Starting phenix.real_space_refine on Fri Jul 3 20:29:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niv_12366/07_2026/7niv_12366.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 54 5.16 5 C 10092 2.51 5 N 2607 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15724 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1578 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Conformer: "B" Number of residues, atoms: 208, 1575 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1598 Chain: "E" Number of atoms: 1702 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 229, 1702 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "A" Number of atoms: 8815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 8815 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 27, 'TRANS': 1110} Chain breaks: 2 Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 250 Unusual residues: {'CLR': 7, 'DLP': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 4.24, per 1000 atoms: 0.27 Number of scatterers: 15724 At special positions: 0 Unit cell: (159.06, 132, 127.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 1 15.00 O 2970 8.00 N 2607 7.00 C 10092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 908.0 milliseconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3732 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 24 sheets defined 36.6% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.911A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 188' Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 213 through 217 Processing helix chain 'A' and resid 50 through 69 Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.929A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 160 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 169 through 190 removed outlier: 4.961A pdb=" N ILE A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 Processing helix chain 'A' and resid 214 through 244 removed outlier: 3.639A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.835A pdb=" N LEU A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.921A pdb=" N VAL A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 322 removed outlier: 4.484A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 Processing helix chain 'A' and resid 350 through 372 removed outlier: 3.741A pdb=" N ALA A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.549A pdb=" N VAL A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 485 through 492 removed outlier: 3.835A pdb=" N TYR A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 540 through 549 removed outlier: 4.168A pdb=" N ALA A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 577 removed outlier: 5.170A pdb=" N ALA A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 696 through 703 removed outlier: 3.536A pdb=" N VAL A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.966A pdb=" N ILE A 736 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 794 removed outlier: 3.639A pdb=" N LYS A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 751 " --> pdb=" O LYS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 853 removed outlier: 3.760A pdb=" N LEU A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 868 removed outlier: 3.587A pdb=" N THR A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Proline residue: A 865 - end of helix Processing helix chain 'A' and resid 869 through 874 Processing helix chain 'A' and resid 881 through 902 removed outlier: 5.391A pdb=" N ILE A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.992A pdb=" N VAL A 906 " --> pdb=" O ASN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 965 removed outlier: 4.943A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 3.630A pdb=" N TYR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 992 removed outlier: 3.895A pdb=" N SER A 978 " --> pdb=" O ILE A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1013 removed outlier: 4.415A pdb=" N LEU A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1104 through 1112 removed outlier: 3.774A pdb=" N GLN A1111 " --> pdb=" O TRP A1107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A1112 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1134 removed outlier: 4.018A pdb=" N GLY A1133 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1151 removed outlier: 3.818A pdb=" N ILE A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.839A pdb=" N GLU A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1183 Processing helix chain 'A' and resid 1185 through 1190 Processing helix chain 'A' and resid 1206 through 1211 removed outlier: 4.187A pdb=" N LYS A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1215 Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 4.374A pdb=" N GLN A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.543A pdb=" N SER C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 35 " --> pdb=" O LEU C 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 35' Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing sheet with id=AA1, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.794A pdb=" N THR D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 66 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 47 removed outlier: 3.591A pdb=" N LYS D 46 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 115 through 118 removed outlier: 5.105A pdb=" N SER D 132 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU D 182 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL D 134 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU D 180 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU D 136 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER D 178 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN D 138 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU D 176 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 146 through 151 Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 25 removed outlier: 3.556A pdb=" N CYS E 25 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 82 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 38 through 41 removed outlier: 7.009A pdb=" N TRP E 39 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 133 through 137 removed outlier: 3.854A pdb=" N GLY E 152 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS E 153 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER E 193 " --> pdb=" O CYS E 153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 194 " --> pdb=" O HIS E 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 164 through 167 removed outlier: 3.761A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS E 222 " --> pdb=" O CYS E 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AB2, first strand: chain 'A' and resid 427 through 428 removed outlier: 3.593A pdb=" N VAL A 428 " --> pdb=" O ALA A 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 472 through 473 removed outlier: 6.493A pdb=" N GLY A 473 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP A 557 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1050 through 1057 removed outlier: 7.040A pdb=" N VAL A1051 " --> pdb=" O ASN A1042 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASN A1042 " --> pdb=" O VAL A1051 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLN A1053 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A1040 " --> pdb=" O GLN A1053 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A1055 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1038 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1195 through 1197 removed outlier: 5.232A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1245 through 1246 Processing sheet with id=AB7, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.804A pdb=" N CYS B 24 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE B 72 " --> pdb=" O CYS B 24 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.578A pdb=" N SER B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 35 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 90 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 115 through 119 removed outlier: 5.931A pdb=" N TYR B 174 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.201A pdb=" N CYS B 195 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 208 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 197 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 206 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N HIS B 199 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER B 204 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.657A pdb=" N SER C 24 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.220A pdb=" N VAL C 15 " --> pdb=" O THR C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.564A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 140 through 142 removed outlier: 5.904A pdb=" N TYR C 196 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 170 through 174 656 hydrogen bonds defined for protein. 1836 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: 2.93 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2524 1.31 - 1.44: 4312 1.44 - 1.57: 9121 1.57 - 1.69: 26 1.69 - 1.82: 81 Bond restraints: 16064 Sorted by residual: bond pdb=" C11 DLP A1301 " pdb=" O3 DLP A1301 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C31 DLP A1301 " pdb=" O2 DLP A1301 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" N DLP A1301 " pdb=" C7 DLP A1301 " ideal model delta sigma weight residual 1.491 1.427 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" N VAL E 124 " pdb=" CA VAL E 124 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.58e+00 bond pdb=" C23 CLR A1307 " pdb=" C24 CLR A1307 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 16059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 21335 3.01 - 6.02: 414 6.02 - 9.03: 49 9.03 - 12.04: 7 12.04 - 15.04: 1 Bond angle restraints: 21806 Sorted by residual: angle pdb=" N TYR E 107 " pdb=" CA TYR E 107 " pdb=" C TYR E 107 " ideal model delta sigma weight residual 111.71 118.65 -6.94 1.15e+00 7.56e-01 3.65e+01 angle pdb=" O3P DLP A1301 " pdb=" P DLP A1301 " pdb=" O4P DLP A1301 " ideal model delta sigma weight residual 93.58 108.62 -15.04 3.00e+00 1.11e-01 2.51e+01 angle pdb=" C ALA E 112 " pdb=" CA ALA E 112 " pdb=" CB ALA E 112 " ideal model delta sigma weight residual 116.54 110.79 5.75 1.15e+00 7.56e-01 2.50e+01 angle pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " ideal model delta sigma weight residual 117.15 120.86 -3.71 7.80e-01 1.64e+00 2.26e+01 angle pdb=" CA ALA E 112 " pdb=" C ALA E 112 " pdb=" N MET E 113 " ideal model delta sigma weight residual 119.52 115.97 3.55 7.90e-01 1.60e+00 2.02e+01 ... (remaining 21801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 8846 23.80 - 47.59: 601 47.59 - 71.38: 57 71.38 - 95.18: 13 95.18 - 118.97: 1 Dihedral angle restraints: 9518 sinusoidal: 3687 harmonic: 5831 Sorted by residual: dihedral pdb=" CA PHE A 732 " pdb=" C PHE A 732 " pdb=" N SER A 733 " pdb=" CA SER A 733 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 195 " pdb=" CB CYS B 195 " ideal model delta sinusoidal sigma weight residual 93.00 45.35 47.65 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CA PHE A 982 " pdb=" C PHE A 982 " pdb=" N GLY A 983 " pdb=" CA GLY A 983 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 9515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2169 0.077 - 0.155: 285 0.155 - 0.232: 27 0.232 - 0.309: 14 0.309 - 0.386: 4 Chirality restraints: 2499 Sorted by residual: chirality pdb=" C17 CLR A1303 " pdb=" C13 CLR A1303 " pdb=" C16 CLR A1303 " pdb=" C20 CLR A1303 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C17 CLR A1302 " pdb=" C13 CLR A1302 " pdb=" C16 CLR A1302 " pdb=" C20 CLR A1302 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C17 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C16 CLR A1304 " pdb=" C20 CLR A1304 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 2496 not shown) Planarity restraints: 2727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " -0.021 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE A 305 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 175 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C THR A 175 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 175 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 176 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 958 " 0.016 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE A 958 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 958 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 958 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 958 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 958 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 958 " 0.002 2.00e-02 2.50e+03 ... (remaining 2724 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1670 2.74 - 3.28: 16241 3.28 - 3.82: 25161 3.82 - 4.36: 30743 4.36 - 4.90: 51375 Nonbonded interactions: 125190 Sorted by model distance: nonbonded pdb=" N ASP A 243 " pdb=" OD1 ASP A 243 " model vdw 2.197 3.120 nonbonded pdb=" OE1 GLN A 443 " pdb=" OG SER A 908 " model vdw 2.200 3.040 nonbonded pdb=" NE2 GLN B 39 " pdb=" O LYS B 43 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASP A 166 " pdb=" OH TYR A 446 " model vdw 2.215 3.040 nonbonded pdb=" O GLY A 845 " pdb=" OG SER A 849 " model vdw 2.216 3.040 ... (remaining 125185 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 'B' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) selection = (chain 'D' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) } ncs_group { reference = (chain 'C' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 109 or resid 111 throug \ h 112 or resid 115 or resid 121 through 236)) selection = (chain 'E' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 103 or resid 105 throug \ h 106 or resid 108 or resid 114 through 229)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.620 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.770 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 16072 Z= 0.350 Angle : 1.042 15.045 21822 Z= 0.568 Chirality : 0.058 0.386 2499 Planarity : 0.006 0.047 2727 Dihedral : 15.416 118.974 5762 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.62 % Favored : 90.33 % Rotamer: Outliers : 0.89 % Allowed : 7.72 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.19 (0.15), residues: 2010 helix: -3.96 (0.12), residues: 688 sheet: -2.34 (0.24), residues: 406 loop : -3.48 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 831 TYR 0.031 0.003 TYR A 710 PHE 0.059 0.003 PHE A 305 TRP 0.022 0.002 TRP C 112 HIS 0.008 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.35 (16064) covalent geometry : angle 1.04190 / 0.57 (21806) SS BOND : bond 0.00375 / 0.22 ( 8) SS BOND : angle 1.45484 / 0.80 ( 16) hydrogen bonds : bond 0.16208 / 10.80 ( 656) hydrogen bonds : angle 8.40589 / 5.66 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 TYR cc_start: 0.5676 (m-80) cc_final: 0.5361 (m-80) REVERT: A 206 PHE cc_start: 0.6256 (t80) cc_final: 0.5800 (t80) REVERT: A 246 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0761 (mt) REVERT: A 738 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (pt) REVERT: B 95 LYS cc_start: 0.5449 (mmmt) cc_final: 0.4585 (mtmt) outliers start: 15 outliers final: 7 residues processed: 193 average time/residue: 0.1578 time to fit residues: 43.3871 Evaluate side-chains 142 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1065 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN E 108 GLN A 151 GLN A 332 ASN A 400 HIS A 537 GLN A 748 GLN A 837 GLN A 838 ASN A 841 ASN A 881 ASN A 902 ASN A 935 HIS A1033 ASN A1111 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1214 GLN B 4 GLN B 90 GLN B 91 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 80 ASN C 87 ASN C 175 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.256980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.239266 restraints weight = 41741.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.236588 restraints weight = 48024.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.234635 restraints weight = 33783.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.234825 restraints weight = 34303.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.233990 restraints weight = 24577.923| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4792 r_free = 0.4792 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4791 r_free = 0.4791 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.4791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16072 Z= 0.134 Angle : 0.659 9.023 21822 Z= 0.340 Chirality : 0.044 0.182 2499 Planarity : 0.005 0.075 2727 Dihedral : 8.911 113.300 2288 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.78 % Allowed : 11.41 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.17), residues: 2010 helix: -1.64 (0.17), residues: 694 sheet: -1.71 (0.24), residues: 406 loop : -2.51 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 494 TYR 0.017 0.002 TYR A 116 PHE 0.026 0.002 PHE A 732 TRP 0.035 0.002 TRP E 106 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16064) covalent geometry : angle 0.65836 / 0.34 (21806) SS BOND : bond 0.00366 / 0.20 ( 8) SS BOND : angle 1.00409 / 0.57 ( 16) hydrogen bonds : bond 0.04871 / 3.23 ( 656) hydrogen bonds : angle 5.84696 / 3.92 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.6463 (t80) cc_final: 0.6234 (t80) REVERT: A 206 PHE cc_start: 0.5706 (t80) cc_final: 0.5287 (t80) REVERT: A 501 GLU cc_start: 0.5779 (mt-10) cc_final: 0.5418 (mt-10) REVERT: A 552 LYS cc_start: 0.6708 (tppt) cc_final: 0.6340 (mmtm) REVERT: A 738 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7669 (pt) REVERT: B 95 LYS cc_start: 0.5327 (mmmt) cc_final: 0.4415 (mtmt) REVERT: C 86 MET cc_start: 0.4695 (ptp) cc_final: 0.4213 (ptm) outliers start: 30 outliers final: 14 residues processed: 177 average time/residue: 0.1198 time to fit residues: 32.0562 Evaluate side-chains 140 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 902 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 121 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 198 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 7 GLN A 67 HIS A 332 ASN A 902 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN B 38 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.251131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.227561 restraints weight = 42470.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.229211 restraints weight = 61371.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.230650 restraints weight = 15744.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.230913 restraints weight = 8875.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.231297 restraints weight = 5409.371| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4692 r_free = 0.4692 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4692 r_free = 0.4692 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16072 Z= 0.182 Angle : 0.668 8.996 21822 Z= 0.343 Chirality : 0.045 0.288 2499 Planarity : 0.005 0.066 2727 Dihedral : 8.674 116.668 2280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.55 % Allowed : 14.68 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.18), residues: 2010 helix: -1.16 (0.18), residues: 703 sheet: -1.42 (0.25), residues: 419 loop : -2.22 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1221 TYR 0.020 0.002 TYR A1132 PHE 0.027 0.002 PHE A 982 TRP 0.019 0.001 TRP E 106 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (16064) covalent geometry : angle 0.66783 / 0.34 (21806) SS BOND : bond 0.00279 / 0.17 ( 8) SS BOND : angle 0.79441 / 0.45 ( 16) hydrogen bonds : bond 0.05342 / 3.55 ( 656) hydrogen bonds : angle 5.70296 / 3.82 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 192 SER cc_start: -0.1354 (OUTLIER) cc_final: -0.1890 (t) REVERT: A 206 PHE cc_start: 0.6013 (t80) cc_final: 0.5792 (t80) REVERT: A 446 TYR cc_start: 0.6628 (m-10) cc_final: 0.6398 (m-10) REVERT: A 501 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5652 (mt-10) REVERT: A 738 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7779 (pt) REVERT: A 800 MET cc_start: 0.6686 (ttt) cc_final: 0.6466 (ttt) REVERT: A 895 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7104 (mp) REVERT: A 927 TYR cc_start: 0.7464 (t80) cc_final: 0.7247 (t80) REVERT: A 1002 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7381 (tp) REVERT: B 95 LYS cc_start: 0.5366 (mmmt) cc_final: 0.4395 (mtmt) outliers start: 43 outliers final: 22 residues processed: 171 average time/residue: 0.1088 time to fit residues: 28.7326 Evaluate side-chains 146 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 26 optimal weight: 0.0980 chunk 160 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 172 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN B 90 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.255105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.236781 restraints weight = 42123.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.234327 restraints weight = 51786.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.231700 restraints weight = 34321.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.230756 restraints weight = 38549.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.229375 restraints weight = 33927.977| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4757 r_free = 0.4757 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4757 r_free = 0.4757 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.4757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16072 Z= 0.129 Angle : 0.604 9.748 21822 Z= 0.307 Chirality : 0.042 0.173 2499 Planarity : 0.004 0.056 2727 Dihedral : 8.310 114.495 2280 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.50 % Allowed : 16.40 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.18), residues: 2010 helix: -0.44 (0.19), residues: 700 sheet: -1.23 (0.25), residues: 422 loop : -1.94 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1221 TYR 0.016 0.001 TYR A1132 PHE 0.029 0.002 PHE A 732 TRP 0.012 0.001 TRP E 167 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16064) covalent geometry : angle 0.60438 / 0.31 (21806) SS BOND : bond 0.00243 / 0.14 ( 8) SS BOND : angle 0.64534 / 0.37 ( 16) hydrogen bonds : bond 0.04502 / 3.00 ( 656) hydrogen bonds : angle 5.26295 / 3.53 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 192 SER cc_start: -0.1538 (OUTLIER) cc_final: -0.1911 (t) REVERT: A 438 THR cc_start: 0.5122 (p) cc_final: 0.4892 (p) REVERT: A 501 GLU cc_start: 0.5799 (mt-10) cc_final: 0.5558 (mt-10) REVERT: A 552 LYS cc_start: 0.6716 (tppt) cc_final: 0.6381 (mmtm) REVERT: A 738 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7697 (pt) REVERT: A 1002 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7254 (tp) REVERT: B 95 LYS cc_start: 0.5281 (mmmt) cc_final: 0.4375 (mtmt) outliers start: 42 outliers final: 20 residues processed: 164 average time/residue: 0.1167 time to fit residues: 29.5018 Evaluate side-chains 144 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 2 optimal weight: 40.0000 chunk 93 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 464 ASN A 841 ASN A 902 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN C 125 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.247208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.216356 restraints weight = 44865.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.215498 restraints weight = 58056.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.212105 restraints weight = 33359.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.211759 restraints weight = 32568.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.210548 restraints weight = 27642.174| |-----------------------------------------------------------------------------| r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16072 Z= 0.270 Angle : 0.747 9.678 21822 Z= 0.381 Chirality : 0.048 0.228 2499 Planarity : 0.005 0.056 2727 Dihedral : 8.811 117.552 2280 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.57 % Allowed : 17.65 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.18), residues: 2010 helix: -1.09 (0.18), residues: 707 sheet: -1.18 (0.25), residues: 410 loop : -1.93 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1187 TYR 0.017 0.002 TYR A 997 PHE 0.040 0.003 PHE A 206 TRP 0.036 0.002 TRP E 106 HIS 0.007 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (16064) covalent geometry : angle 0.74685 / 0.38 (21806) SS BOND : bond 0.00300 / 0.18 ( 8) SS BOND : angle 0.81704 / 0.45 ( 16) hydrogen bonds : bond 0.06119 / 4.11 ( 656) hydrogen bonds : angle 5.74863 / 3.85 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 119 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 86 MET cc_start: 0.6996 (mmt) cc_final: 0.6279 (mmt) REVERT: E 192 SER cc_start: -0.1328 (OUTLIER) cc_final: -0.1856 (t) REVERT: A 123 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6605 (tt) REVERT: A 552 LYS cc_start: 0.6828 (tppt) cc_final: 0.6449 (mmtm) REVERT: A 842 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7659 (tt) REVERT: A 877 LEU cc_start: 0.3804 (OUTLIER) cc_final: 0.3523 (pt) REVERT: A 895 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7045 (mp) REVERT: A 927 TYR cc_start: 0.7473 (t80) cc_final: 0.7255 (t80) REVERT: A 947 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6641 (m-80) REVERT: A 1002 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7412 (tp) REVERT: B 95 LYS cc_start: 0.5282 (mmmt) cc_final: 0.4304 (mtmt) outliers start: 60 outliers final: 33 residues processed: 168 average time/residue: 0.1146 time to fit residues: 30.0236 Evaluate side-chains 148 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 196 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 198 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.249140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.222837 restraints weight = 30417.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.219778 restraints weight = 47401.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.216871 restraints weight = 38939.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.216489 restraints weight = 40248.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.214598 restraints weight = 34800.411| |-----------------------------------------------------------------------------| r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4615 r_free = 0.4615 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4615 r_free = 0.4615 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16072 Z= 0.165 Angle : 0.642 12.173 21822 Z= 0.325 Chirality : 0.043 0.199 2499 Planarity : 0.004 0.056 2727 Dihedral : 8.305 114.931 2278 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.15 % Allowed : 19.01 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.18), residues: 2010 helix: -0.64 (0.19), residues: 702 sheet: -1.08 (0.25), residues: 409 loop : -1.70 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 971 TYR 0.015 0.002 TYR C 122 PHE 0.035 0.002 PHE A 206 TRP 0.026 0.001 TRP E 106 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (16064) covalent geometry : angle 0.64219 / 0.33 (21806) SS BOND : bond 0.00218 / 0.13 ( 8) SS BOND : angle 0.63718 / 0.36 ( 16) hydrogen bonds : bond 0.05044 / 3.38 ( 656) hydrogen bonds : angle 5.34863 / 3.59 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 86 MET cc_start: 0.6880 (mmt) cc_final: 0.6167 (mmt) REVERT: A 552 LYS cc_start: 0.6808 (tppt) cc_final: 0.6452 (mmtm) REVERT: A 877 LEU cc_start: 0.3798 (OUTLIER) cc_final: 0.3546 (pt) REVERT: A 895 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6946 (mp) REVERT: A 947 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: A 1002 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7354 (tp) REVERT: A 1249 ARG cc_start: 0.3191 (OUTLIER) cc_final: 0.2983 (mmt-90) REVERT: B 95 LYS cc_start: 0.5262 (mmmt) cc_final: 0.4344 (mtmt) REVERT: C 89 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.4284 (tp) outliers start: 53 outliers final: 32 residues processed: 162 average time/residue: 0.1012 time to fit residues: 25.1720 Evaluate side-chains 149 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 141 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 172 optimal weight: 50.0000 chunk 57 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 841 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** 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 = 0.4905 r_free = 0.4905 target = 0.247154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.215855 restraints weight = 27690.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.212449 restraints weight = 42069.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.208973 restraints weight = 34174.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.209033 restraints weight = 35948.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.207587 restraints weight = 29587.675| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4530 r_free = 0.4530 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4530 r_free = 0.4530 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16072 Z= 0.271 Angle : 0.755 11.090 21822 Z= 0.384 Chirality : 0.048 0.234 2499 Planarity : 0.005 0.053 2727 Dihedral : 8.645 117.409 2277 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.10 % Allowed : 18.84 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 2010 helix: -1.15 (0.18), residues: 704 sheet: -1.13 (0.25), residues: 410 loop : -1.80 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1187 TYR 0.023 0.002 TYR C 122 PHE 0.036 0.003 PHE A 206 TRP 0.064 0.002 TRP E 106 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (16064) covalent geometry : angle 0.75495 / 0.38 (21806) SS BOND : bond 0.00254 / 0.15 ( 8) SS BOND : angle 0.72915 / 0.40 ( 16) hydrogen bonds : bond 0.06205 / 4.16 ( 656) hydrogen bonds : angle 5.75287 / 3.85 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: E 86 MET cc_start: 0.6991 (mmt) cc_final: 0.6292 (mmt) REVERT: E 192 SER cc_start: -0.1287 (OUTLIER) cc_final: -0.1772 (t) REVERT: A 552 LYS cc_start: 0.6883 (tppt) cc_final: 0.6574 (mmtm) REVERT: A 842 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7607 (tt) REVERT: A 895 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7037 (mp) REVERT: A 923 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7131 (mp) REVERT: A 947 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: A 1002 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7433 (tp) REVERT: A 1137 ARG cc_start: 0.7055 (ptm-80) cc_final: 0.6819 (ttp80) REVERT: A 1238 ASN cc_start: 0.0730 (OUTLIER) cc_final: -0.0558 (t0) REVERT: A 1249 ARG cc_start: 0.3153 (OUTLIER) cc_final: 0.2943 (mmt-90) REVERT: B 95 LYS cc_start: 0.5257 (mmmt) cc_final: 0.4237 (mtmt) outliers start: 69 outliers final: 41 residues processed: 171 average time/residue: 0.1040 time to fit residues: 27.9990 Evaluate side-chains 158 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1043 TYR Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1238 ASN Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 101 optimal weight: 0.0670 chunk 195 optimal weight: 30.0000 chunk 21 optimal weight: 0.0010 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 157 optimal weight: 0.0470 chunk 173 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 overall best weight: 0.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN A 134 GLN A 489 ASN A 841 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.260136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.241636 restraints weight = 40422.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.239753 restraints weight = 53670.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.237826 restraints weight = 31983.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.237489 restraints weight = 30417.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.236231 restraints weight = 29072.268| |-----------------------------------------------------------------------------| r_work (final): 0.4809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4809 r_free = 0.4809 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4809 r_free = 0.4809 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.4809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16072 Z= 0.113 Angle : 0.603 10.360 21822 Z= 0.304 Chirality : 0.042 0.186 2499 Planarity : 0.004 0.058 2727 Dihedral : 7.781 112.252 2277 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.84 % Allowed : 21.33 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.19), residues: 2010 helix: -0.01 (0.20), residues: 698 sheet: -1.01 (0.25), residues: 418 loop : -1.47 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 494 TYR 0.018 0.001 TYR A 116 PHE 0.035 0.002 PHE A 154 TRP 0.075 0.002 TRP E 106 HIS 0.004 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16064) covalent geometry : angle 0.60253 / 0.30 (21806) SS BOND : bond 0.00247 / 0.14 ( 8) SS BOND : angle 0.61177 / 0.36 ( 16) hydrogen bonds : bond 0.04139 / 2.78 ( 656) hydrogen bonds : angle 4.94240 / 3.32 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 552 LYS cc_start: 0.6515 (tppt) cc_final: 0.6202 (mmtm) REVERT: A 1002 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7276 (tp) REVERT: A 1137 ARG cc_start: 0.6440 (ptm-80) cc_final: 0.6221 (ttp80) REVERT: B 28 GLN cc_start: 0.5242 (mp10) cc_final: 0.3599 (tm-30) REVERT: B 95 LYS cc_start: 0.5337 (mmmt) cc_final: 0.4458 (mtmt) REVERT: C 89 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4162 (tp) outliers start: 31 outliers final: 15 residues processed: 148 average time/residue: 0.1171 time to fit residues: 26.8122 Evaluate side-chains 126 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 171 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.256483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.236437 restraints weight = 35172.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.234231 restraints weight = 49907.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.230984 restraints weight = 31332.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.229953 restraints weight = 38820.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.229188 restraints weight = 30348.117| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4790 r_free = 0.4790 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4790 r_free = 0.4790 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16072 Z= 0.131 Angle : 0.604 10.684 21822 Z= 0.304 Chirality : 0.042 0.184 2499 Planarity : 0.004 0.058 2727 Dihedral : 7.723 115.944 2275 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.90 % Allowed : 21.21 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 2010 helix: 0.08 (0.20), residues: 693 sheet: -0.86 (0.26), residues: 409 loop : -1.39 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1249 TYR 0.019 0.001 TYR D 174 PHE 0.038 0.002 PHE A 206 TRP 0.051 0.002 TRP E 106 HIS 0.003 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16064) covalent geometry : angle 0.60365 / 0.30 (21806) SS BOND : bond 0.00229 / 0.13 ( 8) SS BOND : angle 0.54071 / 0.31 ( 16) hydrogen bonds : bond 0.04428 / 2.96 ( 656) hydrogen bonds : angle 4.95216 / 3.32 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.747 Fit side-chains REVERT: A 246 LEU cc_start: 0.2278 (OUTLIER) cc_final: 0.1889 (pt) REVERT: A 552 LYS cc_start: 0.6614 (tppt) cc_final: 0.6344 (mmtm) REVERT: A 947 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: A 1002 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7363 (tp) REVERT: B 95 LYS cc_start: 0.5330 (mmmt) cc_final: 0.4457 (mtmt) REVERT: C 89 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.4185 (tp) outliers start: 32 outliers final: 24 residues processed: 143 average time/residue: 0.1114 time to fit residues: 25.1743 Evaluate side-chains 137 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 88 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 163 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 841 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.253650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.233226 restraints weight = 29865.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.229881 restraints weight = 49028.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.228067 restraints weight = 40436.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.227955 restraints weight = 44942.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.226608 restraints weight = 36320.689| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16072 Z= 0.194 Angle : 0.670 10.311 21822 Z= 0.340 Chirality : 0.045 0.208 2499 Planarity : 0.005 0.058 2727 Dihedral : 8.049 116.587 2275 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.02 % Allowed : 21.75 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 2010 helix: -0.31 (0.19), residues: 698 sheet: -0.90 (0.26), residues: 412 loop : -1.36 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1249 TYR 0.031 0.002 TYR A 952 PHE 0.040 0.002 PHE A 154 TRP 0.063 0.002 TRP E 106 HIS 0.006 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (16064) covalent geometry : angle 0.66977 / 0.34 (21806) SS BOND : bond 0.00211 / 0.12 ( 8) SS BOND : angle 0.72055 / 0.37 ( 16) hydrogen bonds : bond 0.05156 / 3.44 ( 656) hydrogen bonds : angle 5.21922 / 3.50 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.577 Fit side-chains REVERT: E 89 LEU cc_start: 0.5682 (mm) cc_final: 0.5380 (mm) REVERT: A 552 LYS cc_start: 0.6625 (tppt) cc_final: 0.6349 (mmtm) REVERT: A 947 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: A 1002 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7415 (tp) REVERT: A 1137 ARG cc_start: 0.6680 (ptm-80) cc_final: 0.6383 (ttp80) REVERT: B 95 LYS cc_start: 0.5321 (mmmt) cc_final: 0.4378 (mtmt) REVERT: C 89 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4251 (tp) outliers start: 34 outliers final: 29 residues processed: 140 average time/residue: 0.1172 time to fit residues: 25.6642 Evaluate side-chains 138 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 80 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 155 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.255114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.234870 restraints weight = 32849.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.232699 restraints weight = 49042.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.230372 restraints weight = 30600.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.229481 restraints weight = 31797.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.228787 restraints weight = 31206.992| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4750 r_free = 0.4750 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4750 r_free = 0.4750 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16072 Z= 0.145 Angle : 0.624 10.323 21822 Z= 0.316 Chirality : 0.043 0.186 2499 Planarity : 0.004 0.058 2727 Dihedral : 7.857 115.005 2275 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.02 % Allowed : 22.04 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 2010 helix: -0.11 (0.20), residues: 695 sheet: -0.77 (0.26), residues: 407 loop : -1.33 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1249 TYR 0.027 0.002 TYR A 952 PHE 0.042 0.002 PHE B 140 TRP 0.066 0.002 TRP E 106 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16064) covalent geometry : angle 0.62354 / 0.32 (21806) SS BOND : bond 0.00207 / 0.12 ( 8) SS BOND : angle 0.68060 / 0.39 ( 16) hydrogen bonds : bond 0.04628 / 3.09 ( 656) hydrogen bonds : angle 5.05303 / 3.40 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.58 seconds wall clock time: 51 minutes 24.19 seconds (3084.19 seconds total)