Starting phenix.real_space_refine on Wed Jun 18 08:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0o_35907/06_2025/8j0o_35907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0o_35907/06_2025/8j0o_35907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0o_35907/06_2025/8j0o_35907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0o_35907/06_2025/8j0o_35907.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0o_35907/06_2025/8j0o_35907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0o_35907/06_2025/8j0o_35907.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 13430 2.51 5 N 3565 2.21 5 O 3891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20986 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7544 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 43, 'TRANS': 905} Chain breaks: 2 Chain: "B" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2438 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 4, 'TRANS': 291} Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1222 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1114 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "H" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1559 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain breaks: 1 Chain: "J" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1146 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "K" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2162 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.74, per 1000 atoms: 0.56 Number of scatterers: 20986 At special positions: 0 Unit cell: (142.79, 212.55, 123.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3891 8.00 N 3565 7.00 C 13430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG L 1 " - " ASN A 818 " " NAG M 1 " - " ASN A 913 " " NAG N 1 " - " ASN J 182 " Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.6 seconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4914 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 27 sheets defined 35.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 479 through 510 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.753A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 993 removed outlier: 3.897A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.809A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.831A pdb=" N ILE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.792A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.855A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.575A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.739A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.586A pdb=" N TRP B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.582A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.789A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.732A pdb=" N LYS B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.817A pdb=" N LEU B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.550A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 297 removed outlier: 3.740A pdb=" N SER B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.029A pdb=" N LEU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 39 Processing helix chain 'C' and resid 45 through 64 Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 101 through 113 removed outlier: 4.493A pdb=" N MET C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 132 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.842A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 4.206A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.540A pdb=" N LEU C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.626A pdb=" N LYS C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.755A pdb=" N VAL D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 91 removed outlier: 3.658A pdb=" N ILE D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.611A pdb=" N ALA D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP D 107 " --> pdb=" O CYS D 103 " (cutoff:3.500A) Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.809A pdb=" N THR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 155 removed outlier: 3.506A pdb=" N PHE D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.628A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 34 removed outlier: 3.550A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 64 removed outlier: 3.641A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 61 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 4.208A pdb=" N ASN E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.545A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 3.904A pdb=" N VAL E 99 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 45 removed outlier: 3.507A pdb=" N VAL F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.545A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.823A pdb=" N TYR F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.738A pdb=" N LEU F 98 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 4.019A pdb=" N SER G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 178 removed outlier: 3.916A pdb=" N LEU G 171 " --> pdb=" O MET G 167 " (cutoff:3.500A) Proline residue: G 172 - end of helix Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.583A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 83 removed outlier: 3.840A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 119 removed outlier: 4.097A pdb=" N GLY H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 177 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 210 Processing helix chain 'J' and resid 91 through 104 removed outlier: 3.624A pdb=" N LEU J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 140 Processing helix chain 'J' and resid 197 through 207 removed outlier: 3.740A pdb=" N PHE J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.545A pdb=" N CYS A 933 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.485A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.172A pdb=" N ALA A 89 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 99 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 108 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET A 107 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A 120 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A 109 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 135 removed outlier: 3.883A pdb=" N TRP A 163 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.809A pdb=" N LYS A 201 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 211 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 removed outlier: 3.754A pdb=" N GLY A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 236 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 247 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.923A pdb=" N ARG A 275 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 292 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 291 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 303 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 326 removed outlier: 3.518A pdb=" N LEU A 321 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 377 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR A 389 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N LEU A 379 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N LEU A 387 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 412 removed outlier: 3.506A pdb=" N TYR A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 418 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 412 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 430 through 433 removed outlier: 6.797A pdb=" N LEU A 430 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER A 444 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 432 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 458 removed outlier: 3.915A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP A 557 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU A 549 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 555 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 576 removed outlier: 6.666A pdb=" N GLN A 586 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 633 removed outlier: 8.530A pdb=" N LEU A 627 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE A 643 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 629 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 641 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 639 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 699 removed outlier: 6.120A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 696 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 180 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 705 through 711 removed outlier: 7.159A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 757 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 774 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 759 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 772 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A 761 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR J 191 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 786 removed outlier: 5.002A pdb=" N TRP A 796 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 802 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 821 through 822 removed outlier: 3.536A pdb=" N PHE A 822 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AC3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.814A pdb=" N THR C 138 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 84 through 89 removed outlier: 3.725A pdb=" N ASP G 88 " --> pdb=" O PHE G 45 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE G 45 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU G 138 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET G 140 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.616A pdb=" N ARG G 66 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 92 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.704A pdb=" N VAL H 31 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS H 57 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU H 29 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASN H 27 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE H 61 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA H 25 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 26 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR H 92 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE H 125 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL H 127 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS H 153 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 83 through 87 removed outlier: 6.277A pdb=" N LYS J 70 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS J 58 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY J 72 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU J 56 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU J 55 " --> pdb=" O PRO J 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 156 through 162 removed outlier: 6.761A pdb=" N HIS J 149 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL J 159 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR J 147 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL J 161 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN J 145 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL J 150 " --> pdb=" O GLN J 188 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 26 through 34 removed outlier: 3.642A pdb=" N ILE K 243 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS K 256 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU K 280 " --> pdb=" O LYS K 256 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU K 26 " --> pdb=" O LEU K 275 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU K 277 " --> pdb=" O LEU K 26 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 21179 1.54 - 1.86: 275 1.86 - 2.19: 0 2.19 - 2.51: 0 2.51 - 2.83: 2 Bond restraints: 21456 Sorted by residual: bond pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.473 2.828 -1.355 1.40e-02 5.10e+03 9.37e+03 bond pdb=" N PRO A 630 " pdb=" CD PRO A 630 " ideal model delta sigma weight residual 1.473 2.759 -1.286 1.40e-02 5.10e+03 8.44e+03 bond pdb=" N PRO A 260 " pdb=" CD PRO A 260 " ideal model delta sigma weight residual 1.473 1.803 -0.330 1.40e-02 5.10e+03 5.56e+02 bond pdb=" N PRO E 88 " pdb=" CD PRO E 88 " ideal model delta sigma weight residual 1.473 1.698 -0.225 1.40e-02 5.10e+03 2.58e+02 bond pdb=" N PRO G 90 " pdb=" CD PRO G 90 " ideal model delta sigma weight residual 1.473 1.683 -0.210 1.40e-02 5.10e+03 2.24e+02 ... (remaining 21451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.84: 29051 9.84 - 19.68: 12 19.68 - 29.51: 1 29.51 - 39.35: 0 39.35 - 49.19: 4 Bond angle restraints: 29068 Sorted by residual: angle pdb=" N PRO C 83 " pdb=" CD PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 103.20 54.01 49.19 1.50e+00 4.44e-01 1.08e+03 angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 68.27 43.73 1.40e+00 5.10e-01 9.76e+02 angle pdb=" CA PRO A 630 " pdb=" N PRO A 630 " pdb=" CD PRO A 630 " ideal model delta sigma weight residual 112.00 68.51 43.49 1.40e+00 5.10e-01 9.65e+02 angle pdb=" N PRO A 630 " pdb=" CD PRO A 630 " pdb=" CG PRO A 630 " ideal model delta sigma weight residual 103.20 62.67 40.53 1.50e+00 4.44e-01 7.30e+02 angle pdb=" CA PRO A 260 " pdb=" N PRO A 260 " pdb=" CD PRO A 260 " ideal model delta sigma weight residual 112.00 91.02 20.98 1.40e+00 5.10e-01 2.25e+02 ... (remaining 29063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 11378 21.52 - 43.04: 1274 43.04 - 64.55: 217 64.55 - 86.07: 49 86.07 - 107.59: 19 Dihedral angle restraints: 12937 sinusoidal: 5312 harmonic: 7625 Sorted by residual: dihedral pdb=" CA LEU A 929 " pdb=" C LEU A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA PHE A 581 " pdb=" C PHE A 581 " pdb=" N PRO A 582 " pdb=" CA PRO A 582 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLY B 67 " pdb=" C GLY B 67 " pdb=" N ARG B 68 " pdb=" CA ARG B 68 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 12934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3030 0.088 - 0.177: 241 0.177 - 0.265: 3 0.265 - 0.353: 4 0.353 - 0.442: 1 Chirality restraints: 3279 Sorted by residual: chirality pdb=" CG LEU H 16 " pdb=" CB LEU H 16 " pdb=" CD1 LEU H 16 " pdb=" CD2 LEU H 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3276 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 82 " -0.229 5.00e-02 4.00e+02 2.42e-01 9.38e+01 pdb=" N PRO C 83 " 0.406 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " -0.118 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 629 " -0.217 5.00e-02 4.00e+02 2.27e-01 8.21e+01 pdb=" N PRO A 630 " 0.380 5.00e-02 4.00e+02 pdb=" CA PRO A 630 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO A 630 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 259 " 0.116 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO A 260 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.067 5.00e-02 4.00e+02 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 96 2.51 - 3.11: 14136 3.11 - 3.71: 30174 3.71 - 4.30: 39668 4.30 - 4.90: 67826 Nonbonded interactions: 151900 Sorted by model distance: nonbonded pdb=" O GLU H 201 " pdb=" OE2 GLU H 201 " model vdw 1.915 3.040 nonbonded pdb=" NH1 ARG B 224 " pdb=" SD MET C 251 " model vdw 1.990 3.480 nonbonded pdb=" O GLU D 175 " pdb=" OE1 GLU D 175 " model vdw 2.055 3.040 nonbonded pdb=" O MET A 505 " pdb=" CE MET A 505 " model vdw 2.062 3.460 nonbonded pdb=" NH2 ARG B 224 " pdb=" CE MET C 251 " model vdw 2.108 3.540 ... (remaining 151895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 45.370 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2216 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 : 0.014 1.355 21465 Z= 0.956 Angle : 0.973 49.189 29095 Z= 0.567 Chirality : 0.045 0.442 3279 Planarity : 0.008 0.242 3679 Dihedral : 18.117 107.591 8023 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.36 % Favored : 91.37 % Rotamer: Outliers : 0.40 % Allowed : 28.40 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2597 helix: 1.26 (0.18), residues: 859 sheet: 0.32 (0.20), residues: 665 loop : -3.37 (0.15), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 164 HIS 0.014 0.001 HIS D 160 PHE 0.042 0.001 PHE A 581 TYR 0.025 0.001 TYR E 91 ARG 0.011 0.001 ARG B 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 3) link_NAG-ASN : angle 4.27533 ( 9) link_BETA1-4 : bond 0.00705 ( 6) link_BETA1-4 : angle 1.34171 ( 18) hydrogen bonds : bond 0.15931 ( 972) hydrogen bonds : angle 6.34063 ( 2847) covalent geometry : bond 0.01375 (21456) covalent geometry : angle 0.96977 (29068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 533 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.6008 (mp) cc_final: 0.5467 (pt) REVERT: C 222 TRP cc_start: 0.6412 (t60) cc_final: 0.6146 (t60) REVERT: F 90 ILE cc_start: 0.6958 (mt) cc_final: 0.6747 (mp) REVERT: G 47 ILE cc_start: 0.6516 (mt) cc_final: 0.5986 (mt) REVERT: G 162 MET cc_start: 0.4922 (ptp) cc_final: 0.4597 (ttp) REVERT: H 7 THR cc_start: 0.5261 (p) cc_final: 0.5012 (p) outliers start: 9 outliers final: 0 residues processed: 540 average time/residue: 0.3656 time to fit residues: 285.0795 Evaluate side-chains 299 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 201 optimal weight: 0.0670 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 222 HIS A 559 GLN A 575 GLN A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 238 HIS C 39 GLN C 53 GLN C 64 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 124 ASN G 163 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN H 195 ASN H 199 ASN ** J 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.098353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.080622 restraints weight = 82794.449| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 4.92 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3748 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 21465 Z= 0.193 Angle : 0.829 13.502 29095 Z= 0.403 Chirality : 0.047 0.252 3279 Planarity : 0.006 0.067 3679 Dihedral : 6.462 57.899 3028 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.47 % Favored : 91.26 % Rotamer: Outliers : 5.32 % Allowed : 26.99 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2597 helix: 1.18 (0.18), residues: 884 sheet: 0.37 (0.20), residues: 678 loop : -3.26 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 127 HIS 0.013 0.002 HIS A 783 PHE 0.023 0.002 PHE G 160 TYR 0.033 0.002 TYR E 58 ARG 0.009 0.001 ARG C 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 3) link_NAG-ASN : angle 3.33049 ( 9) link_BETA1-4 : bond 0.00586 ( 6) link_BETA1-4 : angle 2.73650 ( 18) hydrogen bonds : bond 0.04366 ( 972) hydrogen bonds : angle 5.34328 ( 2847) covalent geometry : bond 0.00435 (21456) covalent geometry : angle 0.82420 (29068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 325 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ILE cc_start: 0.6069 (mt) cc_final: 0.5503 (mt) REVERT: A 442 LEU cc_start: 0.0523 (OUTLIER) cc_final: 0.0010 (tp) REVERT: A 707 ILE cc_start: 0.4920 (OUTLIER) cc_final: 0.4719 (mm) REVERT: B 32 GLN cc_start: 0.7296 (tp40) cc_final: 0.7080 (tt0) REVERT: B 183 MET cc_start: -0.0444 (ttt) cc_final: -0.1201 (mmm) REVERT: B 234 MET cc_start: 0.5237 (ptt) cc_final: 0.4826 (ptp) REVERT: C 70 LYS cc_start: 0.8160 (tptm) cc_final: 0.7688 (tppt) REVERT: C 74 LEU cc_start: 0.8536 (mt) cc_final: 0.8130 (tt) REVERT: C 203 MET cc_start: 0.0677 (OUTLIER) cc_final: -0.0245 (mmt) REVERT: C 210 MET cc_start: 0.2611 (mmm) cc_final: 0.2290 (mmm) REVERT: C 226 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6484 (tm-30) REVERT: D 49 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8231 (p0) REVERT: D 181 LEU cc_start: 0.1154 (OUTLIER) cc_final: 0.0914 (pt) REVERT: E 85 ARG cc_start: 0.3700 (ttt-90) cc_final: 0.3282 (tmm160) REVERT: F 78 PHE cc_start: 0.3414 (m-80) cc_final: 0.3080 (m-10) REVERT: F 90 ILE cc_start: 0.7095 (mt) cc_final: 0.6860 (mp) REVERT: G 47 ILE cc_start: 0.6542 (mt) cc_final: 0.6340 (mt) REVERT: G 117 LYS cc_start: 0.6411 (tptt) cc_final: 0.5962 (tptt) REVERT: G 124 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6094 (t0) REVERT: G 162 MET cc_start: 0.6906 (ptp) cc_final: 0.5867 (ttp) REVERT: H 14 MET cc_start: 0.4957 (tmm) cc_final: 0.4423 (tmm) REVERT: H 94 GLN cc_start: 0.5513 (OUTLIER) cc_final: 0.4818 (tm-30) REVERT: H 151 TRP cc_start: 0.7205 (OUTLIER) cc_final: 0.6630 (t-100) REVERT: H 166 GLU cc_start: 0.8480 (mp0) cc_final: 0.8244 (mp0) REVERT: J 74 LEU cc_start: -0.0098 (OUTLIER) cc_final: -0.0670 (tt) REVERT: K 189 GLU cc_start: 0.7858 (mp0) cc_final: 0.7440 (mp0) REVERT: K 251 LEU cc_start: 0.2367 (OUTLIER) cc_final: 0.2127 (tp) outliers start: 121 outliers final: 40 residues processed: 420 average time/residue: 0.3526 time to fit residues: 224.8011 Evaluate side-chains 312 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 131 PHE Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 169 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN A 583 HIS A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS C 230 HIS G 124 ASN H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 HIS K 124 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.082171 restraints weight = 82222.487| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.97 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3832 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21465 Z= 0.143 Angle : 0.758 13.213 29095 Z= 0.359 Chirality : 0.044 0.235 3279 Planarity : 0.005 0.063 3679 Dihedral : 5.384 57.168 3028 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.28 % Favored : 91.45 % Rotamer: Outliers : 4.62 % Allowed : 28.22 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2597 helix: 1.40 (0.18), residues: 876 sheet: 0.51 (0.20), residues: 685 loop : -3.26 (0.15), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 443 HIS 0.013 0.001 HIS A 77 PHE 0.022 0.002 PHE E 67 TYR 0.018 0.001 TYR B 66 ARG 0.007 0.001 ARG D 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 3) link_NAG-ASN : angle 4.32618 ( 9) link_BETA1-4 : bond 0.00644 ( 6) link_BETA1-4 : angle 2.49703 ( 18) hydrogen bonds : bond 0.03888 ( 972) hydrogen bonds : angle 4.99316 ( 2847) covalent geometry : bond 0.00317 (21456) covalent geometry : angle 0.75151 (29068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 291 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 HIS cc_start: 0.6163 (t-170) cc_final: 0.5944 (t-170) REVERT: A 442 LEU cc_start: 0.0432 (OUTLIER) cc_final: -0.0014 (mp) REVERT: A 689 ASP cc_start: 0.3855 (t0) cc_final: 0.3233 (t0) REVERT: A 754 ARG cc_start: 0.6794 (mpp80) cc_final: 0.6423 (ptt-90) REVERT: A 853 GLU cc_start: 0.2042 (OUTLIER) cc_final: 0.1815 (mp0) REVERT: B 32 GLN cc_start: 0.7323 (tp40) cc_final: 0.7073 (tt0) REVERT: B 120 ASN cc_start: 0.2420 (OUTLIER) cc_final: 0.1529 (t0) REVERT: B 289 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5601 (pp) REVERT: C 70 LYS cc_start: 0.8056 (tptm) cc_final: 0.7569 (tppt) REVERT: C 74 LEU cc_start: 0.8565 (mt) cc_final: 0.8093 (tt) REVERT: C 81 ASN cc_start: 0.5682 (m-40) cc_final: 0.5288 (t0) REVERT: C 135 PHE cc_start: 0.4030 (OUTLIER) cc_final: 0.1818 (t80) REVERT: C 147 ARG cc_start: 0.1555 (mtt180) cc_final: -0.1053 (mtp85) REVERT: C 151 MET cc_start: 0.4095 (mmt) cc_final: 0.3415 (tpp) REVERT: C 210 MET cc_start: 0.2872 (mmm) cc_final: 0.2534 (mmm) REVERT: C 226 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6306 (tp30) REVERT: D 49 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8288 (p0) REVERT: D 154 MET cc_start: 0.5687 (tpt) cc_final: 0.5341 (tpp) REVERT: E 66 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4607 (mm-30) REVERT: E 70 MET cc_start: 0.1663 (mmm) cc_final: 0.1165 (mmt) REVERT: E 85 ARG cc_start: 0.3519 (ttt-90) cc_final: 0.3231 (tmm160) REVERT: F 76 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6556 (ttpp) REVERT: F 90 ILE cc_start: 0.6971 (mt) cc_final: 0.6746 (mp) REVERT: G 117 LYS cc_start: 0.6270 (tptt) cc_final: 0.5732 (tptt) REVERT: G 118 MET cc_start: -0.1277 (pmm) cc_final: -0.1719 (pmm) REVERT: G 124 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.6061 (t0) REVERT: G 162 MET cc_start: 0.6978 (ptp) cc_final: 0.5818 (ttp) REVERT: H 94 GLN cc_start: 0.5706 (OUTLIER) cc_final: 0.4897 (tm-30) REVERT: H 166 GLU cc_start: 0.8454 (mp0) cc_final: 0.8032 (mp0) REVERT: J 74 LEU cc_start: 0.0796 (OUTLIER) cc_final: 0.0286 (tt) REVERT: K 9 ASP cc_start: 0.8336 (t70) cc_final: 0.7805 (p0) REVERT: K 154 GLN cc_start: 0.8763 (tt0) cc_final: 0.8513 (pt0) REVERT: K 166 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7320 (tp-100) REVERT: K 251 LEU cc_start: 0.2382 (OUTLIER) cc_final: 0.2018 (tp) outliers start: 105 outliers final: 44 residues processed: 368 average time/residue: 0.3238 time to fit residues: 184.4752 Evaluate side-chains 304 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 817 TYR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 221 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 501 HIS A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 163 ASN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.099911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.083006 restraints weight = 84710.898| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 4.99 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4101 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21465 Z= 0.155 Angle : 0.748 12.012 29095 Z= 0.358 Chirality : 0.044 0.235 3279 Planarity : 0.005 0.062 3679 Dihedral : 4.846 58.680 3028 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.36 % Favored : 91.34 % Rotamer: Outliers : 4.31 % Allowed : 28.66 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2597 helix: 1.36 (0.18), residues: 880 sheet: 0.52 (0.19), residues: 692 loop : -3.26 (0.15), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 15 HIS 0.021 0.001 HIS B 238 PHE 0.033 0.002 PHE A 324 TYR 0.026 0.002 TYR B 66 ARG 0.006 0.001 ARG B 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 3) link_NAG-ASN : angle 3.71028 ( 9) link_BETA1-4 : bond 0.00540 ( 6) link_BETA1-4 : angle 2.21766 ( 18) hydrogen bonds : bond 0.03561 ( 972) hydrogen bonds : angle 4.89835 ( 2847) covalent geometry : bond 0.00347 (21456) covalent geometry : angle 0.74324 (29068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 290 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6379 (mt) REVERT: A 96 ASP cc_start: 0.7540 (m-30) cc_final: 0.6940 (t70) REVERT: A 177 MET cc_start: 0.6479 (mtt) cc_final: 0.6212 (mtt) REVERT: A 275 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6093 (tmm160) REVERT: A 406 TYR cc_start: 0.6512 (t80) cc_final: 0.6262 (t80) REVERT: A 442 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.0988 (mp) REVERT: A 632 MET cc_start: 0.3882 (mmt) cc_final: 0.3644 (tpp) REVERT: A 853 GLU cc_start: 0.2144 (OUTLIER) cc_final: 0.1930 (mp0) REVERT: A 889 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 32 GLN cc_start: 0.7410 (tp40) cc_final: 0.7152 (tt0) REVERT: B 251 LYS cc_start: 0.8627 (pptt) cc_final: 0.8383 (pptt) REVERT: B 289 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5341 (pp) REVERT: C 67 TYR cc_start: 0.5111 (m-10) cc_final: 0.4910 (m-80) REVERT: C 70 LYS cc_start: 0.8138 (tptm) cc_final: 0.7621 (tppt) REVERT: C 74 LEU cc_start: 0.8636 (mt) cc_final: 0.8172 (tt) REVERT: C 81 ASN cc_start: 0.5924 (m-40) cc_final: 0.5593 (t0) REVERT: C 130 MET cc_start: 0.5964 (tmm) cc_final: 0.5716 (tmm) REVERT: C 147 ARG cc_start: 0.1940 (mtt180) cc_final: -0.0964 (mtp-110) REVERT: C 182 ILE cc_start: 0.3411 (mm) cc_final: 0.3110 (mm) REVERT: C 210 MET cc_start: 0.3224 (mmm) cc_final: 0.2831 (mmm) REVERT: C 251 MET cc_start: 0.4949 (tmm) cc_final: 0.4605 (tmm) REVERT: E 66 GLU cc_start: 0.5224 (OUTLIER) cc_final: 0.4909 (mm-30) REVERT: E 67 PHE cc_start: 0.5949 (p90) cc_final: 0.5744 (p90) REVERT: E 70 MET cc_start: 0.1655 (mmm) cc_final: 0.1147 (mmt) REVERT: F 76 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7096 (ttpt) REVERT: F 90 ILE cc_start: 0.7162 (mt) cc_final: 0.6945 (mp) REVERT: G 45 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7521 (t80) REVERT: G 117 LYS cc_start: 0.6564 (tptt) cc_final: 0.6208 (tptt) REVERT: G 124 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.6462 (t0) REVERT: G 162 MET cc_start: 0.6950 (ptp) cc_final: 0.5314 (ttp) REVERT: G 167 MET cc_start: 0.6214 (mmp) cc_final: 0.6005 (mmp) REVERT: H 14 MET cc_start: 0.4688 (tmm) cc_final: 0.4305 (tmm) REVERT: H 70 MET cc_start: 0.3599 (ptt) cc_final: 0.3333 (ptt) REVERT: H 94 GLN cc_start: 0.5455 (OUTLIER) cc_final: 0.4963 (tm-30) REVERT: H 132 PHE cc_start: 0.4445 (t80) cc_final: 0.4235 (t80) REVERT: H 163 ASP cc_start: 0.6708 (p0) cc_final: 0.6250 (p0) REVERT: H 166 GLU cc_start: 0.8437 (mp0) cc_final: 0.7889 (mp0) REVERT: J 74 LEU cc_start: 0.0808 (OUTLIER) cc_final: 0.0289 (tt) REVERT: K 9 ASP cc_start: 0.8141 (t70) cc_final: 0.7710 (p0) REVERT: K 130 ASP cc_start: 0.7960 (p0) cc_final: 0.7415 (p0) REVERT: K 166 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7668 (tp-100) REVERT: K 251 LEU cc_start: 0.2088 (OUTLIER) cc_final: 0.1753 (tp) outliers start: 98 outliers final: 55 residues processed: 365 average time/residue: 0.3310 time to fit residues: 191.7486 Evaluate side-chains 317 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 581 PHE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 9 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 chunk 167 optimal weight: 0.3980 chunk 129 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 167 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.097906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.081712 restraints weight = 88489.104| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 5.21 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.8371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 21465 Z= 0.244 Angle : 0.895 14.341 29095 Z= 0.448 Chirality : 0.050 0.249 3279 Planarity : 0.007 0.163 3679 Dihedral : 5.406 59.244 3028 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.93 % Favored : 90.76 % Rotamer: Outliers : 5.98 % Allowed : 27.38 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2597 helix: 0.71 (0.17), residues: 881 sheet: 0.27 (0.20), residues: 683 loop : -3.20 (0.16), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 796 HIS 0.017 0.002 HIS B 238 PHE 0.057 0.003 PHE B 270 TYR 0.028 0.003 TYR G 125 ARG 0.025 0.001 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 3) link_NAG-ASN : angle 4.16230 ( 9) link_BETA1-4 : bond 0.00783 ( 6) link_BETA1-4 : angle 1.90510 ( 18) hydrogen bonds : bond 0.04173 ( 972) hydrogen bonds : angle 5.34888 ( 2847) covalent geometry : bond 0.00515 (21456) covalent geometry : angle 0.89156 (29068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 352 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6611 (tp) cc_final: 0.6209 (tp) REVERT: A 177 MET cc_start: 0.6926 (mtt) cc_final: 0.6299 (mtt) REVERT: A 336 MET cc_start: 0.8342 (mmp) cc_final: 0.8071 (mmm) REVERT: A 442 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.2486 (mp) REVERT: A 494 LEU cc_start: 0.9193 (mt) cc_final: 0.8907 (pp) REVERT: A 632 MET cc_start: 0.4180 (mmt) cc_final: 0.3703 (tpp) REVERT: A 863 ILE cc_start: 0.7665 (mt) cc_final: 0.7334 (mt) REVERT: A 889 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 18 LYS cc_start: 0.2893 (OUTLIER) cc_final: 0.2556 (pttt) REVERT: B 33 ILE cc_start: 0.5971 (mt) cc_final: 0.5720 (mt) REVERT: B 76 LEU cc_start: 0.5205 (mt) cc_final: 0.4982 (mp) REVERT: B 289 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5748 (mt) REVERT: C 67 TYR cc_start: 0.5739 (m-10) cc_final: 0.5460 (m-80) REVERT: C 110 MET cc_start: 0.0067 (ptp) cc_final: -0.0513 (ttp) REVERT: C 135 PHE cc_start: 0.5328 (OUTLIER) cc_final: 0.3568 (t80) REVERT: C 151 MET cc_start: 0.4843 (mmt) cc_final: 0.4180 (tpp) REVERT: E 58 TYR cc_start: 0.3916 (t80) cc_final: 0.3558 (m-80) REVERT: E 66 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4930 (mm-30) REVERT: F 76 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7475 (ttpt) REVERT: F 89 LEU cc_start: 0.7576 (mt) cc_final: 0.7170 (pt) REVERT: F 90 ILE cc_start: 0.7009 (mt) cc_final: 0.6716 (mt) REVERT: G 45 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8160 (t80) REVERT: G 117 LYS cc_start: 0.7261 (tptt) cc_final: 0.6861 (tptt) REVERT: G 162 MET cc_start: 0.7566 (ptp) cc_final: 0.5951 (ttp) REVERT: H 94 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: H 132 PHE cc_start: 0.5526 (t80) cc_final: 0.5306 (t80) REVERT: H 163 ASP cc_start: 0.7053 (p0) cc_final: 0.6667 (p0) REVERT: H 166 GLU cc_start: 0.8562 (mp0) cc_final: 0.8026 (mp0) REVERT: J 74 LEU cc_start: 0.2461 (OUTLIER) cc_final: 0.1736 (tt) REVERT: J 151 ASP cc_start: 0.5399 (m-30) cc_final: 0.4361 (t0) REVERT: J 178 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4364 (pp) REVERT: J 179 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6564 (tm-30) REVERT: K 9 ASP cc_start: 0.8298 (t70) cc_final: 0.7773 (p0) REVERT: K 166 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7748 (tp-100) REVERT: K 181 HIS cc_start: 0.5248 (t70) cc_final: 0.4888 (t-170) REVERT: K 251 LEU cc_start: 0.2067 (OUTLIER) cc_final: 0.1810 (tp) outliers start: 136 outliers final: 74 residues processed: 461 average time/residue: 0.3178 time to fit residues: 225.7090 Evaluate side-chains 375 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 290 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 196 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 137 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS C 81 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 95 HIS H 17 HIS ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.098643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082307 restraints weight = 89145.683| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 5.68 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4918 moved from start: 0.8851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21465 Z= 0.144 Angle : 0.778 14.109 29095 Z= 0.372 Chirality : 0.045 0.256 3279 Planarity : 0.005 0.077 3679 Dihedral : 4.918 59.518 3028 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.01 % Favored : 91.68 % Rotamer: Outliers : 4.26 % Allowed : 29.98 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2597 helix: 1.04 (0.18), residues: 880 sheet: 0.51 (0.20), residues: 665 loop : -3.01 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 992 HIS 0.013 0.001 HIS B 238 PHE 0.043 0.002 PHE B 230 TYR 0.028 0.002 TYR B 66 ARG 0.007 0.001 ARG J 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 3) link_NAG-ASN : angle 3.31171 ( 9) link_BETA1-4 : bond 0.00307 ( 6) link_BETA1-4 : angle 1.63784 ( 18) hydrogen bonds : bond 0.03459 ( 972) hydrogen bonds : angle 5.02267 ( 2847) covalent geometry : bond 0.00318 (21456) covalent geometry : angle 0.77462 (29068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 320 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6754 (mtt) cc_final: 0.6037 (mtt) REVERT: A 221 GLN cc_start: 0.6855 (pm20) cc_final: 0.6549 (pp30) REVERT: A 442 LEU cc_start: 0.2616 (OUTLIER) cc_final: 0.2299 (mp) REVERT: A 457 MET cc_start: 0.5105 (mmt) cc_final: 0.4898 (mmt) REVERT: A 535 MET cc_start: 0.4773 (tpp) cc_final: 0.3110 (ttm) REVERT: A 889 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 923 TYR cc_start: 0.6839 (t80) cc_final: 0.6618 (t80) REVERT: A 957 LYS cc_start: 0.5091 (mtmt) cc_final: 0.4310 (ptpp) REVERT: A 960 TYR cc_start: 0.6267 (t80) cc_final: 0.6061 (t80) REVERT: B 33 ILE cc_start: 0.5982 (mt) cc_final: 0.5737 (mt) REVERT: C 67 TYR cc_start: 0.5549 (m-10) cc_final: 0.4937 (m-80) REVERT: C 70 LYS cc_start: 0.8213 (tptm) cc_final: 0.7624 (tppt) REVERT: C 110 MET cc_start: 0.0159 (ptp) cc_final: -0.0534 (ttp) REVERT: C 135 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.3626 (t80) REVERT: C 147 ARG cc_start: 0.1342 (mtt180) cc_final: -0.0470 (ttp80) REVERT: C 151 MET cc_start: 0.4592 (mmt) cc_final: 0.3973 (tpp) REVERT: C 210 MET cc_start: 0.3390 (mmm) cc_final: 0.2940 (mmm) REVERT: C 226 GLU cc_start: 0.7632 (mm-30) cc_final: 0.5620 (tp30) REVERT: D 137 LEU cc_start: 0.8067 (tp) cc_final: 0.7858 (mt) REVERT: E 58 TYR cc_start: 0.3949 (OUTLIER) cc_final: 0.3356 (m-80) REVERT: E 66 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5110 (mm-30) REVERT: F 89 LEU cc_start: 0.7533 (mt) cc_final: 0.7119 (pt) REVERT: F 90 ILE cc_start: 0.6709 (mt) cc_final: 0.6397 (mp) REVERT: G 45 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8266 (t80) REVERT: G 117 LYS cc_start: 0.7124 (tptt) cc_final: 0.6912 (tptt) REVERT: G 118 MET cc_start: 0.0325 (pmm) cc_final: -0.0151 (pmm) REVERT: G 162 MET cc_start: 0.7621 (ptp) cc_final: 0.5951 (ttp) REVERT: H 132 PHE cc_start: 0.5684 (t80) cc_final: 0.5445 (t80) REVERT: H 163 ASP cc_start: 0.6926 (p0) cc_final: 0.6544 (p0) REVERT: H 166 GLU cc_start: 0.8539 (mp0) cc_final: 0.7990 (mp0) REVERT: J 74 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.2309 (tp) REVERT: J 151 ASP cc_start: 0.4988 (m-30) cc_final: 0.4246 (t0) REVERT: J 157 VAL cc_start: 0.1311 (OUTLIER) cc_final: 0.0899 (m) REVERT: J 178 LEU cc_start: 0.4710 (OUTLIER) cc_final: 0.4313 (pp) REVERT: J 179 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6661 (tm-30) REVERT: J 185 VAL cc_start: 0.8151 (t) cc_final: 0.7846 (p) REVERT: K 9 ASP cc_start: 0.8459 (t70) cc_final: 0.7858 (p0) REVERT: K 154 GLN cc_start: 0.8775 (tt0) cc_final: 0.8386 (mm110) REVERT: K 189 GLU cc_start: 0.8675 (mp0) cc_final: 0.8467 (mp0) REVERT: K 251 LEU cc_start: 0.1951 (OUTLIER) cc_final: 0.1646 (tp) outliers start: 97 outliers final: 60 residues processed: 389 average time/residue: 0.3180 time to fit residues: 194.6349 Evaluate side-chains 364 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 62 TYR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 197 optimal weight: 0.0020 chunk 140 optimal weight: 0.0770 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 69 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 153 optimal weight: 8.9990 overall best weight: 0.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 583 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 944 GLN B 155 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.098921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.082748 restraints weight = 88597.800| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 5.14 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4903 moved from start: 0.9074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21465 Z= 0.138 Angle : 0.797 12.412 29095 Z= 0.379 Chirality : 0.044 0.254 3279 Planarity : 0.005 0.078 3679 Dihedral : 4.737 58.871 3028 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.86 % Favored : 91.84 % Rotamer: Outliers : 4.00 % Allowed : 30.73 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2597 helix: 1.13 (0.18), residues: 882 sheet: 0.58 (0.20), residues: 673 loop : -2.95 (0.16), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 557 HIS 0.011 0.001 HIS B 238 PHE 0.045 0.002 PHE B 230 TYR 0.024 0.001 TYR B 66 ARG 0.012 0.001 ARG B 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 3) link_NAG-ASN : angle 2.97393 ( 9) link_BETA1-4 : bond 0.00402 ( 6) link_BETA1-4 : angle 1.56202 ( 18) hydrogen bonds : bond 0.03373 ( 972) hydrogen bonds : angle 4.85577 ( 2847) covalent geometry : bond 0.00298 (21456) covalent geometry : angle 0.79484 (29068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 302 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6663 (mtt) cc_final: 0.5960 (mtt) REVERT: A 221 GLN cc_start: 0.6847 (pm20) cc_final: 0.6533 (pp30) REVERT: A 310 LEU cc_start: 0.6453 (mm) cc_final: 0.5891 (pp) REVERT: A 442 LEU cc_start: 0.2804 (OUTLIER) cc_final: 0.2460 (mp) REVERT: A 457 MET cc_start: 0.5086 (mmt) cc_final: 0.4061 (mmm) REVERT: A 889 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 957 LYS cc_start: 0.5179 (mtmt) cc_final: 0.4624 (ptpp) REVERT: B 33 ILE cc_start: 0.5928 (mt) cc_final: 0.5724 (mt) REVERT: B 234 MET cc_start: 0.6262 (ptt) cc_final: 0.5937 (ptt) REVERT: C 70 LYS cc_start: 0.8173 (tptm) cc_final: 0.7519 (tppt) REVERT: C 110 MET cc_start: -0.0131 (ptp) cc_final: -0.0512 (ttp) REVERT: C 135 PHE cc_start: 0.5156 (OUTLIER) cc_final: 0.3366 (t80) REVERT: C 147 ARG cc_start: 0.1543 (mtt180) cc_final: -0.0111 (ttp-170) REVERT: C 151 MET cc_start: 0.4837 (mmt) cc_final: 0.4198 (tpp) REVERT: D 137 LEU cc_start: 0.8093 (tp) cc_final: 0.7858 (mt) REVERT: E 58 TYR cc_start: 0.3889 (t80) cc_final: 0.3347 (m-80) REVERT: E 66 GLU cc_start: 0.5244 (OUTLIER) cc_final: 0.4751 (mm-30) REVERT: E 67 PHE cc_start: 0.6470 (p90) cc_final: 0.6235 (p90) REVERT: F 89 LEU cc_start: 0.7530 (mt) cc_final: 0.7120 (pt) REVERT: F 90 ILE cc_start: 0.6624 (mt) cc_final: 0.6388 (mt) REVERT: G 45 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8129 (t80) REVERT: G 118 MET cc_start: 0.0502 (pmm) cc_final: 0.0122 (pmm) REVERT: G 130 GLU cc_start: 0.8598 (mp0) cc_final: 0.8357 (mp0) REVERT: G 162 MET cc_start: 0.7602 (ptp) cc_final: 0.5974 (ttp) REVERT: H 94 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5879 (tm-30) REVERT: H 132 PHE cc_start: 0.5766 (t80) cc_final: 0.5559 (t80) REVERT: H 163 ASP cc_start: 0.6915 (p0) cc_final: 0.6536 (p0) REVERT: H 166 GLU cc_start: 0.8554 (mp0) cc_final: 0.7983 (mp0) REVERT: J 74 LEU cc_start: 0.2198 (OUTLIER) cc_final: 0.1925 (tp) REVERT: J 151 ASP cc_start: 0.4977 (m-30) cc_final: 0.4186 (t0) REVERT: J 157 VAL cc_start: 0.1107 (OUTLIER) cc_final: 0.0751 (m) REVERT: J 178 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.3495 (pp) REVERT: J 185 VAL cc_start: 0.8052 (t) cc_final: 0.7752 (p) REVERT: K 9 ASP cc_start: 0.8550 (t70) cc_final: 0.7983 (p0) REVERT: K 96 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7339 (ptmm) REVERT: K 154 GLN cc_start: 0.8830 (tt0) cc_final: 0.8463 (mm110) REVERT: K 251 LEU cc_start: 0.2060 (OUTLIER) cc_final: 0.1809 (tp) outliers start: 91 outliers final: 59 residues processed: 368 average time/residue: 0.3076 time to fit residues: 179.0041 Evaluate side-chains 347 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 278 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 817 TYR Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 944 GLN Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 583 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.098680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.082550 restraints weight = 90587.779| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 5.22 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 moved from start: 1.0139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21465 Z= 0.168 Angle : 0.828 14.442 29095 Z= 0.400 Chirality : 0.046 0.353 3279 Planarity : 0.005 0.074 3679 Dihedral : 4.900 59.403 3028 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.28 % Favored : 91.41 % Rotamer: Outliers : 3.82 % Allowed : 30.77 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2597 helix: 1.11 (0.18), residues: 881 sheet: 0.56 (0.20), residues: 664 loop : -2.85 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 219 HIS 0.035 0.002 HIS A 222 PHE 0.047 0.002 PHE B 230 TYR 0.029 0.002 TYR A 943 ARG 0.015 0.001 ARG A 946 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 3) link_NAG-ASN : angle 3.69214 ( 9) link_BETA1-4 : bond 0.00294 ( 6) link_BETA1-4 : angle 1.62375 ( 18) hydrogen bonds : bond 0.03672 ( 972) hydrogen bonds : angle 4.92701 ( 2847) covalent geometry : bond 0.00366 (21456) covalent geometry : angle 0.82446 (29068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 315 time to evaluate : 2.188 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 80 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7097 (mmtm) REVERT: A 310 LEU cc_start: 0.6881 (mm) cc_final: 0.6227 (pp) REVERT: A 442 LEU cc_start: 0.3251 (OUTLIER) cc_final: 0.2872 (mp) REVERT: A 457 MET cc_start: 0.5668 (mmt) cc_final: 0.5374 (mmt) REVERT: A 470 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: A 847 MET cc_start: 0.8484 (mpp) cc_final: 0.7826 (mpp) REVERT: A 861 LEU cc_start: 0.7662 (tt) cc_final: 0.7305 (tp) REVERT: A 889 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 986 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6317 (mmmm) REVERT: B 234 MET cc_start: 0.6668 (ptt) cc_final: 0.6374 (ptt) REVERT: C 67 TYR cc_start: 0.5414 (m-10) cc_final: 0.4828 (m-10) REVERT: C 70 LYS cc_start: 0.8290 (tptm) cc_final: 0.7632 (tppt) REVERT: C 110 MET cc_start: 0.0177 (ptp) cc_final: -0.0215 (ttp) REVERT: C 135 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.3936 (t80) REVERT: C 147 ARG cc_start: 0.1742 (mtt180) cc_final: 0.0720 (ttp-170) REVERT: C 151 MET cc_start: 0.5107 (mmt) cc_final: 0.4122 (tpp) REVERT: C 194 ASP cc_start: 0.5526 (m-30) cc_final: 0.5273 (p0) REVERT: C 210 MET cc_start: 0.3401 (mmm) cc_final: 0.2888 (mmm) REVERT: E 58 TYR cc_start: 0.4809 (OUTLIER) cc_final: 0.4158 (m-80) REVERT: E 66 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.5054 (mm-30) REVERT: F 89 LEU cc_start: 0.7657 (mt) cc_final: 0.7266 (pt) REVERT: F 90 ILE cc_start: 0.6890 (mt) cc_final: 0.6648 (mt) REVERT: G 45 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8417 (t80) REVERT: G 118 MET cc_start: 0.1166 (pmm) cc_final: 0.0884 (pmm) REVERT: G 162 MET cc_start: 0.7496 (ptp) cc_final: 0.5876 (ttp) REVERT: H 132 PHE cc_start: 0.5797 (t80) cc_final: 0.5565 (t80) REVERT: H 163 ASP cc_start: 0.6903 (p0) cc_final: 0.6549 (p0) REVERT: H 166 GLU cc_start: 0.8609 (mp0) cc_final: 0.7999 (mp0) REVERT: J 151 ASP cc_start: 0.5625 (m-30) cc_final: 0.4845 (t0) REVERT: J 178 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.3708 (pp) REVERT: J 185 VAL cc_start: 0.8313 (t) cc_final: 0.8037 (p) REVERT: K 154 GLN cc_start: 0.8959 (tt0) cc_final: 0.8511 (mm110) outliers start: 87 outliers final: 56 residues processed: 381 average time/residue: 0.2951 time to fit residues: 177.7020 Evaluate side-chains 349 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 285 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 57 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 252 optimal weight: 30.0000 chunk 169 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 102 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN C 191 ASN ** E 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS H 23 HIS ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.096196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.079755 restraints weight = 98791.527| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 5.63 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 1.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 21465 Z= 0.370 Angle : 1.257 21.747 29095 Z= 0.645 Chirality : 0.064 0.473 3279 Planarity : 0.010 0.089 3679 Dihedral : 7.211 60.426 3028 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.13 % Favored : 89.30 % Rotamer: Outliers : 4.31 % Allowed : 31.03 % Favored : 64.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.12 % 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: -2.29 (0.15), residues: 2597 helix: -0.68 (0.16), residues: 881 sheet: -0.19 (0.20), residues: 657 loop : -3.17 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP A 110 HIS 0.036 0.004 HIS E 87 PHE 0.082 0.005 PHE C 135 TYR 0.066 0.005 TYR E 30 ARG 0.032 0.002 ARG B 126 Details of bonding type rmsd link_NAG-ASN : bond 0.02267 ( 3) link_NAG-ASN : angle 5.68200 ( 9) link_BETA1-4 : bond 0.00751 ( 6) link_BETA1-4 : angle 2.25342 ( 18) hydrogen bonds : bond 0.06216 ( 972) hydrogen bonds : angle 6.79907 ( 2847) covalent geometry : bond 0.00821 (21456) covalent geometry : angle 1.25219 (29068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 416 time to evaluate : 2.339 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 26 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8476 (mm-40) REVERT: A 107 MET cc_start: 0.8418 (tmm) cc_final: 0.8132 (tmm) REVERT: A 177 MET cc_start: 0.7570 (mtt) cc_final: 0.7095 (mtt) REVERT: A 405 LEU cc_start: 0.7699 (tt) cc_final: 0.7143 (tp) REVERT: A 451 GLU cc_start: 0.7426 (pt0) cc_final: 0.6873 (pt0) REVERT: A 453 VAL cc_start: 0.8339 (m) cc_final: 0.8110 (m) REVERT: A 539 VAL cc_start: 0.8877 (t) cc_final: 0.8522 (p) REVERT: A 770 ILE cc_start: 0.6278 (mm) cc_final: 0.5824 (mm) REVERT: A 842 SER cc_start: 0.6995 (m) cc_final: 0.6030 (m) REVERT: A 933 CYS cc_start: 0.7796 (m) cc_final: 0.7529 (m) REVERT: A 986 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7724 (mmmm) REVERT: B 71 LEU cc_start: 0.8165 (mt) cc_final: 0.7584 (tp) REVERT: B 183 MET cc_start: 0.3176 (mtt) cc_final: 0.2565 (ppp) REVERT: B 223 ASN cc_start: 0.5882 (OUTLIER) cc_final: 0.5559 (t0) REVERT: B 234 MET cc_start: 0.7046 (ptt) cc_final: 0.6390 (ptp) REVERT: C 36 ILE cc_start: 0.7862 (mm) cc_final: 0.7583 (mt) REVERT: C 70 LYS cc_start: 0.8642 (tptm) cc_final: 0.7872 (tppt) REVERT: C 74 LEU cc_start: 0.8953 (mt) cc_final: 0.8722 (mt) REVERT: C 148 PHE cc_start: 0.6224 (m-80) cc_final: 0.5658 (m-10) REVERT: C 210 MET cc_start: 0.4397 (mmm) cc_final: 0.3965 (mmm) REVERT: C 242 MET cc_start: 0.7491 (tpp) cc_final: 0.7236 (mpp) REVERT: D 116 ILE cc_start: 0.8347 (pt) cc_final: 0.8044 (mm) REVERT: D 153 SER cc_start: 0.5758 (t) cc_final: 0.5273 (p) REVERT: E 58 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: G 117 LYS cc_start: 0.7964 (tptt) cc_final: 0.7705 (tptt) REVERT: G 130 GLU cc_start: 0.8927 (mp0) cc_final: 0.8613 (mt-10) REVERT: G 140 MET cc_start: 0.8244 (tpt) cc_final: 0.7966 (tpp) REVERT: G 159 ASP cc_start: 0.8649 (m-30) cc_final: 0.7767 (p0) REVERT: H 21 TYR cc_start: 0.7887 (m-80) cc_final: 0.7667 (m-10) REVERT: H 58 ILE cc_start: 0.8115 (mt) cc_final: 0.7598 (tt) REVERT: H 131 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7082 (tttt) REVERT: H 163 ASP cc_start: 0.7330 (p0) cc_final: 0.7070 (p0) REVERT: H 166 GLU cc_start: 0.8524 (mp0) cc_final: 0.8016 (mp0) REVERT: H 170 ILE cc_start: 0.7764 (tt) cc_final: 0.7134 (mm) REVERT: H 174 LEU cc_start: 0.9038 (mt) cc_final: 0.8734 (mt) REVERT: H 204 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8081 (tmtt) REVERT: H 207 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8856 (pp) REVERT: J 151 ASP cc_start: 0.7059 (m-30) cc_final: 0.6764 (t0) REVERT: J 178 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.4576 (mt) REVERT: K 9 ASP cc_start: 0.9056 (t0) cc_final: 0.8430 (p0) REVERT: K 96 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7145 (ptmm) outliers start: 98 outliers final: 58 residues processed: 487 average time/residue: 0.3037 time to fit residues: 231.4828 Evaluate side-chains 406 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 342 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 838 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 172 TYR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 96 TYR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 243 ILE Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 132 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 179 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 233 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 318 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS A 775 GLN B 159 HIS B 167 ASN ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN H 51 HIS H 62 HIS ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.096622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.079781 restraints weight = 96900.924| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 5.63 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 1.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21465 Z= 0.186 Angle : 0.969 15.315 29095 Z= 0.471 Chirality : 0.051 0.358 3279 Planarity : 0.006 0.117 3679 Dihedral : 5.951 57.502 3028 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.55 % Favored : 91.11 % Rotamer: Outliers : 2.81 % Allowed : 35.03 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2597 helix: 0.08 (0.17), residues: 878 sheet: 0.01 (0.19), residues: 679 loop : -3.06 (0.16), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 254 HIS 0.014 0.001 HIS E 87 PHE 0.070 0.003 PHE A 484 TYR 0.033 0.002 TYR E 30 ARG 0.017 0.001 ARG B 126 Details of bonding type rmsd link_NAG-ASN : bond 0.01234 ( 3) link_NAG-ASN : angle 4.29020 ( 9) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 2.24283 ( 18) hydrogen bonds : bond 0.04263 ( 972) hydrogen bonds : angle 5.72346 ( 2847) covalent geometry : bond 0.00419 (21456) covalent geometry : angle 0.96524 (29068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 387 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8443 (mm-40) REVERT: A 46 GLU cc_start: 0.7733 (mp0) cc_final: 0.7065 (tp30) REVERT: A 59 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8133 (mp0) REVERT: A 90 MET cc_start: 0.8676 (tmm) cc_final: 0.8343 (tmm) REVERT: A 177 MET cc_start: 0.7276 (mtt) cc_final: 0.6919 (mtt) REVERT: A 318 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: A 443 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.8471 (p-90) REVERT: A 535 MET cc_start: 0.8703 (tpt) cc_final: 0.8407 (tpp) REVERT: A 588 THR cc_start: 0.7684 (m) cc_final: 0.7042 (p) REVERT: A 770 ILE cc_start: 0.6432 (mm) cc_final: 0.5966 (mm) REVERT: A 860 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: A 955 VAL cc_start: 0.8442 (p) cc_final: 0.8179 (p) REVERT: A 986 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7639 (mmmm) REVERT: A 990 ARG cc_start: 0.8257 (mmp80) cc_final: 0.7333 (ttm-80) REVERT: B 182 MET cc_start: 0.8622 (ptm) cc_final: 0.7893 (ptt) REVERT: B 183 MET cc_start: 0.3027 (mtt) cc_final: 0.2426 (ppp) REVERT: B 234 MET cc_start: 0.6903 (ptt) cc_final: 0.6455 (ptp) REVERT: C 36 ILE cc_start: 0.7739 (mm) cc_final: 0.7378 (mt) REVERT: C 70 LYS cc_start: 0.8499 (tptm) cc_final: 0.7829 (tppt) REVERT: C 130 MET cc_start: 0.8454 (tmm) cc_final: 0.8177 (tmm) REVERT: C 153 GLN cc_start: 0.5152 (mt0) cc_final: 0.4608 (mp10) REVERT: C 210 MET cc_start: 0.4248 (mmm) cc_final: 0.3877 (mmm) REVERT: C 242 MET cc_start: 0.7526 (tpp) cc_final: 0.7312 (mpp) REVERT: D 116 ILE cc_start: 0.8096 (pt) cc_final: 0.7851 (mm) REVERT: D 121 LYS cc_start: 0.5223 (mttt) cc_final: 0.4676 (mmtt) REVERT: E 58 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: F 84 LEU cc_start: 0.6016 (mp) cc_final: 0.5467 (mm) REVERT: F 106 MET cc_start: 0.8083 (tpp) cc_final: 0.7835 (tpp) REVERT: G 106 ASP cc_start: 0.7874 (p0) cc_final: 0.7604 (p0) REVERT: H 58 ILE cc_start: 0.8057 (mt) cc_final: 0.7519 (tt) REVERT: H 131 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7378 (tttt) REVERT: H 163 ASP cc_start: 0.7323 (p0) cc_final: 0.7061 (p0) REVERT: H 166 GLU cc_start: 0.8551 (mp0) cc_final: 0.8002 (mp0) REVERT: H 170 ILE cc_start: 0.7786 (tt) cc_final: 0.7160 (mm) REVERT: H 174 LEU cc_start: 0.8974 (mt) cc_final: 0.8663 (mt) REVERT: J 151 ASP cc_start: 0.6769 (m-30) cc_final: 0.6525 (t0) REVERT: K 9 ASP cc_start: 0.9079 (t0) cc_final: 0.8419 (p0) outliers start: 64 outliers final: 49 residues processed: 435 average time/residue: 0.3000 time to fit residues: 205.9549 Evaluate side-chains 405 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 351 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 371 GLN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 85 PHE Chi-restraints excluded: chain F residue 96 TYR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.096453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.079495 restraints weight = 96802.584| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 5.62 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 1.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.406 21465 Z= 0.379 Angle : 1.168 57.299 29095 Z= 0.636 Chirality : 0.054 0.501 3279 Planarity : 0.008 0.190 3679 Dihedral : 5.953 57.649 3028 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.70 % Favored : 90.95 % Rotamer: Outliers : 3.21 % Allowed : 35.56 % Favored : 61.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2597 helix: 0.06 (0.17), residues: 884 sheet: 0.00 (0.19), residues: 680 loop : -3.06 (0.16), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 254 HIS 0.138 0.003 HIS H 62 PHE 0.072 0.003 PHE A 484 TYR 0.060 0.003 TYR J 108 ARG 0.109 0.001 ARG J 109 Details of bonding type rmsd link_NAG-ASN : bond 0.01223 ( 3) link_NAG-ASN : angle 4.29843 ( 9) link_BETA1-4 : bond 0.00457 ( 6) link_BETA1-4 : angle 2.17656 ( 18) hydrogen bonds : bond 0.04266 ( 972) hydrogen bonds : angle 5.71800 ( 2847) covalent geometry : bond 0.00893 (21456) covalent geometry : angle 1.16528 (29068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10015.80 seconds wall clock time: 173 minutes 0.41 seconds (10380.41 seconds total)