Starting phenix.real_space_refine on Mon Aug 10 06:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpb_18547/08_2026/8qpb_18547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpb_18547/08_2026/8qpb_18547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpb_18547/08_2026/8qpb_18547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpb_18547/08_2026/8qpb_18547.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpb_18547/08_2026/8qpb_18547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpb_18547/08_2026/8qpb_18547.cif" } resolution = 3.7 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= 0.005 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 226 5.49 5 S 167 5.16 5 C 27014 2.51 5 N 7699 2.21 5 O 8698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43804 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 158 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "G" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 484 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "J" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2886 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "F" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 488 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "N" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3502 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 23, 'TRANS': 433} Chain breaks: 4 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'HIS:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 3, 'TRP:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 16409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1977, 16409 Classifications: {'peptide': 1977} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 105, 'TRANS': 1869} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "U" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3749 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain: "S" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1164 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 4 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 6592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6592 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 48, 'TRANS': 787} Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "D" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1170 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1660 Classifications: {'RNA': 79} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 25, 'rna3p_pyr': 39} Link IDs: {'rna2p': 15, 'rna3p': 63} Chain: "7" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 846 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Chain: "4" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1699 Classifications: {'RNA': 80} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 18, 'rna3p': 61} Chain: "6" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1034 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 28, 'rna3p_pyr': 15} Link IDs: {'rna2p': 5, 'rna3p': 42} Chain: "z" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 286 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.35, per 1000 atoms: 0.17 Number of scatterers: 43804 At special positions: 0 Unit cell: (203, 196.04, 175.16, 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 167 16.00 P 226 15.00 O 8698 8.00 N 7699 7.00 C 27014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9212 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 38 sheets defined 51.3% alpha, 11.1% beta 51 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 308 through 316 Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'J' and resid 441 through 466 Processing helix chain 'J' and resid 477 through 485 removed outlier: 4.638A pdb=" N MET J 482 " --> pdb=" O ILE J 478 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG J 483 " --> pdb=" O SER J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 490 removed outlier: 4.035A pdb=" N VAL J 490 " --> pdb=" O GLY J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 519 Processing helix chain 'L' and resid 53 through 79 removed outlier: 3.534A pdb=" N ILE L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU L 69 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR L 70 " --> pdb=" O LYS L 66 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 122 removed outlier: 4.099A pdb=" N VAL L 92 " --> pdb=" O PRO L 88 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL L 101 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 146 through 150 removed outlier: 3.775A pdb=" N LYS L 150 " --> pdb=" O ASP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 157 removed outlier: 3.619A pdb=" N GLN L 156 " --> pdb=" O ASN L 152 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN L 157 " --> pdb=" O GLU L 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 152 through 157' Processing helix chain 'L' and resid 160 through 173 removed outlier: 3.565A pdb=" N MET L 165 " --> pdb=" O ASN L 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL L 166 " --> pdb=" O ALA L 162 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR L 173 " --> pdb=" O VAL L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 216 removed outlier: 4.823A pdb=" N SER L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA L 216 " --> pdb=" O MET L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 223 Processing helix chain 'L' and resid 224 through 236 Processing helix chain 'L' and resid 237 through 243 Processing helix chain 'L' and resid 245 through 250 removed outlier: 3.765A pdb=" N MET L 250 " --> pdb=" O ALA L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.556A pdb=" N VAL L 267 " --> pdb=" O SER L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 283 through 286 removed outlier: 6.065A pdb=" N ASP L 286 " --> pdb=" O LEU L 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 283 through 286' Processing helix chain 'L' and resid 287 through 307 Processing helix chain 'L' and resid 314 through 333 removed outlier: 4.165A pdb=" N GLU L 323 " --> pdb=" O GLU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 367 Processing helix chain 'L' and resid 369 through 376 removed outlier: 3.508A pdb=" N ASN L 376 " --> pdb=" O ARG L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 417 Processing helix chain 'L' and resid 421 through 431 Processing helix chain 'F' and resid 81 through 98 Processing helix chain 'F' and resid 104 through 116 Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'N' and resid 98 through 114 removed outlier: 3.744A pdb=" N ASP N 102 " --> pdb=" O ASP N 98 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE N 104 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 135 removed outlier: 4.203A pdb=" N GLU N 134 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 142 through 149 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 153 through 159 Processing helix chain 'N' and resid 168 through 173 Processing helix chain 'N' and resid 183 through 193 removed outlier: 4.199A pdb=" N PHE N 187 " --> pdb=" O PRO N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 305 Processing helix chain 'N' and resid 308 through 323 removed outlier: 3.592A pdb=" N TRP N 312 " --> pdb=" O HIS N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 339 removed outlier: 3.636A pdb=" N ARG N 329 " --> pdb=" O LEU N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 353 removed outlier: 4.248A pdb=" N TRP N 346 " --> pdb=" O SER N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 369 Processing helix chain 'N' and resid 373 through 383 Processing helix chain 'N' and resid 385 through 400 Processing helix chain 'N' and resid 403 through 408 Processing helix chain 'N' and resid 409 through 414 Processing helix chain 'N' and resid 793 through 807 Processing helix chain 'N' and resid 810 through 821 Processing helix chain 'N' and resid 822 through 827 removed outlier: 4.284A pdb=" N ARG N 827 " --> pdb=" O ARG N 823 " (cutoff:3.500A) Processing helix chain 'N' and resid 829 through 838 removed outlier: 3.574A pdb=" N ALA N 833 " --> pdb=" O LYS N 829 " (cutoff:3.500A) Processing helix chain 'N' and resid 840 through 854 Processing helix chain 'N' and resid 856 through 871 Processing helix chain 'N' and resid 876 through 888 removed outlier: 4.126A pdb=" N PHE N 880 " --> pdb=" O ASP N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 890 through 901 Processing helix chain 'N' and resid 910 through 919 Processing helix chain 'N' and resid 923 through 930 removed outlier: 3.870A pdb=" N GLY N 927 " --> pdb=" O GLN N 923 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP N 928 " --> pdb=" O LYS N 924 " (cutoff:3.500A) Processing helix chain 'N' and resid 934 through 940 removed outlier: 4.023A pdb=" N LYS N 938 " --> pdb=" O ALA N 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.158A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 removed outlier: 3.872A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.687A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.150A pdb=" N TYR A 254 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.434A pdb=" N ASP A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.837A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.593A pdb=" N ASN A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.545A pdb=" N ARG A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.611A pdb=" N ALA A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 567 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 598 through 617 removed outlier: 4.005A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 656 removed outlier: 3.852A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 680 through 697 removed outlier: 4.230A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 732 through 763 removed outlier: 4.071A pdb=" N GLU A 759 " --> pdb=" O HIS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 798 removed outlier: 3.789A pdb=" N CYS A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 933 removed outlier: 3.791A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 989 through 999 Processing helix chain 'A' and resid 1002 through 1013 Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 4.308A pdb=" N HIS A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 3.933A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 4.077A pdb=" N ILE A1125 " --> pdb=" O ASN A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.515A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1203 removed outlier: 4.156A pdb=" N SER A1203 " --> pdb=" O LYS A1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1199 through 1203' Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1341 removed outlier: 4.137A pdb=" N ARG A1341 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.755A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1400 removed outlier: 4.068A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A1399 " --> pdb=" O GLU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1479 through 1487 removed outlier: 4.117A pdb=" N GLY A1483 " --> pdb=" O GLY A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1494 Processing helix chain 'A' and resid 1507 through 1513 Processing helix chain 'A' and resid 1519 through 1527 Processing helix chain 'A' and resid 1528 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 removed outlier: 3.502A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1621 Processing helix chain 'A' and resid 1675 through 1690 Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 3.941A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1767 through 1772 removed outlier: 3.856A pdb=" N PHE A1772 " --> pdb=" O TYR A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1827 Processing helix chain 'A' and resid 1832 through 1852 removed outlier: 3.609A pdb=" N LEU A1836 " --> pdb=" O ARG A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1867 No H-bonds generated for 'chain 'A' and resid 1865 through 1867' Processing helix chain 'A' and resid 1868 through 1876 removed outlier: 3.847A pdb=" N GLU A1873 " --> pdb=" O LEU A1869 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1898 Processing helix chain 'A' and resid 1899 through 1908 removed outlier: 4.276A pdb=" N ASP A1904 " --> pdb=" O GLU A1900 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A1905 " --> pdb=" O LYS A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1926 Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1948 through 1955 removed outlier: 3.634A pdb=" N LYS A1955 " --> pdb=" O LYS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1996 Processing helix chain 'A' and resid 2003 through 2013 Processing helix chain 'A' and resid 2020 through 2027 removed outlier: 4.195A pdb=" N ARG A2023 " --> pdb=" O SER A2020 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 111 Processing helix chain 'U' and resid 112 through 116 removed outlier: 3.567A pdb=" N LEU U 116 " --> pdb=" O ARG U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 186 through 194 Processing helix chain 'U' and resid 198 through 205 Processing helix chain 'U' and resid 233 through 244 removed outlier: 3.806A pdb=" N ASN U 237 " --> pdb=" O ASN U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 246 through 255 removed outlier: 4.347A pdb=" N GLU U 255 " --> pdb=" O ASN U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 259 Processing helix chain 'U' and resid 269 through 285 removed outlier: 3.737A pdb=" N LEU U 273 " --> pdb=" O ILE U 269 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY U 278 " --> pdb=" O VAL U 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 296 through 308 removed outlier: 3.716A pdb=" N LYS U 308 " --> pdb=" O VAL U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 334 Processing helix chain 'U' and resid 343 through 350 Processing helix chain 'U' and resid 366 through 376 Processing helix chain 'U' and resid 415 through 420 Processing helix chain 'U' and resid 481 through 484 Processing helix chain 'U' and resid 538 through 542 removed outlier: 3.542A pdb=" N MET U 541 " --> pdb=" O LEU U 538 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 185 removed outlier: 3.686A pdb=" N LYS S 183 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 219 Processing helix chain 'S' and resid 291 through 310 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.772A pdb=" N GLY C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 249 removed outlier: 4.115A pdb=" N THR C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 240 " --> pdb=" O MET C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 270 through 291 Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.683A pdb=" N LEU C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.670A pdb=" N VAL C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.502A pdb=" N LEU C 410 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 438 Processing helix chain 'C' and resid 440 through 453 removed outlier: 5.422A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 467 removed outlier: 3.575A pdb=" N ASP C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 removed outlier: 3.614A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 755 through 776 removed outlier: 3.536A pdb=" N LEU C 759 " --> pdb=" O ASP C 755 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 804 through 823 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 842 through 853 removed outlier: 3.533A pdb=" N ARG C 853 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 941 removed outlier: 4.377A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ARG C 931 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 937 " --> pdb=" O PHE C 933 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 32 removed outlier: 3.593A pdb=" N LYS M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 21 " --> pdb=" O HIS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 49 Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.685A pdb=" N LEU M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU M 69 " --> pdb=" O ILE M 65 " (cutoff:3.500A) Proline residue: M 70 - end of helix Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 112 through 127 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.725A pdb=" N GLU D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.564A pdb=" N MET D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain '7' and resid 424 through 431 Processing helix chain '7' and resid 435 through 451 removed outlier: 3.721A pdb=" N LEU 7 439 " --> pdb=" O ASP 7 435 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 473 Processing helix chain '7' and resid 505 through 507 No H-bonds generated for 'chain '7' and resid 505 through 507' Processing helix chain '7' and resid 508 through 519 Processing sheet with id=AA1, first strand: chain 'L' and resid 377 through 379 Processing sheet with id=AA2, first strand: chain 'N' and resid 180 through 181 Processing sheet with id=AA3, first strand: chain 'N' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 294 removed outlier: 6.799A pdb=" N TRP A 293 " --> pdb=" O LEU A1142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA9, first strand: chain 'A' and resid 905 through 910 removed outlier: 6.294A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1085 through 1089 removed outlier: 5.312A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 3.751A pdb=" N ALA A1226 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1334 through 1335 Processing sheet with id=AB4, first strand: chain 'A' and resid 1342 through 1346 removed outlier: 9.612A pdb=" N VAL S 151 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N HIS A1352 " --> pdb=" O VAL S 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id=AB6, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 7.154A pdb=" N PHE A1632 " --> pdb=" O GLU A1607 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL A1609 " --> pdb=" O LEU A1630 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A1630 " --> pdb=" O VAL A1609 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1643 through 1644 removed outlier: 6.426A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1762 through 1763 removed outlier: 6.233A pdb=" N ILE A1861 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER A1887 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1863 " --> pdb=" O SER A1887 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A1818 " --> pdb=" O ILE A1809 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 349 through 350 removed outlier: 7.136A pdb=" N THR S 258 " --> pdb=" O LEU S 289 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 142 through 143 removed outlier: 3.859A pdb=" N LYS U 171 " --> pdb=" O ASN U 166 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE U 172 " --> pdb=" O ILE U 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 226 through 227 removed outlier: 6.296A pdb=" N GLY U 226 " --> pdb=" O VAL U 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'U' and resid 381 through 388 removed outlier: 6.511A pdb=" N SER U 352 " --> pdb=" O THR U 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 391 through 393 removed outlier: 6.382A pdb=" N LEU U 391 " --> pdb=" O CYS U 453 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR U 548 " --> pdb=" O ILE U 454 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE U 503 " --> pdb=" O TYR U 548 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN U 550 " --> pdb=" O ALA U 501 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA U 501 " --> pdb=" O GLN U 550 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP U 552 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU U 499 " --> pdb=" O TRP U 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 391 through 393 removed outlier: 6.382A pdb=" N LEU U 391 " --> pdb=" O CYS U 453 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR U 548 " --> pdb=" O ILE U 454 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE U 503 " --> pdb=" O TYR U 548 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN U 550 " --> pdb=" O ALA U 501 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA U 501 " --> pdb=" O GLN U 550 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP U 552 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU U 499 " --> pdb=" O TRP U 552 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE U 500 " --> pdb=" O LEU U 519 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE U 516 " --> pdb=" O LEU U 529 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP U 526 " --> pdb=" O ILE U 537 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 412 through 414 removed outlier: 6.401A pdb=" N VAL U 413 " --> pdb=" O ASN U 472 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'U' and resid 458 through 459 Processing sheet with id=AC8, first strand: chain 'C' and resid 184 through 191 removed outlier: 8.969A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 225 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N CYS C 256 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 227 " --> pdb=" O CYS C 256 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN C 258 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE C 229 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AD1, first strand: chain 'C' and resid 523 through 527 removed outlier: 6.359A pdb=" N MET C 475 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AD3, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.409A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.720A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.720A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.495A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 663 through 666 removed outlier: 7.134A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 900 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 835 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 898 " --> pdb=" O GLU C 835 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.507A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 35 through 37 removed outlier: 3.876A pdb=" N PHE M 53 " --> pdb=" O VAL M 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.404A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N VAL D 81 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE D 92 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE D 83 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 411 through 412 1874 hydrogen bonds defined for protein. 5346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 119 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 11.63 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13224 1.34 - 1.46: 8249 1.46 - 1.58: 23032 1.58 - 1.70: 442 1.70 - 1.82: 277 Bond restraints: 45224 Sorted by residual: bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.603 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.609 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.609 0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" O14 IHP A2401 " pdb=" P4 IHP A2401 " ideal model delta sigma weight residual 1.671 1.609 0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 45219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 60926 1.87 - 3.74: 1217 3.74 - 5.60: 104 5.60 - 7.47: 18 7.47 - 9.34: 6 Bond angle restraints: 62271 Sorted by residual: angle pdb=" N1 C 6 37 " pdb=" C2 C 6 37 " pdb=" O2 C 6 37 " ideal model delta sigma weight residual 118.90 121.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" C3' U 5 78 " pdb=" O3' U 5 78 " pdb=" P C 5 79 " ideal model delta sigma weight residual 119.70 125.23 -5.53 1.20e+00 6.94e-01 2.12e+01 angle pdb=" C ALA C 535 " pdb=" CA ALA C 535 " pdb=" CB ALA C 535 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" C3' C 6 77 " pdb=" O3' C 6 77 " pdb=" P A 6 78 " ideal model delta sigma weight residual 119.70 125.15 -5.45 1.20e+00 6.94e-01 2.06e+01 angle pdb=" C1' C 6 37 " pdb=" N1 C 6 37 " pdb=" C2 C 6 37 " ideal model delta sigma weight residual 118.80 123.77 -4.97 1.10e+00 8.26e-01 2.04e+01 ... (remaining 62266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 26699 35.96 - 71.92: 913 71.92 - 107.88: 100 107.88 - 143.84: 4 143.84 - 179.80: 9 Dihedral angle restraints: 27725 sinusoidal: 13524 harmonic: 14201 Sorted by residual: dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual 232.00 52.20 179.80 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 4 19 " pdb=" C1' U 4 19 " pdb=" N1 U 4 19 " pdb=" C2 U 4 19 " ideal model delta sinusoidal sigma weight residual -128.00 51.73 -179.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 5 78 " pdb=" C1' U 5 78 " pdb=" N1 U 5 78 " pdb=" C2 U 5 78 " ideal model delta sinusoidal sigma weight residual -128.00 49.21 -177.21 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 27722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.002: 7050 1.002 - 2.004: 0 2.004 - 3.006: 0 3.006 - 4.008: 0 4.008 - 5.010: 4 Chirality restraints: 7054 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.27e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.49 -4.91 2.00e-01 2.50e+01 6.02e+02 chirality pdb=" C3 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" O13 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.34 2.52 -4.86 2.00e-01 2.50e+01 5.91e+02 ... (remaining 7051 not shown) Planarity restraints: 7183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1879 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A1880 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A1880 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1880 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1416 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A1417 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1417 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1417 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL U 246 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO U 247 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO U 247 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO U 247 " 0.025 5.00e-02 4.00e+02 ... (remaining 7180 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3461 2.74 - 3.28: 44906 3.28 - 3.82: 78315 3.82 - 4.36: 92894 4.36 - 4.90: 151848 Nonbonded interactions: 371424 Sorted by model distance: nonbonded pdb=" OG1 THR A1102 " pdb=" OD1 ASP A1104 " model vdw 2.195 3.040 nonbonded pdb=" O LYS A 465 " pdb=" N4 C 5 23 " model vdw 2.197 3.120 nonbonded pdb=" O GLU C 776 " pdb=" OH TYR C 817 " model vdw 2.201 3.040 nonbonded pdb=" O MET A1622 " pdb=" OH TYR A1687 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 783 " pdb=" OE2 GLU A 986 " model vdw 2.211 3.040 ... (remaining 371419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 : 0.003 0.068 45224 Z= 0.149 Angle : 0.566 9.338 62271 Z= 0.338 Chirality : 0.124 5.010 7054 Planarity : 0.004 0.062 7183 Dihedral : 17.306 179.798 18513 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.02 % Allowed : 0.38 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.72 (0.12), residues: 4796 helix: 1.42 (0.11), residues: 2211 sheet: 0.02 (0.23), residues: 501 loop : -0.36 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 536 TYR 0.014 0.001 TYR A1371 PHE 0.017 0.001 PHE A1794 TRP 0.021 0.001 TRP A1375 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (45224) covalent geometry : angle 0.56564 / 0.34 (62271) hydrogen bonds : bond 0.15124 / 10.15 ( 1975) hydrogen bonds : angle 6.29060 / 4.56 ( 5540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.297 Fit side-chains REVERT: A 1357 MET cc_start: 0.2415 (tpt) cc_final: 0.1156 (mmt) REVERT: M 15 ASP cc_start: 0.7844 (m-30) cc_final: 0.7483 (m-30) REVERT: M 64 GLU cc_start: 0.8839 (mp0) cc_final: 0.8576 (mp0) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.2213 time to fit residues: 64.6203 Evaluate side-chains 146 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 531 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.2980 chunk 494 optimal weight: 40.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 431 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 284 HIS ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 GLN A1944 HIS U 166 ASN ** U 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 316 GLN C 538 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.053392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.044154 restraints weight = 310530.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.045064 restraints weight = 179803.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.045660 restraints weight = 126426.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.046017 restraints weight = 101543.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.046273 restraints weight = 88521.532| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45224 Z= 0.190 Angle : 0.593 25.555 62271 Z= 0.300 Chirality : 0.043 0.776 7054 Planarity : 0.004 0.046 7183 Dihedral : 16.775 179.469 8719 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.24 % Allowed : 5.58 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.74 (0.12), residues: 4796 helix: 1.45 (0.11), residues: 2263 sheet: 0.02 (0.23), residues: 493 loop : -0.41 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 642 TYR 0.015 0.001 TYR C 722 PHE 0.020 0.001 PHE A1187 TRP 0.021 0.001 TRP A 293 HIS 0.007 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (45224) covalent geometry : angle 0.59261 / 0.30 (62271) hydrogen bonds : bond 0.05275 / 3.51 ( 1975) hydrogen bonds : angle 4.85533 / 3.54 ( 5540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: L 362 MET cc_start: 0.7918 (mtt) cc_final: 0.7699 (mtm) REVERT: A 599 MET cc_start: 0.8218 (tpt) cc_final: 0.7802 (tpt) REVERT: A 1357 MET cc_start: 0.2359 (tpt) cc_final: 0.1190 (mmt) REVERT: U 316 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: U 353 MET cc_start: 0.6919 (tmm) cc_final: 0.6442 (tmm) REVERT: M 15 ASP cc_start: 0.7810 (m-30) cc_final: 0.7472 (m-30) REVERT: M 64 GLU cc_start: 0.8749 (mp0) cc_final: 0.8484 (mp0) REVERT: M 115 GLN cc_start: 0.7540 (tp-100) cc_final: 0.6394 (mp10) outliers start: 10 outliers final: 6 residues processed: 153 average time/residue: 0.2301 time to fit residues: 61.9669 Evaluate side-chains 152 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain U residue 316 GLN Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 531 TRP Chi-restraints excluded: chain M residue 124 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 325 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 511 HIS J 515 ASN ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 190 HIS ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS A 752 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 GLN ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 316 GLN ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.053112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.044002 restraints weight = 311055.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044768 restraints weight = 180720.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.045339 restraints weight = 127762.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.045636 restraints weight = 102803.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.045914 restraints weight = 90694.958| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 45224 Z= 0.183 Angle : 0.554 9.573 62271 Z= 0.285 Chirality : 0.042 0.572 7054 Planarity : 0.004 0.045 7183 Dihedral : 16.753 178.273 8719 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.69 % Allowed : 9.18 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.65 (0.12), residues: 4796 helix: 1.40 (0.11), residues: 2276 sheet: -0.14 (0.23), residues: 501 loop : -0.48 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 642 TYR 0.015 0.001 TYR N 882 PHE 0.016 0.002 PHE S 349 TRP 0.023 0.001 TRP A 293 HIS 0.006 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (45224) covalent geometry : angle 0.55401 / 0.28 (62271) hydrogen bonds : bond 0.04602 / 3.02 ( 1975) hydrogen bonds : angle 4.66958 / 3.40 ( 5540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 362 MET cc_start: 0.7745 (mtt) cc_final: 0.7528 (mtm) REVERT: N 333 MET cc_start: 0.8234 (mmm) cc_final: 0.7992 (mmm) REVERT: A 147 MET cc_start: 0.8594 (mmt) cc_final: 0.8313 (mmt) REVERT: A 1271 MET cc_start: 0.8175 (mmm) cc_final: 0.7866 (tpt) REVERT: A 1357 MET cc_start: 0.2366 (tpt) cc_final: 0.1297 (mmt) REVERT: U 316 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6681 (tt0) REVERT: U 353 MET cc_start: 0.7207 (tmm) cc_final: 0.6552 (tmm) REVERT: M 15 ASP cc_start: 0.7835 (m-30) cc_final: 0.7583 (m-30) REVERT: M 64 GLU cc_start: 0.8714 (mp0) cc_final: 0.8421 (mp0) REVERT: M 115 GLN cc_start: 0.7763 (tp-100) cc_final: 0.6452 (mp10) outliers start: 29 outliers final: 14 residues processed: 166 average time/residue: 0.2479 time to fit residues: 71.8499 Evaluate side-chains 161 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain U residue 316 GLN Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 531 TRP Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain D residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 424 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 423 optimal weight: 10.0000 chunk 357 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 472 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 ASN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 316 GLN ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** 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 = 0.3633 r_free = 0.3633 target = 0.052424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.043273 restraints weight = 312676.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.044004 restraints weight = 184302.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.044554 restraints weight = 130951.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.044844 restraints weight = 105481.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.045132 restraints weight = 93734.015| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 45224 Z= 0.272 Angle : 0.647 8.409 62271 Z= 0.332 Chirality : 0.044 0.462 7054 Planarity : 0.005 0.048 7183 Dihedral : 16.879 177.238 8719 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.25 % Allowed : 12.38 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.26 (0.12), residues: 4796 helix: 1.09 (0.11), residues: 2265 sheet: -0.40 (0.24), residues: 481 loop : -0.66 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 642 TYR 0.016 0.002 TYR A1091 PHE 0.018 0.002 PHE S 349 TRP 0.030 0.002 TRP A 293 HIS 0.008 0.001 HIS D 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.27 (45224) covalent geometry : angle 0.64722 / 0.33 (62271) hydrogen bonds : bond 0.04893 / 3.23 ( 1975) hydrogen bonds : angle 4.82530 / 3.52 ( 5540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 270 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.7919 (m-70) REVERT: L 362 MET cc_start: 0.7833 (mtt) cc_final: 0.7593 (mtm) REVERT: N 112 MET cc_start: 0.8379 (tpp) cc_final: 0.7992 (tpp) REVERT: N 133 MET cc_start: 0.8279 (mmm) cc_final: 0.8044 (mmm) REVERT: A 1330 MET cc_start: 0.8414 (tpt) cc_final: 0.8144 (tpt) REVERT: A 1357 MET cc_start: 0.2496 (tpt) cc_final: 0.1400 (mmt) REVERT: U 281 MET cc_start: 0.8360 (ttp) cc_final: 0.8000 (ttp) REVERT: U 353 MET cc_start: 0.7256 (tmm) cc_final: 0.6535 (tmm) REVERT: U 542 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7668 (mm) REVERT: C 303 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8041 (pp) REVERT: M 15 ASP cc_start: 0.7688 (m-30) cc_final: 0.7418 (m-30) REVERT: M 64 GLU cc_start: 0.8745 (mp0) cc_final: 0.8461 (mp0) REVERT: M 115 GLN cc_start: 0.7733 (tp-100) cc_final: 0.6458 (mp10) REVERT: 7 429 MET cc_start: 0.8879 (mmm) cc_final: 0.8427 (mmm) outliers start: 53 outliers final: 31 residues processed: 195 average time/residue: 0.2185 time to fit residues: 75.0167 Evaluate side-chains 181 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain L residue 270 HIS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 541 MET Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain 7 residue 416 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 215 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 448 optimal weight: 4.9990 chunk 467 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 484 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.053021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.044116 restraints weight = 309578.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.045115 restraints weight = 192400.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.045426 restraints weight = 130948.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.045620 restraints weight = 108835.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.045645 restraints weight = 98013.104| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45224 Z= 0.153 Angle : 0.533 9.391 62271 Z= 0.276 Chirality : 0.040 0.406 7054 Planarity : 0.004 0.047 7183 Dihedral : 16.840 177.950 8717 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.25 % Allowed : 13.35 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.44 (0.12), residues: 4796 helix: 1.30 (0.11), residues: 2258 sheet: -0.45 (0.23), residues: 504 loop : -0.60 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 642 TYR 0.014 0.001 TYR A 431 PHE 0.019 0.001 PHE A1099 TRP 0.016 0.001 TRP A 293 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (45224) covalent geometry : angle 0.53294 / 0.28 (62271) hydrogen bonds : bond 0.04257 / 2.79 ( 1975) hydrogen bonds : angle 4.56754 / 3.33 ( 5540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 112 MET cc_start: 0.8404 (tpp) cc_final: 0.7994 (tpp) REVERT: N 133 MET cc_start: 0.8330 (mmm) cc_final: 0.8091 (mmm) REVERT: A 611 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8746 (tp) REVERT: A 710 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8853 (tt) REVERT: A 1357 MET cc_start: 0.2421 (tpt) cc_final: 0.1452 (mmt) REVERT: U 116 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4509 (mm) REVERT: U 281 MET cc_start: 0.8344 (ttp) cc_final: 0.7862 (ttp) REVERT: U 353 MET cc_start: 0.7159 (tmm) cc_final: 0.6404 (tmm) REVERT: U 542 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7716 (mm) REVERT: M 15 ASP cc_start: 0.7599 (m-30) cc_final: 0.7382 (m-30) REVERT: M 64 GLU cc_start: 0.8756 (mp0) cc_final: 0.8464 (mp0) REVERT: M 115 GLN cc_start: 0.7470 (tp-100) cc_final: 0.6310 (mp10) outliers start: 53 outliers final: 29 residues processed: 196 average time/residue: 0.2299 time to fit residues: 79.4983 Evaluate side-chains 181 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1906 ILE Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain D residue 72 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 357 optimal weight: 20.0000 chunk 327 optimal weight: 0.9980 chunk 421 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 252 optimal weight: 0.0870 chunk 183 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 101 optimal weight: 40.0000 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 GLN ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1563 HIS ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 GLN ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.053585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.044727 restraints weight = 307530.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.045764 restraints weight = 190241.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.046006 restraints weight = 133614.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.046244 restraints weight = 107237.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.046242 restraints weight = 95481.045| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 45224 Z= 0.109 Angle : 0.491 9.157 62271 Z= 0.254 Chirality : 0.039 0.351 7054 Planarity : 0.004 0.045 7183 Dihedral : 16.751 178.942 8717 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.21 % Allowed : 14.01 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.71 (0.12), residues: 4796 helix: 1.50 (0.11), residues: 2272 sheet: -0.30 (0.24), residues: 481 loop : -0.45 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1195 TYR 0.014 0.001 TYR A1178 PHE 0.022 0.001 PHE A1187 TRP 0.015 0.001 TRP S 203 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (45224) covalent geometry : angle 0.49136 / 0.25 (62271) hydrogen bonds : bond 0.03862 / 2.52 ( 1975) hydrogen bonds : angle 4.37047 / 3.18 ( 5540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 212 MET cc_start: 0.8263 (mmm) cc_final: 0.8050 (tpp) REVERT: L 362 MET cc_start: 0.7735 (mtt) cc_final: 0.7469 (mtm) REVERT: F 134 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8005 (ttm-80) REVERT: N 112 MET cc_start: 0.8381 (tpp) cc_final: 0.7998 (tpp) REVERT: A 696 MET cc_start: 0.7875 (mmt) cc_final: 0.7390 (mmt) REVERT: A 1335 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (mt) REVERT: A 1357 MET cc_start: 0.2345 (tpt) cc_final: 0.1463 (mmt) REVERT: U 116 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4656 (mm) REVERT: U 281 MET cc_start: 0.8403 (ttp) cc_final: 0.7952 (ttp) REVERT: U 353 MET cc_start: 0.6992 (tmm) cc_final: 0.6356 (tmm) REVERT: M 15 ASP cc_start: 0.7584 (m-30) cc_final: 0.7356 (m-30) REVERT: M 64 GLU cc_start: 0.8724 (mp0) cc_final: 0.8409 (mp0) REVERT: M 115 GLN cc_start: 0.7478 (tp-100) cc_final: 0.6232 (mp10) outliers start: 51 outliers final: 31 residues processed: 196 average time/residue: 0.2217 time to fit residues: 76.3408 Evaluate side-chains 181 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1330 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 274 VAL Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain M residue 124 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 484 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 436 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 404 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 HIS ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.053432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.044575 restraints weight = 307667.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.045618 restraints weight = 191384.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.045866 restraints weight = 134689.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.046075 restraints weight = 107160.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.046147 restraints weight = 97166.197| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45224 Z= 0.125 Angle : 0.499 10.493 62271 Z= 0.256 Chirality : 0.039 0.329 7054 Planarity : 0.004 0.045 7183 Dihedral : 16.725 179.310 8717 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.42 % Allowed : 14.17 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.73 (0.12), residues: 4796 helix: 1.52 (0.11), residues: 2271 sheet: -0.26 (0.24), residues: 478 loop : -0.46 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 134 TYR 0.014 0.001 TYR A 431 PHE 0.021 0.001 PHE A1099 TRP 0.015 0.001 TRP A 293 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (45224) covalent geometry : angle 0.49900 / 0.26 (62271) hydrogen bonds : bond 0.03860 / 2.52 ( 1975) hydrogen bonds : angle 4.33339 / 3.16 ( 5540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 362 MET cc_start: 0.7524 (mtt) cc_final: 0.7195 (mtm) REVERT: L 398 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.5844 (m170) REVERT: F 134 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8097 (ttm-80) REVERT: N 112 MET cc_start: 0.8397 (tpp) cc_final: 0.8026 (tpp) REVERT: A 61 MET cc_start: 0.7325 (mmp) cc_final: 0.6722 (mmt) REVERT: A 448 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: A 696 MET cc_start: 0.7864 (mmt) cc_final: 0.7351 (mmt) REVERT: A 1357 MET cc_start: 0.2401 (tpt) cc_final: 0.1569 (mmt) REVERT: U 116 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4648 (mm) REVERT: U 281 MET cc_start: 0.8706 (ttp) cc_final: 0.8087 (ttp) REVERT: U 353 MET cc_start: 0.7010 (tmm) cc_final: 0.6368 (tmm) REVERT: U 542 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7664 (mm) REVERT: C 603 MET cc_start: 0.8005 (tmm) cc_final: 0.7201 (tmm) REVERT: M 15 ASP cc_start: 0.7580 (m-30) cc_final: 0.7344 (m-30) REVERT: M 64 GLU cc_start: 0.8732 (mp0) cc_final: 0.8411 (mp0) REVERT: M 115 GLN cc_start: 0.7451 (tp-100) cc_final: 0.6285 (mp10) outliers start: 60 outliers final: 41 residues processed: 200 average time/residue: 0.2390 time to fit residues: 84.6893 Evaluate side-chains 194 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain L residue 398 HIS Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1330 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1906 ILE Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 274 VAL Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain M residue 124 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 150 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 473 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 413 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 458 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 470 optimal weight: 20.0000 chunk 258 optimal weight: 4.9990 chunk 389 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 HIS ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** 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 = 0.3660 r_free = 0.3660 target = 0.053162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.044268 restraints weight = 310628.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.045239 restraints weight = 191949.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.045516 restraints weight = 133758.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.045768 restraints weight = 111240.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.045801 restraints weight = 99701.986| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45224 Z= 0.164 Angle : 0.528 10.396 62271 Z= 0.269 Chirality : 0.040 0.329 7054 Planarity : 0.004 0.045 7183 Dihedral : 16.732 179.346 8717 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.40 % Allowed : 14.43 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.67 (0.12), residues: 4796 helix: 1.48 (0.11), residues: 2272 sheet: -0.28 (0.24), residues: 492 loop : -0.50 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.014 0.001 TYR A 431 PHE 0.021 0.001 PHE A1099 TRP 0.019 0.001 TRP A 293 HIS 0.030 0.001 HIS L 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (45224) covalent geometry : angle 0.52783 / 0.27 (62271) hydrogen bonds : bond 0.03965 / 2.59 ( 1975) hydrogen bonds : angle 4.37703 / 3.19 ( 5540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 212 MET cc_start: 0.8296 (mmm) cc_final: 0.8080 (tpp) REVERT: L 362 MET cc_start: 0.7760 (mtt) cc_final: 0.7489 (mtm) REVERT: N 112 MET cc_start: 0.8528 (tpp) cc_final: 0.8174 (tpp) REVERT: A 61 MET cc_start: 0.7438 (mmp) cc_final: 0.6793 (mmt) REVERT: A 70 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7084 (mt) REVERT: A 448 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: A 1357 MET cc_start: 0.2360 (tpt) cc_final: 0.1542 (mmt) REVERT: A 1762 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.5633 (t80) REVERT: U 116 LEU cc_start: 0.4728 (OUTLIER) cc_final: 0.4435 (mm) REVERT: U 281 MET cc_start: 0.8723 (ttp) cc_final: 0.8100 (ttp) REVERT: U 353 MET cc_start: 0.7025 (tmm) cc_final: 0.6396 (tmm) REVERT: U 542 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7724 (mm) REVERT: C 603 MET cc_start: 0.8045 (tmm) cc_final: 0.7223 (tmm) REVERT: M 15 ASP cc_start: 0.7571 (m-30) cc_final: 0.7344 (m-30) REVERT: M 64 GLU cc_start: 0.8750 (mp0) cc_final: 0.8436 (mp0) REVERT: M 115 GLN cc_start: 0.7333 (tp-100) cc_final: 0.6216 (mp10) outliers start: 59 outliers final: 46 residues processed: 198 average time/residue: 0.2309 time to fit residues: 80.3354 Evaluate side-chains 198 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1330 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1906 ILE Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 274 VAL Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 541 MET Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 400 optimal weight: 0.8980 chunk 361 optimal weight: 7.9990 chunk 484 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 389 optimal weight: 0.9990 chunk 263 optimal weight: 0.0020 chunk 100 optimal weight: 6.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** 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 = 0.3677 r_free = 0.3677 target = 0.053600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.044749 restraints weight = 306781.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045797 restraints weight = 189628.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.046042 restraints weight = 133132.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.046268 restraints weight = 106978.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.046293 restraints weight = 96004.278| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45224 Z= 0.109 Angle : 0.490 10.590 62271 Z= 0.251 Chirality : 0.039 0.572 7054 Planarity : 0.004 0.044 7183 Dihedral : 16.708 179.638 8717 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 14.84 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.78 (0.12), residues: 4796 helix: 1.57 (0.11), residues: 2271 sheet: -0.25 (0.24), residues: 478 loop : -0.43 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 134 TYR 0.016 0.001 TYR A 431 PHE 0.021 0.001 PHE A1099 TRP 0.017 0.001 TRP S 203 HIS 0.008 0.001 HIS L 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (45224) covalent geometry : angle 0.49026 / 0.25 (62271) hydrogen bonds : bond 0.03743 / 2.43 ( 1975) hydrogen bonds : angle 4.27354 / 3.11 ( 5540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 212 MET cc_start: 0.8318 (mmm) cc_final: 0.8089 (tpp) REVERT: L 362 MET cc_start: 0.7672 (mtt) cc_final: 0.7406 (mtm) REVERT: N 112 MET cc_start: 0.8503 (tpp) cc_final: 0.8125 (tpp) REVERT: A 61 MET cc_start: 0.7398 (mmp) cc_final: 0.6796 (mmt) REVERT: A 448 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: A 1335 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8204 (mt) REVERT: A 1357 MET cc_start: 0.2332 (tpt) cc_final: 0.1553 (mmt) REVERT: A 1762 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.5599 (t80) REVERT: U 116 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4633 (mm) REVERT: U 281 MET cc_start: 0.8722 (ttp) cc_final: 0.8090 (ttp) REVERT: U 353 MET cc_start: 0.6896 (tmm) cc_final: 0.6337 (tmm) REVERT: U 542 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7669 (mm) REVERT: C 303 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7804 (pp) REVERT: C 603 MET cc_start: 0.8008 (tmm) cc_final: 0.7140 (tmm) REVERT: M 15 ASP cc_start: 0.7560 (m-30) cc_final: 0.7328 (m-30) REVERT: M 64 GLU cc_start: 0.8710 (mp0) cc_final: 0.8376 (mp0) REVERT: M 115 GLN cc_start: 0.7310 (tp-100) cc_final: 0.6133 (mp10) outliers start: 55 outliers final: 43 residues processed: 196 average time/residue: 0.2161 time to fit residues: 75.0906 Evaluate side-chains 197 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1330 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1906 ILE Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 274 VAL Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 452 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 292 optimal weight: 0.0270 chunk 301 optimal weight: 0.4980 chunk 252 optimal weight: 7.9990 chunk 434 optimal weight: 3.9990 chunk 409 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 313 optimal weight: 20.0000 overall best weight: 2.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.053225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.044105 restraints weight = 310261.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.044910 restraints weight = 180089.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.045486 restraints weight = 126887.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045877 restraints weight = 101608.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.046057 restraints weight = 88685.524| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45224 Z= 0.154 Angle : 0.515 10.388 62271 Z= 0.263 Chirality : 0.040 0.329 7054 Planarity : 0.004 0.045 7183 Dihedral : 16.703 179.653 8717 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.25 % Allowed : 14.98 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.73 (0.12), residues: 4796 helix: 1.53 (0.11), residues: 2271 sheet: -0.26 (0.24), residues: 478 loop : -0.48 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1090 TYR 0.014 0.001 TYR A 431 PHE 0.022 0.001 PHE A1099 TRP 0.022 0.001 TRP S 203 HIS 0.004 0.001 HIS A1674 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (45224) covalent geometry : angle 0.51538 / 0.26 (62271) hydrogen bonds : bond 0.03903 / 2.55 ( 1975) hydrogen bonds : angle 4.32125 / 3.14 ( 5540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 469 MET cc_start: 0.6566 (tpt) cc_final: 0.6309 (tpt) REVERT: L 212 MET cc_start: 0.8336 (mmm) cc_final: 0.7381 (tpp) REVERT: L 362 MET cc_start: 0.7717 (mtt) cc_final: 0.7439 (mtm) REVERT: N 112 MET cc_start: 0.8524 (tpp) cc_final: 0.8147 (tpp) REVERT: N 333 MET cc_start: 0.8173 (mmm) cc_final: 0.7924 (mmm) REVERT: A 61 MET cc_start: 0.7367 (mmp) cc_final: 0.6787 (mmt) REVERT: A 448 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: A 1257 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7859 (m) REVERT: A 1357 MET cc_start: 0.2349 (tpt) cc_final: 0.1581 (mmt) REVERT: A 1762 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.5645 (t80) REVERT: U 116 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4860 (mm) REVERT: U 281 MET cc_start: 0.8749 (ttp) cc_final: 0.8124 (ttp) REVERT: U 353 MET cc_start: 0.7025 (tmm) cc_final: 0.6408 (tmm) REVERT: U 542 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7708 (mm) REVERT: C 303 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7880 (pp) REVERT: C 603 MET cc_start: 0.8040 (tmm) cc_final: 0.7195 (tmm) REVERT: M 15 ASP cc_start: 0.7659 (m-30) cc_final: 0.7387 (m-30) REVERT: M 64 GLU cc_start: 0.8667 (mp0) cc_final: 0.8452 (mp0) REVERT: M 115 GLN cc_start: 0.7336 (tp-100) cc_final: 0.6129 (mp10) outliers start: 53 outliers final: 45 residues processed: 195 average time/residue: 0.2250 time to fit residues: 77.5025 Evaluate side-chains 199 residues out of total 4314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1330 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1906 ILE Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 274 VAL Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 516 ILE Chi-restraints excluded: chain U residue 518 VAL Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain M residue 124 GLU Chi-restraints excluded: chain D residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 327 optimal weight: 0.4980 chunk 17 optimal weight: 20.0000 chunk 414 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 441 optimal weight: 1.9990 chunk 463 optimal weight: 8.9990 chunk 437 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.053725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.044845 restraints weight = 308849.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.045980 restraints weight = 186402.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.046271 restraints weight = 120923.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.046426 restraints weight = 103210.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.046511 restraints weight = 94121.134| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 45224 Z= 0.100 Angle : 0.487 11.421 62271 Z= 0.247 Chirality : 0.038 0.329 7054 Planarity : 0.004 0.044 7183 Dihedral : 16.676 179.913 8717 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.18 % Allowed : 15.22 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.84 (0.12), residues: 4796 helix: 1.65 (0.11), residues: 2265 sheet: -0.23 (0.24), residues: 492 loop : -0.44 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1310 TYR 0.016 0.001 TYR A 431 PHE 0.021 0.001 PHE A1099 TRP 0.023 0.001 TRP S 203 HIS 0.003 0.001 HIS 7 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (45224) covalent geometry : angle 0.48691 / 0.25 (62271) hydrogen bonds : bond 0.03690 / 2.41 ( 1975) hydrogen bonds : angle 4.21562 / 3.06 ( 5540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6130.61 seconds wall clock time: 107 minutes 51.72 seconds (6471.72 seconds total)