Starting phenix.real_space_refine on Sun Sep 29 01:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0o_35907/09_2024/8j0o_35907.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0o_35907/09_2024/8j0o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0o_35907/09_2024/8j0o_35907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0o_35907/09_2024/8j0o_35907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0o_35907/09_2024/8j0o_35907.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0o_35907/09_2024/8j0o_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.59, per 1000 atoms: 0.60 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: 5.36 Conformation dependent library (CDL) restraints added in 2.9 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: 2.44 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: 7.33 Time building geometry restraints manager: 6.21 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: 2.750 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: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 47.060 Find NCS groups from input model: 0.240 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.290 ------------------------------------------------------------------------------- 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 21456 Z= 0.569 Angle : 0.970 49.189 29068 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 533 time to evaluate : 2.532 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: 0.3852 time to fit residues: 300.9071 Evaluate side-chains 299 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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: 0.4980 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.2522 ------------------------------------------------------------------------------- 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 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2901 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 21456 Z= 0.286 Angle : 0.822 13.773 29068 Z= 0.401 Chirality : 0.046 0.282 3279 Planarity : 0.006 0.076 3679 Dihedral : 6.574 58.022 3028 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.24 % Favored : 91.49 % Rotamer: Outliers : 5.10 % Allowed : 27.30 % Favored : 67.60 % 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: -1.00 (0.16), residues: 2597 helix: 1.22 (0.18), residues: 884 sheet: 0.39 (0.20), residues: 678 loop : -3.27 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 127 HIS 0.015 0.002 HIS A 294 PHE 0.022 0.002 PHE G 160 TYR 0.034 0.002 TYR E 58 ARG 0.008 0.001 ARG F 20 *********************** 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 437 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 321 time to evaluate : 2.379 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 375 ILE cc_start: 0.5407 (mt) cc_final: 0.5136 (mt) REVERT: A 442 LEU cc_start: 0.0896 (OUTLIER) cc_final: 0.0402 (tp) REVERT: A 847 MET cc_start: 0.1166 (OUTLIER) cc_final: 0.0524 (ptt) REVERT: B 183 MET cc_start: -0.0664 (ttt) cc_final: -0.0977 (mmm) REVERT: B 234 MET cc_start: 0.4001 (ptt) cc_final: 0.3773 (ptp) REVERT: C 70 LYS cc_start: 0.7207 (tptm) cc_final: 0.6878 (tppt) REVERT: C 74 LEU cc_start: 0.8125 (mt) cc_final: 0.7660 (tt) REVERT: C 203 MET cc_start: 0.0069 (OUTLIER) cc_final: -0.0201 (mmt) REVERT: C 210 MET cc_start: 0.2543 (mmm) cc_final: 0.2231 (mmm) REVERT: C 226 GLU cc_start: 0.6349 (mt-10) cc_final: 0.5912 (tm-30) REVERT: F 90 ILE cc_start: 0.7181 (mt) cc_final: 0.6976 (mp) REVERT: G 117 LYS cc_start: 0.5723 (tptt) cc_final: 0.5432 (tptt) REVERT: G 124 ASN cc_start: 0.6437 (OUTLIER) cc_final: 0.6039 (t0) REVERT: H 14 MET cc_start: 0.4400 (tmm) cc_final: 0.4001 (tmm) REVERT: H 151 TRP cc_start: 0.6676 (OUTLIER) cc_final: 0.6227 (t-100) REVERT: H 166 GLU cc_start: 0.8406 (mp0) cc_final: 0.8181 (mp0) REVERT: J 69 ARG cc_start: 0.2908 (tmt170) cc_final: 0.2659 (tmt170) REVERT: J 74 LEU cc_start: -0.1474 (OUTLIER) cc_final: -0.1955 (tt) REVERT: K 251 LEU cc_start: 0.0597 (OUTLIER) cc_final: 0.0220 (tp) outliers start: 116 outliers final: 36 residues processed: 412 average time/residue: 0.3378 time to fit residues: 209.7002 Evaluate side-chains 303 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 260 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 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 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 238 HIS 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 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 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 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 130 SER 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 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 129 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 194 optimal weight: 0.0370 chunk 158 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 chunk 208 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN A 501 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 771 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 120 ASN B 150 GLN B 159 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS B 253 ASN C 230 HIS E 94 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 HIS ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN K 154 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4089 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 21456 Z= 0.452 Angle : 1.004 12.615 29068 Z= 0.509 Chirality : 0.055 0.316 3279 Planarity : 0.007 0.064 3679 Dihedral : 6.181 52.114 3028 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.05 % Favored : 90.53 % Rotamer: Outliers : 7.43 % Allowed : 26.64 % Favored : 65.93 % 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: -1.56 (0.16), residues: 2597 helix: 0.46 (0.17), residues: 887 sheet: 0.17 (0.20), residues: 678 loop : -3.35 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 197 HIS 0.076 0.003 HIS B 238 PHE 0.032 0.004 PHE H 119 TYR 0.033 0.003 TYR B 147 ARG 0.026 0.001 ARG E 102 *********************** 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 538 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 369 time to evaluate : 2.569 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 22 VAL cc_start: 0.6664 (m) cc_final: 0.5962 (t) REVERT: A 177 MET cc_start: 0.6669 (mtt) cc_final: 0.6378 (mtt) REVERT: A 327 THR cc_start: 0.7792 (OUTLIER) cc_final: 0.7434 (m) REVERT: A 442 LEU cc_start: 0.2876 (OUTLIER) cc_final: 0.2555 (mp) REVERT: A 457 MET cc_start: 0.4316 (mmt) cc_final: 0.3926 (mmt) REVERT: A 470 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 644 ASP cc_start: 0.2796 (OUTLIER) cc_final: 0.0365 (m-30) REVERT: A 689 ASP cc_start: 0.4227 (t0) cc_final: 0.3829 (t0) REVERT: A 690 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.4028 (mt) REVERT: A 889 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6802 (tm-30) REVERT: B 83 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5637 (m-80) REVERT: B 183 MET cc_start: 0.1891 (ttt) cc_final: 0.0633 (tmm) REVERT: C 70 LYS cc_start: 0.7425 (tptm) cc_final: 0.6935 (tppt) REVERT: C 147 ARG cc_start: 0.0833 (mtt180) cc_final: -0.0143 (ttp80) REVERT: C 151 MET cc_start: 0.2852 (mmt) cc_final: 0.2517 (tpp) REVERT: C 182 ILE cc_start: 0.3769 (mm) cc_final: 0.3519 (mm) REVERT: F 90 ILE cc_start: 0.7033 (mt) cc_final: 0.6777 (mt) REVERT: G 45 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7170 (t80) REVERT: G 118 MET cc_start: 0.0673 (pmm) cc_final: 0.0053 (pmm) REVERT: H 166 GLU cc_start: 0.8335 (mp0) cc_final: 0.7767 (mp0) REVERT: J 69 ARG cc_start: 0.3459 (tmt170) cc_final: 0.3082 (tmt170) REVERT: J 74 LEU cc_start: -0.0715 (OUTLIER) cc_final: -0.1163 (tp) REVERT: K 251 LEU cc_start: 0.1287 (OUTLIER) cc_final: 0.0715 (tp) outliers start: 169 outliers final: 78 residues processed: 503 average time/residue: 0.3233 time to fit residues: 248.9087 Evaluate side-chains 374 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 288 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 97 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 275 ARG Chi-restraints excluded: chain A residue 292 PHE 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 410 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 SER 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 186 ILE Chi-restraints excluded: chain C residue 259 SER 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 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL 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 89 ILE Chi-restraints excluded: chain G residue 103 TYR 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 7 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 151 TRP 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 128 VAL 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 K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 180 LEU 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 231 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 0.0770 chunk 234 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 222 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 294 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4049 moved from start: 0.8155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21456 Z= 0.217 Angle : 0.797 12.948 29068 Z= 0.381 Chirality : 0.045 0.268 3279 Planarity : 0.005 0.068 3679 Dihedral : 6.364 107.718 3028 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.16 % Favored : 91.49 % Rotamer: Outliers : 4.88 % Allowed : 29.41 % Favored : 65.71 % 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: -1.17 (0.16), residues: 2597 helix: 0.90 (0.17), residues: 883 sheet: 0.40 (0.20), residues: 670 loop : -3.22 (0.15), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 155 HIS 0.017 0.001 HIS B 238 PHE 0.030 0.002 PHE D 85 TYR 0.033 0.002 TYR B 66 ARG 0.008 0.001 ARG D 108 *********************** 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 439 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 328 time to evaluate : 2.669 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: A 90 MET cc_start: 0.7494 (tmm) cc_final: 0.7147 (tmm) REVERT: A 174 HIS cc_start: 0.6826 (t70) cc_final: 0.6494 (t70) REVERT: A 177 MET cc_start: 0.6547 (mtt) cc_final: 0.6271 (mtt) REVERT: A 327 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7410 (m) REVERT: A 442 LEU cc_start: 0.2840 (OUTLIER) cc_final: 0.2461 (mp) REVERT: A 470 GLU cc_start: 0.7548 (mt-10) cc_final: 0.4755 (mt-10) REVERT: A 640 LEU cc_start: -0.0884 (OUTLIER) cc_final: -0.1258 (tt) REVERT: A 689 ASP cc_start: 0.4003 (t0) cc_final: 0.3770 (t0) REVERT: A 871 LEU cc_start: 0.3650 (OUTLIER) cc_final: 0.3222 (pp) REVERT: A 889 GLN cc_start: 0.7099 (tm-30) cc_final: 0.6837 (tm-30) REVERT: A 904 ILE cc_start: 0.4955 (mt) cc_final: 0.4748 (mt) REVERT: B 18 LYS cc_start: 0.2213 (OUTLIER) cc_final: 0.1870 (pttt) REVERT: C 70 LYS cc_start: 0.7333 (tptm) cc_final: 0.6990 (tppt) REVERT: C 74 LEU cc_start: 0.8167 (mt) cc_final: 0.7509 (tt) REVERT: C 147 ARG cc_start: 0.0923 (mtt180) cc_final: -0.0198 (ttp80) REVERT: C 151 MET cc_start: 0.2575 (mmt) cc_final: 0.2312 (tpp) REVERT: D 142 MET cc_start: 0.5720 (tmm) cc_final: 0.5150 (tpt) REVERT: E 70 MET cc_start: -0.0334 (mmt) cc_final: -0.0768 (mmt) REVERT: G 45 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7113 (t80) REVERT: G 118 MET cc_start: 0.1392 (pmm) cc_final: 0.1114 (pmm) REVERT: G 162 MET cc_start: 0.5079 (ttp) cc_final: 0.4810 (tmm) REVERT: H 151 TRP cc_start: 0.6950 (OUTLIER) cc_final: 0.6672 (t-100) REVERT: H 163 ASP cc_start: 0.6242 (p0) cc_final: 0.5997 (p0) REVERT: H 166 GLU cc_start: 0.8266 (mp0) cc_final: 0.7716 (mp0) REVERT: H 207 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8191 (pp) REVERT: J 74 LEU cc_start: 0.0222 (OUTLIER) cc_final: -0.0450 (tt) REVERT: K 251 LEU cc_start: 0.0817 (OUTLIER) cc_final: 0.0412 (tp) outliers start: 111 outliers final: 60 residues processed: 411 average time/residue: 0.3329 time to fit residues: 213.3600 Evaluate side-chains 352 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 282 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU 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 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 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 417 VAL 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 469 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 909 PHE 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 214 TYR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 176 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 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 96 ARG 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 H residue 26 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 164 HIS 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 150 LEU 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 206 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 0.0270 chunk 211 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- 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 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** 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 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** C 231 GLN ** 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 58 HIS ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4382 moved from start: 0.9150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21456 Z= 0.238 Angle : 0.797 15.054 29068 Z= 0.385 Chirality : 0.045 0.255 3279 Planarity : 0.005 0.063 3679 Dihedral : 5.657 83.471 3028 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.55 % Favored : 91.14 % Rotamer: Outliers : 5.32 % Allowed : 29.80 % Favored : 64.88 % 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: -1.01 (0.16), residues: 2597 helix: 1.02 (0.18), residues: 879 sheet: 0.49 (0.20), residues: 664 loop : -3.08 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 992 HIS 0.034 0.002 HIS A 222 PHE 0.051 0.002 PHE D 85 TYR 0.032 0.002 TYR E 30 ARG 0.013 0.001 ARG H 194 *********************** 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 448 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 327 time to evaluate : 2.486 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 174 HIS cc_start: 0.7124 (t70) cc_final: 0.6722 (t70) REVERT: A 177 MET cc_start: 0.6536 (mtt) cc_final: 0.6177 (mtt) REVERT: A 275 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6300 (tmm160) REVERT: A 327 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7491 (m) REVERT: A 336 MET cc_start: 0.8145 (mmp) cc_final: 0.7888 (mmm) REVERT: A 442 LEU cc_start: 0.3547 (OUTLIER) cc_final: 0.3038 (mp) REVERT: A 470 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6734 (mt-10) REVERT: A 889 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6873 (tm-30) REVERT: C 110 MET cc_start: -0.1480 (ptp) cc_final: -0.1884 (ttp) REVERT: C 147 ARG cc_start: 0.1128 (mtt180) cc_final: -0.0389 (mtp85) REVERT: C 151 MET cc_start: 0.3269 (mmt) cc_final: 0.2908 (tpp) REVERT: C 203 MET cc_start: -0.0082 (mmt) cc_final: -0.0386 (mmp) REVERT: C 210 MET cc_start: 0.3497 (mmm) cc_final: 0.3058 (mmm) REVERT: E 70 MET cc_start: -0.0279 (mmt) cc_final: -0.0573 (mmt) REVERT: G 118 MET cc_start: 0.1316 (pmm) cc_final: 0.0988 (pmm) REVERT: G 162 MET cc_start: 0.5645 (ttp) cc_final: 0.5161 (ttp) REVERT: H 151 TRP cc_start: 0.6800 (OUTLIER) cc_final: 0.6554 (t-100) REVERT: H 166 GLU cc_start: 0.8329 (mp0) cc_final: 0.7671 (mp0) REVERT: H 207 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8248 (pp) REVERT: J 60 PHE cc_start: -0.0253 (OUTLIER) cc_final: -0.1728 (t80) REVERT: J 185 VAL cc_start: 0.7372 (t) cc_final: 0.7071 (p) REVERT: K 251 LEU cc_start: 0.0707 (OUTLIER) cc_final: 0.0468 (tp) outliers start: 121 outliers final: 65 residues processed: 427 average time/residue: 0.3280 time to fit residues: 218.0335 Evaluate side-chains 368 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 296 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 LEU 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 246 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 186 ILE 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 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 96 ARG 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 80 THR Chi-restraints excluded: chain G residue 103 TYR 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 57 CYS Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 60 PHE 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 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 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 194 ILE Chi-restraints excluded: chain K residue 217 THR 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 83 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 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 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 GLN B 82 GLN B 87 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN E 62 HIS F 108 HIS ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 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 195 ASN J 87 GLN J 89 GLN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 1.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.216 21456 Z= 0.556 Angle : 1.255 22.141 29068 Z= 0.636 Chirality : 0.061 0.399 3279 Planarity : 0.010 0.158 3679 Dihedral : 7.040 59.765 3028 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 30.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.82 % Favored : 88.79 % Rotamer: Outliers : 7.56 % Allowed : 28.75 % Favored : 63.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2597 helix: -0.52 (0.17), residues: 874 sheet: -0.37 (0.19), residues: 659 loop : -3.35 (0.15), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.005 TRP K 64 HIS 0.031 0.004 HIS A 77 PHE 0.051 0.005 PHE B 83 TYR 0.088 0.004 TYR B 191 ARG 0.031 0.002 ARG J 69 *********************** 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 585 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 413 time to evaluate : 2.415 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 26 GLN cc_start: 0.8089 (mp10) cc_final: 0.7455 (pm20) REVERT: A 174 HIS cc_start: 0.7531 (t70) cc_final: 0.7271 (t70) REVERT: A 275 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5921 (ttp-170) REVERT: A 407 ILE cc_start: 0.6823 (mm) cc_final: 0.6573 (mm) REVERT: A 457 MET cc_start: 0.8116 (mmm) cc_final: 0.7822 (tpp) REVERT: A 754 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7735 (mpp80) REVERT: A 986 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7536 (mmmm) REVERT: C 185 LEU cc_start: 0.6779 (tt) cc_final: 0.6359 (tt) REVERT: C 210 MET cc_start: 0.4382 (mmm) cc_final: 0.3965 (mmm) REVERT: D 142 MET cc_start: 0.6707 (tmm) cc_final: 0.6373 (tpt) REVERT: E 70 MET cc_start: 0.1785 (mmt) cc_final: 0.1444 (mmt) REVERT: G 117 LYS cc_start: 0.7512 (tptt) cc_final: 0.7136 (tptt) REVERT: H 70 MET cc_start: 0.3838 (ptp) cc_final: 0.3555 (ptt) REVERT: H 166 GLU cc_start: 0.8479 (mp0) cc_final: 0.8268 (mp0) REVERT: H 170 ILE cc_start: 0.7399 (tt) cc_final: 0.6476 (mm) REVERT: H 174 LEU cc_start: 0.8407 (mt) cc_final: 0.8096 (mt) REVERT: H 207 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8449 (pp) REVERT: J 63 ASP cc_start: 0.6754 (t0) cc_final: 0.5812 (t0) REVERT: K 114 ILE cc_start: 0.0529 (OUTLIER) cc_final: 0.0291 (pt) REVERT: K 251 LEU cc_start: 0.2004 (OUTLIER) cc_final: 0.1784 (tp) outliers start: 172 outliers final: 78 residues processed: 548 average time/residue: 0.3073 time to fit residues: 262.2684 Evaluate side-chains 404 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 320 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 417 VAL 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 469 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 44 LEU 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 149 PHE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 142 HIS Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 150 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 251 LEU Chi-restraints excluded: chain K residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 0.0570 chunk 181 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 209 optimal weight: 0.4980 chunk 138 optimal weight: 0.5980 chunk 247 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 151 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN A 583 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS B 82 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 175 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN H 51 HIS ** 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** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 1.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21456 Z= 0.243 Angle : 0.907 14.074 29068 Z= 0.437 Chirality : 0.048 0.265 3279 Planarity : 0.006 0.073 3679 Dihedral : 5.690 59.747 3028 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.91 % Rotamer: Outliers : 4.35 % Allowed : 32.92 % Favored : 62.73 % 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: -1.68 (0.16), residues: 2597 helix: 0.33 (0.17), residues: 867 sheet: -0.08 (0.20), residues: 669 loop : -3.13 (0.16), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 64 HIS 0.029 0.002 HIS B 87 PHE 0.050 0.002 PHE A 484 TYR 0.035 0.002 TYR E 30 ARG 0.011 0.001 ARG J 95 *********************** 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 462 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 363 time to evaluate : 2.471 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: A 46 GLU cc_start: 0.6358 (mp0) cc_final: 0.5750 (tp30) REVERT: A 174 HIS cc_start: 0.7835 (t70) cc_final: 0.7463 (t70) REVERT: A 457 MET cc_start: 0.8154 (mmm) cc_final: 0.7872 (mmt) REVERT: A 632 MET cc_start: 0.3256 (tpp) cc_final: 0.2966 (mmt) REVERT: A 986 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7803 (mmmm) REVERT: B 29 ASN cc_start: 0.6409 (p0) cc_final: 0.6079 (p0) REVERT: B 32 GLN cc_start: 0.8312 (pm20) cc_final: 0.7861 (pm20) REVERT: B 42 ASN cc_start: 0.4842 (m-40) cc_final: 0.4611 (m110) REVERT: B 71 LEU cc_start: 0.7193 (mt) cc_final: 0.6750 (mt) REVERT: B 254 MET cc_start: 0.6689 (mpp) cc_final: 0.6180 (mpp) REVERT: C 36 ILE cc_start: 0.6652 (mt) cc_final: 0.6306 (mt) REVERT: C 185 LEU cc_start: 0.6985 (tt) cc_final: 0.6610 (tt) REVERT: C 203 MET cc_start: 0.1245 (mmt) cc_final: 0.1006 (mmp) REVERT: C 210 MET cc_start: 0.4800 (mmm) cc_final: 0.4404 (mmm) REVERT: D 142 MET cc_start: 0.6053 (tmm) cc_final: 0.5783 (tpt) REVERT: E 70 MET cc_start: 0.1601 (mmt) cc_final: 0.1234 (mmt) REVERT: H 166 GLU cc_start: 0.8358 (mp0) cc_final: 0.8111 (mp0) REVERT: H 170 ILE cc_start: 0.7443 (tt) cc_final: 0.6581 (mm) REVERT: H 174 LEU cc_start: 0.8608 (mt) cc_final: 0.8322 (mt) REVERT: H 207 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (pp) outliers start: 99 outliers final: 66 residues processed: 436 average time/residue: 0.2821 time to fit residues: 196.9813 Evaluate side-chains 387 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 319 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 163 ASP 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 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 103 TYR 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 50 HIS Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 58 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 191 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 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 0.1980 chunk 98 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 253 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN K 166 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 1.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21456 Z= 0.294 Angle : 0.928 13.779 29068 Z= 0.452 Chirality : 0.049 0.366 3279 Planarity : 0.006 0.085 3679 Dihedral : 5.479 58.062 3028 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.16 % Favored : 90.53 % Rotamer: Outliers : 4.57 % Allowed : 33.76 % Favored : 61.67 % 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: -1.56 (0.16), residues: 2597 helix: 0.39 (0.17), residues: 870 sheet: 0.13 (0.20), residues: 646 loop : -3.10 (0.16), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 254 HIS 0.019 0.002 HIS A 93 PHE 0.049 0.003 PHE A 484 TYR 0.039 0.002 TYR E 30 ARG 0.013 0.001 ARG C 59 *********************** 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 476 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 372 time to evaluate : 2.349 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 174 HIS cc_start: 0.7675 (t70) cc_final: 0.7277 (t70) REVERT: A 177 MET cc_start: 0.6374 (mtt) cc_final: 0.6131 (mtt) REVERT: A 457 MET cc_start: 0.8593 (mmm) cc_final: 0.8267 (mmt) REVERT: A 632 MET cc_start: 0.4307 (tpp) cc_final: 0.3568 (mmt) REVERT: A 754 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7811 (ptt-90) REVERT: A 826 ASP cc_start: 0.5800 (p0) cc_final: 0.5452 (t0) REVERT: A 986 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8011 (mmmm) REVERT: B 42 ASN cc_start: 0.5399 (m-40) cc_final: 0.5057 (m110) REVERT: B 254 MET cc_start: 0.7151 (mpp) cc_final: 0.6737 (mpp) REVERT: C 36 ILE cc_start: 0.7197 (mt) cc_final: 0.6984 (mt) REVERT: C 110 MET cc_start: -0.1655 (ttp) cc_final: -0.2136 (ttm) REVERT: C 203 MET cc_start: 0.1595 (mmt) cc_final: 0.1349 (mmp) REVERT: C 210 MET cc_start: 0.4738 (mmm) cc_final: 0.4415 (mmm) REVERT: D 121 LYS cc_start: 0.4729 (mttt) cc_final: 0.4162 (mptt) REVERT: E 31 MET cc_start: 0.5547 (tpt) cc_final: 0.5008 (mmt) REVERT: E 70 MET cc_start: 0.1751 (mmt) cc_final: 0.1382 (mmt) REVERT: F 40 THR cc_start: 0.8107 (m) cc_final: 0.7790 (t) REVERT: H 150 ARG cc_start: 0.4930 (OUTLIER) cc_final: 0.4688 (tpt90) REVERT: H 166 GLU cc_start: 0.8355 (mp0) cc_final: 0.8147 (mp0) REVERT: H 170 ILE cc_start: 0.7605 (tt) cc_final: 0.6844 (mm) REVERT: H 174 LEU cc_start: 0.8731 (mt) cc_final: 0.8430 (mt) REVERT: H 207 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8380 (pp) outliers start: 104 outliers final: 77 residues processed: 444 average time/residue: 0.3321 time to fit residues: 234.5836 Evaluate side-chains 413 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 332 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 186 ILE 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 163 ASP Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 96 TYR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 103 TYR 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 7 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 131 PHE 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 243 ILE 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 225 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 HIS ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 1.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21456 Z= 0.294 Angle : 0.958 14.555 29068 Z= 0.463 Chirality : 0.049 0.292 3279 Planarity : 0.006 0.077 3679 Dihedral : 5.459 56.048 3028 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.16 % Favored : 91.53 % Rotamer: Outliers : 3.69 % Allowed : 35.08 % Favored : 61.23 % 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: -1.56 (0.16), residues: 2597 helix: 0.35 (0.17), residues: 881 sheet: 0.01 (0.20), residues: 677 loop : -3.08 (0.16), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 222 HIS 0.022 0.002 HIS A 663 PHE 0.042 0.002 PHE A 484 TYR 0.028 0.002 TYR E 30 ARG 0.012 0.001 ARG J 69 *********************** 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 449 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 365 time to evaluate : 2.499 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 174 HIS cc_start: 0.7874 (t70) cc_final: 0.7455 (t70) REVERT: A 177 MET cc_start: 0.7016 (mtt) cc_final: 0.6385 (mtt) REVERT: A 436 LEU cc_start: 0.8024 (pt) cc_final: 0.7764 (tt) REVERT: A 456 GLU cc_start: 0.8289 (tp30) cc_final: 0.7993 (tp30) REVERT: A 457 MET cc_start: 0.8739 (mmm) cc_final: 0.7514 (mmt) REVERT: A 536 MET cc_start: 0.8221 (ptp) cc_final: 0.7963 (ptp) REVERT: A 717 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7001 (mm-30) REVERT: B 42 ASN cc_start: 0.5523 (m-40) cc_final: 0.5194 (m110) REVERT: B 160 GLU cc_start: 0.6275 (tm-30) cc_final: 0.6039 (tm-30) REVERT: B 182 MET cc_start: 0.8073 (mmm) cc_final: 0.7797 (mmm) REVERT: B 254 MET cc_start: 0.7663 (mpp) cc_final: 0.7166 (mpp) REVERT: C 110 MET cc_start: -0.0693 (ttp) cc_final: -0.1239 (ttm) REVERT: C 121 MET cc_start: 0.7546 (ttp) cc_final: 0.7338 (ttp) REVERT: C 203 MET cc_start: 0.1677 (mmt) cc_final: 0.1413 (mmp) REVERT: C 210 MET cc_start: 0.4759 (mmm) cc_final: 0.4515 (mmm) REVERT: D 121 LYS cc_start: 0.4869 (mttt) cc_final: 0.4311 (mmtt) REVERT: D 142 MET cc_start: 0.6999 (tmm) cc_final: 0.6440 (tpt) REVERT: D 174 MET cc_start: 0.6275 (pmm) cc_final: 0.5937 (pmm) REVERT: E 31 MET cc_start: 0.6171 (tpt) cc_final: 0.5721 (tpt) REVERT: E 70 MET cc_start: 0.1953 (mmt) cc_final: 0.1652 (mmt) REVERT: G 117 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7424 (tmtt) REVERT: G 165 MET cc_start: 0.6771 (tmm) cc_final: 0.4239 (mmt) REVERT: H 150 ARG cc_start: 0.5133 (OUTLIER) cc_final: 0.4914 (tpt90) REVERT: H 166 GLU cc_start: 0.8298 (mp0) cc_final: 0.8034 (mp0) REVERT: H 174 LEU cc_start: 0.8940 (mt) cc_final: 0.8647 (mt) REVERT: H 207 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8327 (pp) outliers start: 84 outliers final: 67 residues processed: 425 average time/residue: 0.2948 time to fit residues: 199.2467 Evaluate side-chains 406 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 337 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 96 TYR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 58 HIS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 132 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 71 PHE 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 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 157 optimal weight: 0.0370 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 0.0980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 1.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21456 Z= 0.239 Angle : 0.932 16.287 29068 Z= 0.442 Chirality : 0.047 0.248 3279 Planarity : 0.005 0.089 3679 Dihedral : 5.301 56.727 3028 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.05 % Favored : 91.64 % Rotamer: Outliers : 3.25 % Allowed : 36.00 % Favored : 60.75 % 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: -1.34 (0.16), residues: 2597 helix: 0.57 (0.17), residues: 883 sheet: 0.17 (0.20), residues: 673 loop : -3.02 (0.16), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 222 HIS 0.021 0.001 HIS A 663 PHE 0.045 0.002 PHE C 80 TYR 0.025 0.002 TYR B 8 ARG 0.011 0.001 ARG E 85 ********************** 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 430 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 356 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6823 (mtt) cc_final: 0.6473 (mtt) REVERT: A 456 GLU cc_start: 0.8303 (tp30) cc_final: 0.7962 (tp30) REVERT: A 457 MET cc_start: 0.8730 (mmm) cc_final: 0.7424 (mmt) REVERT: A 536 MET cc_start: 0.8140 (ptp) cc_final: 0.7864 (ptp) REVERT: A 632 MET cc_start: 0.4358 (tpp) cc_final: 0.3965 (tpp) REVERT: A 847 MET cc_start: 0.8184 (mmm) cc_final: 0.7922 (mtt) REVERT: B 19 MET cc_start: 0.5187 (ppp) cc_final: 0.4969 (ppp) REVERT: B 42 ASN cc_start: 0.5725 (m-40) cc_final: 0.5428 (m110) REVERT: B 71 LEU cc_start: 0.8286 (mm) cc_final: 0.8061 (mp) REVERT: B 226 MET cc_start: 0.2954 (mmt) cc_final: 0.2517 (ppp) REVERT: B 254 MET cc_start: 0.7584 (mpp) cc_final: 0.7255 (mpp) REVERT: B 264 ILE cc_start: 0.7226 (mt) cc_final: 0.6907 (tp) REVERT: C 110 MET cc_start: -0.0432 (ttp) cc_final: -0.1136 (ttm) REVERT: C 203 MET cc_start: 0.1647 (mmt) cc_final: 0.1390 (mmp) REVERT: C 210 MET cc_start: 0.4739 (mmm) cc_final: 0.4519 (mmm) REVERT: D 87 MET cc_start: 0.5336 (mtt) cc_final: 0.5048 (ttp) REVERT: D 121 LYS cc_start: 0.4742 (mttt) cc_final: 0.4176 (mmtt) REVERT: D 142 MET cc_start: 0.6715 (tmm) cc_final: 0.6093 (tpt) REVERT: E 70 MET cc_start: 0.2245 (mmt) cc_final: 0.1993 (mmt) REVERT: G 117 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7468 (tptt) REVERT: G 165 MET cc_start: 0.6652 (tmm) cc_final: 0.4311 (mmt) REVERT: H 110 LYS cc_start: 0.6450 (mttt) cc_final: 0.5530 (tptp) REVERT: H 126 MET cc_start: 0.8772 (tmm) cc_final: 0.8543 (tmm) REVERT: H 150 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.5109 (tpt90) REVERT: H 166 GLU cc_start: 0.8314 (mp0) cc_final: 0.8051 (mp0) REVERT: H 174 LEU cc_start: 0.9002 (mt) cc_final: 0.8696 (mt) REVERT: H 207 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (pp) REVERT: J 128 VAL cc_start: 0.4761 (OUTLIER) cc_final: 0.4462 (p) outliers start: 74 outliers final: 60 residues processed: 407 average time/residue: 0.2864 time to fit residues: 186.5229 Evaluate side-chains 398 residues out of total 2275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 335 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 57 CYS Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 204 LYS Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 71 PHE 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 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS C 191 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 HIS ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.089712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.071433 restraints weight = 92669.165| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 5.35 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 1.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21456 Z= 0.342 Angle : 1.024 20.236 29068 Z= 0.499 Chirality : 0.052 0.456 3279 Planarity : 0.006 0.109 3679 Dihedral : 5.703 56.365 3028 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.70 % Favored : 89.99 % Rotamer: Outliers : 3.74 % Allowed : 35.87 % Favored : 60.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2597 helix: 0.24 (0.17), residues: 868 sheet: -0.00 (0.19), residues: 676 loop : -3.08 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 557 HIS 0.020 0.002 HIS E 62 PHE 0.033 0.003 PHE G 77 TYR 0.061 0.003 TYR A 898 ARG 0.018 0.001 ARG C 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5337.72 seconds wall clock time: 95 minutes 38.76 seconds (5738.76 seconds total)