Starting phenix.real_space_refine on Thu Dec 26 08:49:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qoz_18542/12_2024/8qoz_18542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qoz_18542/12_2024/8qoz_18542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qoz_18542/12_2024/8qoz_18542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qoz_18542/12_2024/8qoz_18542.map" model { file = "/net/cci-nas-00/data/ceres_data/8qoz_18542/12_2024/8qoz_18542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qoz_18542/12_2024/8qoz_18542.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 224 5.49 5 S 168 5.16 5 C 27372 2.51 5 N 7806 2.21 5 O 8790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44360 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: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1077 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 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: {'PHE:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP: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: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1977, 16419 Classifications: {'peptide': 1977} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 105, 'TRANS': 1869} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} 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: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 787} Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, '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': 9, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 39} Link IDs: {'rna2p': 16, 'rna3p': 62} Chain: "z" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 8} 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: "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: 23.93, per 1000 atoms: 0.54 Number of scatterers: 44360 At special positions: 0 Unit cell: (189.08, 211.12, 178.64, 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 168 16.00 P 224 15.00 O 8790 8.00 N 7806 7.00 C 27372 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: 11.69 Conformation dependent library (CDL) restraints added in 5.6 seconds 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9350 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 32 sheets defined 51.3% alpha, 9.8% beta 54 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 17.21 Creating SS restraints... Processing helix chain 'G' and resid 242 through 255 removed outlier: 3.508A pdb=" N GLU G 246 " --> pdb=" O ASP G 242 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 247 " --> pdb=" O LYS G 243 " (cutoff:3.500A) 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 315 removed outlier: 3.684A pdb=" N ARG G 314 " --> pdb=" O LYS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 354 removed outlier: 3.690A pdb=" N GLN G 335 " --> pdb=" O GLU G 331 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 360 Processing helix chain 'G' and resid 366 through 376 Processing helix chain 'J' and resid 441 through 466 Processing helix chain 'J' and resid 480 through 485 Processing helix chain 'J' and resid 492 through 519 Processing helix chain 'L' and resid 53 through 79 removed outlier: 3.604A pdb=" N ILE L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU L 69 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR L 70 " --> pdb=" O LYS L 66 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 119 removed outlier: 3.675A pdb=" N VAL L 101 " --> pdb=" O ASN L 97 " (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: 3.867A pdb=" N LYS L 150 " --> pdb=" O ASP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 159 removed outlier: 3.520A pdb=" N GLN L 156 " --> pdb=" O ASN L 152 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN L 157 " --> pdb=" O GLU L 153 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE L 158 " --> pdb=" O ASN L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 172 removed outlier: 3.740A pdb=" N MET L 165 " --> pdb=" O ASN L 161 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL L 166 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 216 removed outlier: 4.529A pdb=" N SER L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE L 214 " --> pdb=" O SER L 210 " (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: 3.862A pdb=" N MET L 250 " --> pdb=" O ALA L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 277 Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 284 through 286 No H-bonds generated for 'chain 'L' and resid 284 through 286' Processing helix chain 'L' and resid 287 through 307 removed outlier: 3.569A pdb=" N ALA L 291 " --> pdb=" O LEU L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 332 removed outlier: 3.914A 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: 3.881A 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 430 Processing helix chain 'F' and resid 81 through 97 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: 4.011A pdb=" N ALA N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE N 104 " --> pdb=" O GLU N 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR N 105 " --> pdb=" O ALA N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 122 Processing helix chain 'N' and resid 122 through 135 removed outlier: 3.619A pdb=" N GLU N 134 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 141 No H-bonds generated for 'chain 'N' and resid 139 through 141' 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: 4.078A 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: 3.556A pdb=" N GLU N 319 " --> pdb=" O SER N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 339 removed outlier: 3.728A pdb=" N ALA N 328 " --> pdb=" O LYS N 324 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG N 329 " --> pdb=" O LEU N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 353 removed outlier: 3.603A pdb=" N TRP N 346 " --> pdb=" O SER N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 369 removed outlier: 4.294A pdb=" N ARG N 367 " --> pdb=" O ALA N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 383 removed outlier: 3.693A pdb=" N TYR N 376 " --> pdb=" O SER N 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 397 Processing helix chain 'N' and resid 403 through 408 Processing helix chain 'N' and resid 408 through 414 removed outlier: 4.527A pdb=" N GLU N 412 " --> pdb=" O LYS N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 807 Processing helix chain 'N' and resid 810 through 821 removed outlier: 3.882A pdb=" N PHE N 819 " --> pdb=" O SER N 815 " (cutoff:3.500A) Processing helix chain 'N' and resid 824 through 829 removed outlier: 4.822A pdb=" N THR N 828 " --> pdb=" O PRO N 824 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS N 829 " --> pdb=" O GLN N 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 824 through 829' Processing helix chain 'N' and resid 831 through 838 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: 4.303A 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: 3.663A pdb=" N GLY N 927 " --> pdb=" O GLN N 923 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP N 928 " --> pdb=" O LYS N 924 " (cutoff:3.500A) Processing helix chain 'N' and resid 935 through 940 Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.764A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.510A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.940A 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: 3.579A pdb=" N ASP A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.933A pdb=" N ASN A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.506A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.693A pdb=" N ASN A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.780A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 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 598 through 617 removed outlier: 3.613A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 654 removed outlier: 3.622A 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 Processing helix chain 'A' and resid 704 through 722 removed outlier: 4.408A pdb=" N THR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 834 through 849 removed outlier: 3.717A pdb=" N LEU A 839 " --> pdb=" O ASP A 835 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) 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: 3.822A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 984 through 988 removed outlier: 4.016A pdb=" N ILE A 988 " --> pdb=" O TYR A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.620A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1013 Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.570A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1063 removed outlier: 4.241A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 4.019A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 4.078A pdb=" N ILE A1125 " --> pdb=" O ASN A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.556A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1203 removed outlier: 3.870A pdb=" N THR A1202 " --> pdb=" O PRO A1198 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A1203 " --> pdb=" O LYS A1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1198 through 1203' Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1275 Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 4.122A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 removed outlier: 3.524A pdb=" N LEU A1285 " --> pdb=" O THR A1281 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A1286 " --> pdb=" O GLN A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.503A pdb=" N TYR A1317 " --> pdb=" O PRO A1313 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A1318 " --> pdb=" O VAL A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1313 through 1318' Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1341 removed outlier: 4.086A pdb=" N ARG A1341 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1399 Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 4.508A pdb=" N ASP A1410 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 Processing helix chain 'A' and resid 1429 through 1433 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 1486 Processing helix chain 'A' and resid 1511 through 1516 removed outlier: 3.933A pdb=" N TRP A1515 " --> pdb=" O SER A1512 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A1516 " --> pdb=" O MET A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1527 Processing helix chain 'A' and resid 1528 through 1538 removed outlier: 3.507A pdb=" N LEU A1536 " --> pdb=" O ARG A1532 " (cutoff:3.500A) 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: 3.967A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1689 Processing helix chain 'A' and resid 1722 through 1736 Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1768 through 1772 Processing helix chain 'A' and resid 1832 through 1852 removed outlier: 3.672A pdb=" N LYS A1838 " --> pdb=" O GLY A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1868 Processing helix chain 'A' and resid 1869 through 1876 Processing helix chain 'A' and resid 1892 through 1899 removed outlier: 3.549A pdb=" N ALA A1895 " --> pdb=" O PRO A1892 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS A1896 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A1897 " --> pdb=" O GLN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1908 removed outlier: 3.580A pdb=" N LYS A1908 " --> pdb=" O ASP A1904 " (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: 3.686A pdb=" N VAL A1952 " --> pdb=" O ASP A1948 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A1955 " --> pdb=" O LYS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1995 removed outlier: 3.692A pdb=" N ASP A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1991 " --> pdb=" O ILE A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2013 removed outlier: 3.734A pdb=" N ARG A2008 " --> pdb=" O GLN A2004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A2009 " --> pdb=" O SER A2005 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2027 removed outlier: 3.791A pdb=" N ARG A2023 " --> pdb=" O SER A2020 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2074 Processing helix chain 'U' and resid 107 through 111 removed outlier: 3.536A pdb=" N ILE U 111 " --> pdb=" O LEU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 183 through 185 No H-bonds generated for 'chain 'U' and resid 183 through 185' Processing helix chain 'U' and resid 186 through 194 Processing helix chain 'U' and resid 198 through 204 removed outlier: 3.516A pdb=" N ALA U 203 " --> pdb=" O LYS U 199 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN U 204 " --> pdb=" O GLN U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 246 removed outlier: 3.561A pdb=" N ASN U 237 " --> pdb=" O ASN U 233 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL U 246 " --> pdb=" O ALA U 242 " (cutoff:3.500A) Processing helix chain 'U' and resid 246 through 255 removed outlier: 4.049A 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: 3.891A pdb=" N LEU U 273 " --> pdb=" O ILE U 269 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG U 276 " --> pdb=" O LEU U 272 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU U 279 " --> pdb=" O GLN U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 296 through 308 removed outlier: 3.676A pdb=" N GLN U 301 " --> pdb=" O HIS U 297 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA U 302 " --> pdb=" O GLU U 298 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 334 Processing helix chain 'U' and resid 366 through 376 Processing helix chain 'U' and resid 415 through 419 Processing helix chain 'U' and resid 480 through 484 removed outlier: 3.553A pdb=" N LEU U 484 " --> pdb=" O ARG U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 485 through 490 removed outlier: 4.244A pdb=" N ALA U 490 " --> pdb=" O GLU U 486 " (cutoff:3.500A) Processing helix chain 'U' and resid 539 through 543 removed outlier: 3.558A pdb=" N THR U 543 " --> pdb=" O GLN U 540 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 185 removed outlier: 3.632A pdb=" N LYS S 183 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 199 through 219 removed outlier: 3.571A pdb=" N ASP S 215 " --> pdb=" O GLN S 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 266 removed outlier: 3.503A pdb=" N PHE S 266 " --> pdb=" O ILE S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 291 through 310 removed outlier: 3.594A pdb=" N LYS S 310 " --> pdb=" O LEU S 306 " (cutoff:3.500A) 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: 3.644A pdb=" N GLY C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 260 through 265 removed outlier: 3.828A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 290 Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.763A 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 387 Processing helix chain 'C' and resid 391 through 400 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: 5.547A 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: 3.747A pdb=" N ASP C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 522 removed outlier: 4.174A pdb=" N ASP C 521 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 522 " --> pdb=" O GLU C 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 518 through 522' 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: 3.510A 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 721 removed outlier: 3.664A pdb=" N PHE C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.529A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 776 Processing helix chain 'C' and resid 799 through 803 removed outlier: 3.808A pdb=" N ARG C 803 " --> pdb=" O PRO C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 823 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 841 No H-bonds generated for 'chain 'C' and resid 839 through 841' Processing helix chain 'C' and resid 842 through 853 Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.733A pdb=" N THR C 937 " --> pdb=" O PHE C 933 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 32 removed outlier: 3.501A pdb=" N LYS M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 3.888A 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 67 through 77 removed outlier: 4.192A pdb=" N LEU M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 112 through 127 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.851A 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: 4.025A pdb=" N MET D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain '7' and resid 424 through 432 Processing helix chain '7' and resid 435 through 452 removed outlier: 3.704A pdb=" N LEU 7 439 " --> pdb=" O ASP 7 435 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 471 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 253 through 254 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 910 Processing sheet with id=AA7, first strand: chain 'A' and resid 1085 through 1089 removed outlier: 6.521A pdb=" N PHE A1098 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A1088 " --> pdb=" O HIS A1096 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS A1096 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1185 through 1189 Processing sheet with id=AA9, first strand: chain 'A' and resid 1334 through 1335 Processing sheet with id=AB1, first strand: chain 'A' and resid 1342 through 1346 removed outlier: 9.323A pdb=" N VAL S 151 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A1352 " --> pdb=" O VAL S 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AB3, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 7.774A pdb=" N ILE A1606 " --> pdb=" O SER A1634 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER A1634 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1762 through 1763 removed outlier: 6.373A pdb=" N ILE A1861 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER A1887 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A1863 " --> pdb=" O SER A1887 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A1818 " --> pdb=" O ILE A1809 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1799 through 1803 removed outlier: 4.365A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 142 through 143 removed outlier: 4.298A pdb=" N PHE U 172 " --> pdb=" O ILE U 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 382 through 388 removed outlier: 6.300A pdb=" N SER U 352 " --> pdb=" O THR U 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 391 through 393 removed outlier: 5.674A pdb=" N TYR U 548 " --> pdb=" O ILE U 454 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA U 547 " --> pdb=" O HIS U 505 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS U 505 " --> pdb=" O ALA U 547 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE U 549 " --> pdb=" O ILE U 503 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS U 553 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU U 499 " --> pdb=" O LYS U 553 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE U 500 " --> pdb=" O LEU U 519 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE U 516 " --> pdb=" O LEU U 529 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 412 through 414 removed outlier: 6.656A pdb=" N VAL U 413 " --> pdb=" O ASN U 472 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 458 through 459 Processing sheet with id=AC2, first strand: chain 'S' and resid 258 through 259 Processing sheet with id=AC3, first strand: chain 'C' and resid 184 through 190 removed outlier: 6.593A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL C 225 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS C 256 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 227 " --> pdb=" O CYS C 256 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN C 258 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE C 229 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AC5, first strand: chain 'C' and resid 523 through 527 removed outlier: 7.420A pdb=" N CYS C 476 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 497 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AC7, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.598A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.598A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.472A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 783 through 784 removed outlier: 7.292A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 835 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 896 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.601A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 35 through 37 removed outlier: 3.707A pdb=" N PHE M 53 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N VAL M 81 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE M 54 " --> pdb=" O VAL M 81 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL M 83 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET M 56 " --> pdb=" O VAL M 83 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.339A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N VAL D 81 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE D 92 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE D 83 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 410 through 412 1858 hydrogen bonds defined for protein. 5286 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 26.54 Time building geometry restraints manager: 13.52 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: 13549 1.34 - 1.46: 8629 1.46 - 1.58: 22889 1.58 - 1.70: 438 1.70 - 1.82: 279 Bond restraints: 45784 Sorted by residual: 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 9.64e+00 bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.613 0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.608 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.616 0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" O11 IHP A2401 " pdb=" P1 IHP A2401 " ideal model delta sigma weight residual 1.666 1.613 0.053 2.00e-02 2.50e+03 7.12e+00 ... (remaining 45779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 62434 2.23 - 4.46: 496 4.46 - 6.69: 58 6.69 - 8.92: 8 8.92 - 11.15: 2 Bond angle restraints: 62998 Sorted by residual: angle pdb=" C1 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" C5 IHP A2401 " ideal model delta sigma weight residual 108.26 119.41 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" N GLU A1276 " pdb=" CA GLU A1276 " pdb=" C GLU A1276 " ideal model delta sigma weight residual 114.62 110.80 3.82 1.14e+00 7.69e-01 1.12e+01 angle pdb=" C VAL C 534 " pdb=" CA VAL C 534 " pdb=" CB VAL C 534 " ideal model delta sigma weight residual 111.23 114.51 -3.28 1.01e+00 9.80e-01 1.06e+01 angle pdb=" C3' U 5 78 " pdb=" O3' U 5 78 " pdb=" P C 5 79 " ideal model delta sigma weight residual 120.20 125.08 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" C3' C 6 77 " pdb=" O3' C 6 77 " pdb=" P A 6 78 " ideal model delta sigma weight residual 120.20 125.04 -4.84 1.50e+00 4.44e-01 1.04e+01 ... (remaining 62993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 27016 35.95 - 71.89: 956 71.89 - 107.84: 92 107.84 - 143.78: 7 143.78 - 179.73: 9 Dihedral angle restraints: 28080 sinusoidal: 13676 harmonic: 14404 Sorted by residual: dihedral pdb=" O4' C 5 71 " pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sinusoidal sigma weight residual 200.00 35.28 164.72 1 1.50e+01 4.44e-03 8.38e+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 51.73 -179.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 5 80 " pdb=" C1' U 5 80 " pdb=" N1 U 5 80 " pdb=" C2 U 5 80 " ideal model delta sinusoidal sigma weight residual -128.00 50.56 -178.56 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 28077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.975: 7119 0.975 - 1.950: 0 1.950 - 2.925: 0 2.925 - 3.899: 0 3.899 - 4.874: 4 Chirality restraints: 7123 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 2.36 -4.87 2.00e-01 2.50e+01 5.94e+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 2.43 -4.84 2.00e-01 2.50e+01 5.86e+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 2.47 -4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 7120 not shown) Planarity restraints: 7283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " 0.029 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP A 293 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL U 246 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO U 247 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO U 247 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO U 247 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1395 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" CD GLU A1395 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A1395 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A1395 " 0.011 2.00e-02 2.50e+03 ... (remaining 7280 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4005 2.74 - 3.28: 44140 3.28 - 3.82: 78930 3.82 - 4.36: 95128 4.36 - 4.90: 155619 Nonbonded interactions: 377822 Sorted by model distance: nonbonded pdb=" OD1 ASP N 252 " pdb=" OH TYR N 273 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.205 3.040 nonbonded pdb=" O LYS A 465 " pdb=" N4 C 5 23 " model vdw 2.208 3.120 nonbonded pdb=" OD2 ASP C 261 " pdb=" OG SER C 311 " model vdw 2.215 3.040 nonbonded pdb=" O VAL A1314 " pdb=" OG1 THR A1318 " model vdw 2.225 3.040 ... (remaining 377817 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.000 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: 0.080 Extract box with map and model: 1.820 Check model and map are aligned: 0.310 Set scattering table: 0.420 Process input model: 115.260 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 0.062 45784 Z= 0.170 Angle : 0.502 11.146 62998 Z= 0.258 Chirality : 0.120 4.874 7123 Planarity : 0.004 0.049 7283 Dihedral : 17.452 179.730 18730 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.02 % Allowed : 0.42 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4859 helix: 1.15 (0.11), residues: 2256 sheet: -0.38 (0.23), residues: 508 loop : -0.14 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP A 293 HIS 0.013 0.001 HIS A 680 PHE 0.022 0.001 PHE A1099 TYR 0.010 0.001 TYR A 140 ARG 0.007 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 4.976 Fit side-chains REVERT: F 115 LEU cc_start: 0.7559 (pp) cc_final: 0.7262 (pp) REVERT: M 75 ASP cc_start: 0.7969 (t0) cc_final: 0.7757 (t0) REVERT: D 106 MET cc_start: 0.7591 (mtm) cc_final: 0.7360 (mtm) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.6489 time to fit residues: 387.7401 Evaluate side-chains 295 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 395 optimal weight: 0.0870 chunk 153 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 294 optimal weight: 0.0870 chunk 458 optimal weight: 1.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 515 ASN ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 398 HIS N 289 ASN N 308 HIS ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1424 GLN A1965 HIS U 275 GLN ** U 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 45784 Z= 0.189 Angle : 0.560 22.386 62998 Z= 0.274 Chirality : 0.042 0.794 7123 Planarity : 0.004 0.048 7283 Dihedral : 17.049 179.597 8750 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.28 % Allowed : 6.39 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.12), residues: 4859 helix: 1.36 (0.11), residues: 2298 sheet: -0.33 (0.23), residues: 493 loop : -0.13 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 293 HIS 0.012 0.001 HIS A 680 PHE 0.018 0.001 PHE U 271 TYR 0.011 0.001 TYR A1369 ARG 0.005 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 323 time to evaluate : 5.344 Fit side-chains REVERT: N 203 ARG cc_start: 0.7152 (ptm-80) cc_final: 0.6840 (ptm160) REVERT: A 598 LEU cc_start: 0.8489 (tt) cc_final: 0.8239 (tt) REVERT: A 1165 VAL cc_start: 0.8448 (p) cc_final: 0.8179 (p) REVERT: A 1620 TYR cc_start: 0.7395 (m-10) cc_final: 0.7155 (m-10) REVERT: A 2002 LEU cc_start: 0.7709 (mt) cc_final: 0.7493 (mt) REVERT: 7 447 ARG cc_start: 0.5623 (mmp80) cc_final: 0.5298 (mmt-90) outliers start: 12 outliers final: 7 residues processed: 331 average time/residue: 0.6699 time to fit residues: 359.7933 Evaluate side-chains 302 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 295 time to evaluate : 5.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain 7 residue 423 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 254 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 381 optimal weight: 0.8980 chunk 312 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 459 optimal weight: 0.0270 chunk 496 optimal weight: 6.9990 chunk 409 optimal weight: 4.9990 chunk 455 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 457 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A1246 GLN A1383 GLN A1835 GLN U 151 HIS U 208 GLN ** U 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 45784 Z= 0.267 Angle : 0.555 10.556 62998 Z= 0.279 Chirality : 0.041 0.373 7123 Planarity : 0.004 0.049 7283 Dihedral : 16.960 179.602 8750 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.14 % Allowed : 8.76 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.12), residues: 4859 helix: 1.32 (0.11), residues: 2302 sheet: -0.42 (0.23), residues: 491 loop : -0.18 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 293 HIS 0.012 0.001 HIS A 680 PHE 0.020 0.001 PHE M 53 TYR 0.012 0.001 TYR A1762 ARG 0.006 0.000 ARG S 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 5.227 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 598 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 1165 VAL cc_start: 0.8421 (p) cc_final: 0.8170 (p) REVERT: A 1620 TYR cc_start: 0.7474 (m-10) cc_final: 0.7221 (m-10) REVERT: A 2002 LEU cc_start: 0.7723 (mt) cc_final: 0.7515 (mt) REVERT: S 336 LYS cc_start: 0.5293 (mtmm) cc_final: 0.4687 (ptmm) REVERT: C 249 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: M 117 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6647 (mp-120) REVERT: 7 447 ARG cc_start: 0.5648 (mmp80) cc_final: 0.5339 (mmt-90) outliers start: 49 outliers final: 28 residues processed: 345 average time/residue: 0.6239 time to fit residues: 358.5102 Evaluate side-chains 323 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 291 time to evaluate : 4.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 496 VAL Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain 7 residue 423 SER Chi-restraints excluded: chain 7 residue 488 ILE Chi-restraints excluded: chain 7 residue 501 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 0.7980 chunk 345 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 chunk 461 optimal weight: 4.9990 chunk 488 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 436 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN N 353 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS A1246 GLN A1383 GLN U 208 GLN U 517 HIS M 117 GLN 7 428 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 45784 Z= 0.176 Angle : 0.507 8.905 62998 Z= 0.256 Chirality : 0.039 0.394 7123 Planarity : 0.004 0.050 7283 Dihedral : 16.864 179.983 8750 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.98 % Allowed : 10.84 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.12), residues: 4859 helix: 1.43 (0.11), residues: 2303 sheet: -0.30 (0.23), residues: 490 loop : -0.18 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 293 HIS 0.013 0.001 HIS A 680 PHE 0.017 0.001 PHE U 271 TYR 0.012 0.001 TYR A1369 ARG 0.006 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 4.694 Fit side-chains revert: symmetry clash REVERT: J 482 MET cc_start: 0.8281 (mmt) cc_final: 0.8079 (mmt) REVERT: A 299 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 598 LEU cc_start: 0.8517 (tt) cc_final: 0.8302 (tt) REVERT: A 1165 VAL cc_start: 0.8335 (p) cc_final: 0.8122 (p) REVERT: A 2002 LEU cc_start: 0.7752 (mt) cc_final: 0.7534 (mt) REVERT: U 376 ASN cc_start: 0.4552 (m110) cc_final: 0.4299 (m110) REVERT: S 336 LYS cc_start: 0.5500 (mtmm) cc_final: 0.5285 (ptpp) REVERT: C 249 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6630 (mp0) outliers start: 42 outliers final: 23 residues processed: 348 average time/residue: 0.6490 time to fit residues: 371.4289 Evaluate side-chains 317 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 416 THR Chi-restraints excluded: chain 7 residue 423 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 363 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 416 optimal weight: 6.9990 chunk 337 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 438 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 457 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN M 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45784 Z= 0.230 Angle : 0.524 9.253 62998 Z= 0.263 Chirality : 0.040 0.396 7123 Planarity : 0.004 0.051 7283 Dihedral : 16.819 179.964 8750 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.38 % Allowed : 11.82 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.12), residues: 4859 helix: 1.41 (0.11), residues: 2309 sheet: -0.27 (0.23), residues: 490 loop : -0.20 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 293 HIS 0.012 0.001 HIS A 680 PHE 0.017 0.001 PHE U 271 TYR 0.012 0.001 TYR U 483 ARG 0.006 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 6.740 Fit side-chains revert: symmetry clash REVERT: J 482 MET cc_start: 0.8270 (mmt) cc_final: 0.8002 (mmt) REVERT: A 598 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 1165 VAL cc_start: 0.8302 (p) cc_final: 0.8082 (p) REVERT: A 1868 MET cc_start: 0.7236 (mmm) cc_final: 0.6993 (tpp) REVERT: A 2002 LEU cc_start: 0.7773 (mt) cc_final: 0.7554 (mt) REVERT: U 376 ASN cc_start: 0.4704 (m110) cc_final: 0.4437 (m110) REVERT: C 249 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: M 106 ILE cc_start: 0.7414 (mm) cc_final: 0.6866 (mt) outliers start: 59 outliers final: 41 residues processed: 348 average time/residue: 0.6384 time to fit residues: 367.1877 Evaluate side-chains 339 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 250 MET Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 423 SER Chi-restraints excluded: chain 7 residue 488 ILE Chi-restraints excluded: chain 7 residue 501 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 3.9990 chunk 439 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 405 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45784 Z= 0.227 Angle : 0.523 9.349 62998 Z= 0.263 Chirality : 0.040 0.391 7123 Planarity : 0.004 0.051 7283 Dihedral : 16.794 179.910 8750 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.61 % Allowed : 12.10 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.12), residues: 4859 helix: 1.42 (0.11), residues: 2309 sheet: -0.27 (0.24), residues: 478 loop : -0.19 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 293 HIS 0.014 0.001 HIS A 680 PHE 0.021 0.001 PHE U 271 TYR 0.012 0.001 TYR A1762 ARG 0.007 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 309 time to evaluate : 5.240 Fit side-chains revert: symmetry clash REVERT: N 381 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: A 1165 VAL cc_start: 0.8312 (p) cc_final: 0.8108 (p) REVERT: A 1395 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: A 2002 LEU cc_start: 0.7779 (mt) cc_final: 0.7539 (mt) REVERT: C 249 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6663 (mp0) outliers start: 69 outliers final: 43 residues processed: 365 average time/residue: 0.6262 time to fit residues: 376.0097 Evaluate side-chains 339 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 4.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1395 GLU Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1515 TRP Chi-restraints excluded: chain A residue 1554 GLN Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 423 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 356 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 486 optimal weight: 0.8980 chunk 304 optimal weight: 1.9990 chunk 296 optimal weight: 0.0670 chunk 224 optimal weight: 4.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1554 GLN A1965 HIS ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45784 Z= 0.194 Angle : 0.511 9.236 62998 Z= 0.257 Chirality : 0.039 0.371 7123 Planarity : 0.004 0.050 7283 Dihedral : 16.771 179.866 8750 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.40 % Allowed : 12.73 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.12), residues: 4859 helix: 1.50 (0.11), residues: 2307 sheet: -0.27 (0.23), residues: 492 loop : -0.18 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 637 HIS 0.013 0.001 HIS A 680 PHE 0.020 0.001 PHE U 271 TYR 0.013 0.001 TYR A1762 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 5.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 381 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: A 1165 VAL cc_start: 0.8294 (p) cc_final: 0.8090 (p) REVERT: A 1395 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: A 2002 LEU cc_start: 0.7721 (mt) cc_final: 0.7493 (mt) REVERT: U 511 GLU cc_start: 0.5289 (tm-30) cc_final: 0.4528 (tt0) REVERT: C 249 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6492 (mp0) outliers start: 60 outliers final: 42 residues processed: 363 average time/residue: 0.6367 time to fit residues: 383.1078 Evaluate side-chains 342 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1395 GLU Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1554 GLN Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 423 SER Chi-restraints excluded: chain 7 residue 488 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 331 optimal weight: 0.0870 chunk 240 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 457 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1965 HIS ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45784 Z= 0.168 Angle : 0.503 9.208 62998 Z= 0.253 Chirality : 0.039 0.352 7123 Planarity : 0.004 0.050 7283 Dihedral : 16.745 179.622 8750 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.24 % Allowed : 13.26 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.12), residues: 4859 helix: 1.55 (0.11), residues: 2307 sheet: -0.27 (0.23), residues: 498 loop : -0.17 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 637 HIS 0.014 0.001 HIS A 680 PHE 0.021 0.001 PHE U 271 TYR 0.012 0.001 TYR A1762 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 90 PHE cc_start: 0.7218 (t80) cc_final: 0.6812 (t80) REVERT: N 381 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: A 1395 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: A 2002 LEU cc_start: 0.7715 (mt) cc_final: 0.7495 (mt) REVERT: U 511 GLU cc_start: 0.5191 (tm-30) cc_final: 0.4408 (tt0) REVERT: C 249 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6518 (mp0) outliers start: 53 outliers final: 46 residues processed: 351 average time/residue: 0.6480 time to fit residues: 372.9371 Evaluate side-chains 343 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 5.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1395 GLU Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 423 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 442 optimal weight: 0.4980 chunk 466 optimal weight: 0.9980 chunk 425 optimal weight: 2.9990 chunk 453 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 139 optimal weight: 0.0050 chunk 409 optimal weight: 3.9990 chunk 428 optimal weight: 2.9990 chunk 451 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 491 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1965 HIS ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45784 Z= 0.163 Angle : 0.500 10.639 62998 Z= 0.251 Chirality : 0.038 0.337 7123 Planarity : 0.004 0.050 7283 Dihedral : 16.720 179.373 8750 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.26 % Allowed : 13.45 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 4859 helix: 1.61 (0.11), residues: 2306 sheet: -0.23 (0.23), residues: 492 loop : -0.17 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 637 HIS 0.013 0.001 HIS A 680 PHE 0.018 0.001 PHE U 271 TYR 0.013 0.001 TYR A1762 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 5.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 90 PHE cc_start: 0.7208 (t80) cc_final: 0.6799 (t80) REVERT: A 1395 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: A 2002 LEU cc_start: 0.7714 (mt) cc_final: 0.7480 (mt) REVERT: U 511 GLU cc_start: 0.5200 (tm-30) cc_final: 0.4405 (tt0) REVERT: C 249 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: C 922 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7558 (mp0) outliers start: 54 outliers final: 45 residues processed: 347 average time/residue: 0.6379 time to fit residues: 364.2178 Evaluate side-chains 339 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 5.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1395 GLU Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 240 LEU Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 423 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 297 optimal weight: 3.9990 chunk 479 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 503 optimal weight: 5.9990 chunk 463 optimal weight: 0.7980 chunk 400 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 491 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1965 HIS ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 45784 Z= 0.224 Angle : 0.529 10.128 62998 Z= 0.265 Chirality : 0.039 0.347 7123 Planarity : 0.004 0.051 7283 Dihedral : 16.723 179.753 8750 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.31 % Allowed : 13.43 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.12), residues: 4859 helix: 1.53 (0.11), residues: 2307 sheet: -0.28 (0.23), residues: 486 loop : -0.19 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 293 HIS 0.015 0.001 HIS A 680 PHE 0.022 0.001 PHE U 271 TYR 0.016 0.001 TYR A1762 ARG 0.008 0.000 ARG F 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 5.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 115 LEU cc_start: 0.7200 (pp) cc_final: 0.6926 (pt) REVERT: A 1395 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: A 2002 LEU cc_start: 0.7731 (mt) cc_final: 0.7506 (mt) REVERT: U 511 GLU cc_start: 0.5108 (tm-30) cc_final: 0.4314 (tt0) REVERT: C 249 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: C 922 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7635 (mp0) outliers start: 56 outliers final: 49 residues processed: 336 average time/residue: 0.6429 time to fit residues: 355.0603 Evaluate side-chains 341 residues out of total 4376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1395 GLU Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1614 ILE Chi-restraints excluded: chain A residue 1753 LEU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain U residue 240 LEU Chi-restraints excluded: chain U residue 297 HIS Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 535 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 259 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 922 GLU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 117 GLN Chi-restraints excluded: chain M residue 119 ILE Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain 7 residue 420 ILE Chi-restraints excluded: chain 7 residue 423 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 0.0040 chunk 426 optimal weight: 0.5980 chunk 122 optimal weight: 0.0470 chunk 369 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 401 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 412 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 491 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1965 HIS ** U 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 291 ASN M 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092785 restraints weight = 86494.451| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.71 r_work: 0.3294 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 45784 Z= 0.134 Angle : 0.492 10.080 62998 Z= 0.246 Chirality : 0.038 0.303 7123 Planarity : 0.003 0.049 7283 Dihedral : 16.674 179.192 8750 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.14 % Allowed : 13.68 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.12), residues: 4859 helix: 1.68 (0.11), residues: 2305 sheet: -0.23 (0.23), residues: 498 loop : -0.14 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 750 HIS 0.013 0.001 HIS A 680 PHE 0.016 0.001 PHE U 271 TYR 0.012 0.001 TYR A1762 ARG 0.008 0.000 ARG F 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9206.36 seconds wall clock time: 171 minutes 50.24 seconds (10310.24 seconds total)