 (p) REVERT: B 70 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8079 (p) REVERT: B 122 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.6407 (mtt90) REVERT: B 125 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7357 (pm20) REVERT: C 1 MET cc_start: 0.1185 (ptt) cc_final: 0.0934 (mmt) REVERT: C 20 PHE cc_start: 0.2449 (OUTLIER) cc_final: 0.1216 (m-80) REVERT: D 25 MET cc_start: 0.1805 (mtt) cc_final: 0.1258 (ptt) REVERT: D 56 MET cc_start: 0.3211 (mtt) cc_final: 0.2711 (mmt) REVERT: D 99 LYS cc_start: 0.3855 (OUTLIER) cc_final: 0.3588 (ptmm) REVERT: E 1 MET cc_start: 0.5443 (tpp) cc_final: 0.5001 (tpp) REVERT: E 56 ASP cc_start: 0.8783 (m-30) cc_final: 0.8498 (m-30) REVERT: E 106 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7939 (ptpp) REVERT: E 112 ASN cc_start: 0.7332 (p0) cc_final: 0.6672 (p0) REVERT: E 123 ASP cc_start: 0.7750 (m-30) cc_final: 0.7490 (m-30) REVERT: F 21 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7513 (ptt-90) REVERT: F 24 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5830 (pmm150) REVERT: F 33 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7425 (mm) REVERT: F 61 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7611 (p) REVERT: F 102 MET cc_start: 0.7500 (mmt) cc_final: 0.7294 (mmt) REVERT: F 147 ASN cc_start: 0.8033 (m-40) cc_final: 0.7699 (m110) REVERT: F 153 ARG cc_start: 0.7957 (ttt90) cc_final: 0.7555 (ttt-90) REVERT: G 43 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8066 (mttt) REVERT: G 44 ILE cc_start: 0.7954 (mm) cc_final: 0.7612 (tt) REVERT: G 47 ARG cc_start: 0.6443 (mtt90) cc_final: 0.6076 (mtp85) REVERT: G 53 MET cc_start: 0.8324 (tpp) cc_final: 0.8047 (tpt) REVERT: H 34 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7439 (ptt90) REVERT: I 32 LYS cc_start: 0.4663 (OUTLIER) cc_final: 0.3814 (mmmt) REVERT: I 111 ASN cc_start: 0.6251 (p0) cc_final: 0.5854 (p0) REVERT: J 68 LYS cc_start: 0.3214 (OUTLIER) cc_final: 0.3008 (ttmt) REVERT: J 126 ARG cc_start: 0.1101 (mtm180) cc_final: 0.0465 (ttt90) REVERT: J 165 MET cc_start: 0.2096 (mtm) cc_final: 0.1195 (tpt) outliers start: 113 outliers final: 81 residues processed: 350 average time/residue: 0.5580 time to fit residues: 311.6672 Evaluate side-chains 361 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 263 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 228 optimal weight: 30.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS C 83 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42871 Z= 0.259 Angle : 0.668 13.384 63548 Z= 0.341 Chirality : 0.040 0.254 8123 Planarity : 0.005 0.154 3754 Dihedral : 23.395 179.998 19865 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.18 % Favored : 90.29 % Rotamer: Outliers : 6.91 % Allowed : 21.65 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.47 (0.18), residues: 1885 helix: 0.15 (0.25), residues: 445 sheet: -1.67 (0.30), residues: 240 loop : -2.49 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 125 HIS 0.007 0.001 HIS A 276 PHE 0.018 0.002 PHE J 57 TYR 0.021 0.002 TYR A 286 ARG 0.011 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 271 time to evaluate : 2.304 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8509 (t0) cc_final: 0.8031 (t0) REVERT: A 36 ASP cc_start: 0.4715 (OUTLIER) cc_final: 0.4028 (m-30) REVERT: A 59 ASP cc_start: 0.7865 (p0) cc_final: 0.7271 (p0) REVERT: A 89 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8831 (tp) REVERT: A 100 LYS cc_start: 0.4960 (tptp) cc_final: 0.4632 (mmmt) REVERT: A 117 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5302 (mtt-85) REVERT: A 135 VAL cc_start: 0.2520 (OUTLIER) cc_final: 0.2132 (t) REVERT: A 137 GLN cc_start: 0.4195 (OUTLIER) cc_final: 0.3939 (tm-30) REVERT: A 233 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 341 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7623 (pttt) REVERT: A 347 ARG cc_start: 0.8117 (mtt90) cc_final: 0.6378 (ttp-170) REVERT: A 388 PHE cc_start: 0.5808 (m-10) cc_final: 0.5504 (m-80) REVERT: A 395 SER cc_start: 0.3528 (OUTLIER) cc_final: 0.2739 (m) REVERT: B 14 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6760 (pm20) REVERT: B 21 LYS cc_start: 0.7677 (tttp) cc_final: 0.6928 (tmtt) REVERT: B 26 LYS cc_start: 0.7745 (mttm) cc_final: 0.7364 (tttt) REVERT: B 54 THR cc_start: 0.7430 (t) cc_final: 0.6980 (p) REVERT: B 70 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 122 ARG cc_start: 0.6951 (ttm-80) cc_final: 0.6489 (mtt90) REVERT: B 125 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7212 (pm20) REVERT: C 1 MET cc_start: 0.1343 (ptt) cc_final: 0.1073 (mmm) REVERT: D 25 MET cc_start: 0.2282 (mtt) cc_final: 0.1932 (mtt) REVERT: D 56 MET cc_start: 0.3258 (mtt) cc_final: 0.2741 (mmt) REVERT: D 99 LYS cc_start: 0.3831 (OUTLIER) cc_final: 0.3585 (ptmm) REVERT: E 1 MET cc_start: 0.5508 (tpp) cc_final: 0.5061 (tpp) REVERT: E 106 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7949 (ptpp) REVERT: E 112 ASN cc_start: 0.7294 (p0) cc_final: 0.6646 (p0) REVERT: E 119 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7275 (tmtt) REVERT: F 21 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7439 (ptt-90) REVERT: F 24 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5730 (pmm150) REVERT: F 33 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7510 (mm) REVERT: F 147 ASN cc_start: 0.8164 (m-40) cc_final: 0.7884 (m110) REVERT: F 153 ARG cc_start: 0.7933 (ttt90) cc_final: 0.7554 (ttt-90) REVERT: F 183 LYS cc_start: 0.7884 (tttt) cc_final: 0.7636 (tttp) REVERT: G 27 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8065 (mtpp) REVERT: G 43 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8051 (mttt) REVERT: G 44 ILE cc_start: 0.7953 (mm) cc_final: 0.7620 (tt) REVERT: G 47 ARG cc_start: 0.6435 (mtt90) cc_final: 0.6078 (mtp85) REVERT: G 53 MET cc_start: 0.8328 (tpp) cc_final: 0.8079 (tpt) REVERT: H 34 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7421 (ptt90) REVERT: I 17 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7077 (tt) REVERT: I 32 LYS cc_start: 0.4651 (OUTLIER) cc_final: 0.3804 (mmmt) REVERT: I 111 ASN cc_start: 0.6214 (p0) cc_final: 0.5784 (p0) REVERT: J 52 GLN cc_start: 0.4392 (mm-40) cc_final: 0.4172 (tp40) REVERT: J 126 ARG cc_start: 0.1090 (mtm180) cc_final: 0.0455 (ttt90) REVERT: J 165 MET cc_start: 0.1801 (mtm) cc_final: 0.1093 (tpt) REVERT: J 213 ASP cc_start: 0.4382 (p0) cc_final: 0.2744 (t0) outliers start: 113 outliers final: 86 residues processed: 346 average time/residue: 0.5669 time to fit residues: 310.6024 Evaluate side-chains 364 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 262 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 263 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.094 42871 Z= 0.618 Angle : 1.003 12.769 63548 Z= 0.494 Chirality : 0.055 0.304 8123 Planarity : 0.007 0.155 3754 Dihedral : 23.680 179.637 19863 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.25 % Favored : 87.16 % Rotamer: Outliers : 6.97 % Allowed : 22.20 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -3.09 (0.17), residues: 1885 helix: -0.71 (0.24), residues: 452 sheet: -1.97 (0.29), residues: 244 loop : -2.78 (0.15), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 171 HIS 0.020 0.003 HIS A 276 PHE 0.033 0.003 PHE A 131 TYR 0.046 0.004 TYR A 286 ARG 0.012 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 267 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8029 (p0) cc_final: 0.7592 (p0) REVERT: A 61 GLU cc_start: 0.7571 (pm20) cc_final: 0.6436 (tp30) REVERT: A 89 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8921 (tp) REVERT: A 100 LYS cc_start: 0.4828 (tptp) cc_final: 0.4588 (mmmt) REVERT: A 117 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5343 (mtt-85) REVERT: A 137 GLN cc_start: 0.4312 (OUTLIER) cc_final: 0.3430 (tm-30) REVERT: A 214 GLU cc_start: 0.8061 (tp30) cc_final: 0.7769 (tp30) REVERT: A 225 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8225 (ttpp) REVERT: A 233 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 341 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8076 (pttt) REVERT: A 347 ARG cc_start: 0.8251 (mtt90) cc_final: 0.6183 (ttp-110) REVERT: A 388 PHE cc_start: 0.6452 (m-10) cc_final: 0.6119 (m-80) REVERT: A 395 SER cc_start: 0.3726 (OUTLIER) cc_final: 0.2845 (m) REVERT: B 14 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6782 (pm20) REVERT: B 21 LYS cc_start: 0.8012 (tttp) cc_final: 0.7115 (tmtt) REVERT: B 26 LYS cc_start: 0.7696 (mttm) cc_final: 0.7346 (tttt) REVERT: B 54 THR cc_start: 0.7730 (t) cc_final: 0.7168 (p) REVERT: B 122 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.6463 (mtt90) REVERT: B 125 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7182 (pm20) REVERT: C 1 MET cc_start: 0.1104 (ptt) cc_final: 0.0846 (mmt) REVERT: C 20 PHE cc_start: 0.2859 (OUTLIER) cc_final: 0.1750 (m-80) REVERT: D 56 MET cc_start: 0.3890 (mtt) cc_final: 0.3161 (mmt) REVERT: E 1 MET cc_start: 0.5502 (tpp) cc_final: 0.5043 (tpp) REVERT: E 33 ASN cc_start: 0.8095 (m-40) cc_final: 0.7827 (m-40) REVERT: E 112 ASN cc_start: 0.7584 (p0) cc_final: 0.6927 (p0) REVERT: E 119 LYS cc_start: 0.7724 (tmtt) cc_final: 0.7487 (tmtt) REVERT: F 21 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7667 (ptt-90) REVERT: F 24 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5607 (pmm150) REVERT: F 33 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7433 (mm) REVERT: F 153 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7600 (ttt-90) REVERT: G 12 LYS cc_start: 0.8131 (tptp) cc_final: 0.7833 (tptt) REVERT: G 44 ILE cc_start: 0.8096 (mm) cc_final: 0.7758 (tt) REVERT: I 32 LYS cc_start: 0.4821 (OUTLIER) cc_final: 0.3974 (mmmt) REVERT: I 111 ASN cc_start: 0.6137 (p0) cc_final: 0.5928 (p0) REVERT: J 52 GLN cc_start: 0.4505 (mm-40) cc_final: 0.4267 (tp40) REVERT: J 94 GLN cc_start: 0.4919 (tt0) cc_final: 0.4416 (tt0) REVERT: J 126 ARG cc_start: 0.1661 (mtm180) cc_final: 0.1069 (ttt90) REVERT: J 165 MET cc_start: 0.1673 (mtm) cc_final: 0.0853 (tpt) REVERT: J 213 ASP cc_start: 0.4143 (p0) cc_final: 0.2820 (t70) outliers start: 114 outliers final: 86 residues processed: 347 average time/residue: 0.5543 time to fit residues: 304.8290 Evaluate side-chains 355 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 257 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 ASN Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 219 GLU Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 40.0000 chunk 285 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42871 Z= 0.212 Angle : 0.650 13.467 63548 Z= 0.333 Chirality : 0.039 0.266 8123 Planarity : 0.005 0.154 3754 Dihedral : 23.433 179.353 19863 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.17 % Favored : 91.30 % Rotamer: Outliers : 4.95 % Allowed : 24.10 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.57 (0.18), residues: 1885 helix: -0.03 (0.25), residues: 447 sheet: -1.71 (0.30), residues: 239 loop : -2.52 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 125 HIS 0.008 0.001 HIS A 246 PHE 0.020 0.002 PHE J 57 TYR 0.021 0.002 TYR A 286 ARG 0.010 0.001 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 276 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8534 (t0) cc_final: 0.8048 (t0) REVERT: A 59 ASP cc_start: 0.7887 (p0) cc_final: 0.7634 (p0) REVERT: A 69 LYS cc_start: 0.7267 (mtmt) cc_final: 0.6645 (mptt) REVERT: A 89 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8944 (tt) REVERT: A 100 LYS cc_start: 0.4867 (tptp) cc_final: 0.4540 (mmmt) REVERT: A 117 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5243 (mtt-85) REVERT: A 131 PHE cc_start: 0.6314 (OUTLIER) cc_final: 0.6025 (m-10) REVERT: A 137 GLN cc_start: 0.4205 (OUTLIER) cc_final: 0.3383 (tm-30) REVERT: A 233 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 278 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7224 (ppp80) REVERT: A 341 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7589 (pttt) REVERT: A 347 ARG cc_start: 0.8130 (mtt90) cc_final: 0.6447 (ttp-170) REVERT: A 395 SER cc_start: 0.3695 (OUTLIER) cc_final: 0.2991 (m) REVERT: B 14 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6838 (pm20) REVERT: B 20 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8068 (t) REVERT: B 21 LYS cc_start: 0.7826 (tttp) cc_final: 0.6912 (tmtt) REVERT: B 26 LYS cc_start: 0.7702 (mttm) cc_final: 0.7193 (ptmt) REVERT: B 54 THR cc_start: 0.7540 (t) cc_final: 0.7022 (p) REVERT: B 125 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6994 (pm20) REVERT: C 20 PHE cc_start: 0.2594 (OUTLIER) cc_final: 0.1517 (m-80) REVERT: C 111 LYS cc_start: 0.1334 (OUTLIER) cc_final: 0.0305 (tptm) REVERT: D 56 MET cc_start: 0.2988 (mtt) cc_final: 0.2510 (mmt) REVERT: E 1 MET cc_start: 0.5556 (tpp) cc_final: 0.5053 (tpp) REVERT: E 56 ASP cc_start: 0.8767 (m-30) cc_final: 0.8471 (m-30) REVERT: E 112 ASN cc_start: 0.7546 (p0) cc_final: 0.6933 (p0) REVERT: E 119 LYS cc_start: 0.7319 (tmtt) cc_final: 0.6819 (mttp) REVERT: F 21 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7605 (ptt-90) REVERT: F 33 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7326 (mm) REVERT: F 135 ILE cc_start: 0.9116 (pt) cc_final: 0.8816 (mt) REVERT: F 153 ARG cc_start: 0.7989 (ttt90) cc_final: 0.7615 (ttt-90) REVERT: G 44 ILE cc_start: 0.8102 (mm) cc_final: 0.7815 (tt) REVERT: I 8 GLU cc_start: 0.5597 (mt-10) cc_final: 0.5324 (mt-10) REVERT: I 32 LYS cc_start: 0.4620 (OUTLIER) cc_final: 0.3734 (mmmt) REVERT: I 39 GLU cc_start: 0.6209 (mt-10) cc_final: 0.6004 (tt0) REVERT: I 111 ASN cc_start: 0.6079 (p0) cc_final: 0.5649 (p0) REVERT: J 52 GLN cc_start: 0.4419 (mm-40) cc_final: 0.4155 (tp40) REVERT: J 94 GLN cc_start: 0.5239 (tt0) cc_final: 0.5015 (tt0) REVERT: J 126 ARG cc_start: 0.1299 (mtm180) cc_final: 0.0678 (tpp-160) REVERT: J 165 MET cc_start: 0.1921 (mtm) cc_final: 0.1076 (tpt) REVERT: J 213 ASP cc_start: 0.4110 (p0) cc_final: 0.2762 (t70) outliers start: 81 outliers final: 61 residues processed: 331 average time/residue: 0.5718 time to fit residues: 300.0492 Evaluate side-chains 335 residues out of total 1635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 260 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 0.1980 chunk 239 optimal weight: 6.9990 chunk 100 optimal weight: 0.0470 chunk 245 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN F 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.181118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.158355 restraints weight = 55768.937| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.53 r_work: 0.3356 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 42871 Z= 0.295 Angle : 0.703 13.214 63548 Z= 0.357 Chirality : 0.041 0.258 8123 Planarity : 0.005 0.154 3754 Dihedral : 23.433 179.328 19863 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.45 % Favored : 89.07 % Rotamer: Outliers : 5.63 % Allowed : 23.06 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -2.65 (0.18), residues: 1885 helix: -0.10 (0.25), residues: 453 sheet: -2.04 (0.28), residues: 251 loop : -2.51 (0.16), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 125 HIS 0.009 0.001 HIS A 276 PHE 0.021 0.002 PHE J 57 TYR 0.026 0.002 TYR A 286 ARG 0.009 0.001 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7240.35 seconds wall clock time: 136 minutes 22.99 seconds (8182.99 seconds total)