Starting phenix.real_space_refine on Wed Apr 8 09:14:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2n_22012/04_2026/6x2n_22012.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2n_22012/04_2026/6x2n_22012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x2n_22012/04_2026/6x2n_22012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2n_22012/04_2026/6x2n_22012.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2n_22012/04_2026/6x2n_22012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2n_22012/04_2026/6x2n_22012.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.081 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 115 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 22308 2.51 5 N 6402 2.21 5 O 7110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36079 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8951 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 9, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10368 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23160 SG CYS J 70 26.018 98.800 103.950 1.00156.22 S ATOM 23174 SG CYS J 72 25.542 102.314 102.985 1.00158.71 S ATOM 23282 SG CYS J 85 24.097 99.462 100.857 1.00148.19 S ATOM 23306 SG CYS J 88 27.680 99.944 100.646 1.00151.65 S ATOM 28982 SG CYS J 814 52.446 37.176 110.486 1.00114.64 S ATOM 29547 SG CYS J 888 52.836 39.793 109.324 1.00 90.94 S ATOM 29598 SG CYS J 895 52.659 39.553 112.068 1.00 91.36 S ATOM 29619 SG CYS J 898 54.816 37.963 111.582 1.00 92.44 S Time building chain proxies: 8.12, per 1000 atoms: 0.23 Number of scatterers: 36079 At special positions: 0 Unit cell: (137.8, 209.3, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 115 15.00 Mg 1 11.99 O 7110 8.00 N 6402 7.00 C 22308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 56 sheets defined 38.4% alpha, 14.7% beta 53 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.706A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.630A pdb=" N ILE A 88 " --> pdb=" O HIS A 84 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 256 through 265 Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.754A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.550A pdb=" N ALA A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 564 through 578 Processing helix chain 'A' and resid 587 through 597 removed outlier: 3.794A pdb=" N PHE A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 removed outlier: 3.555A pdb=" N ASP A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 647 removed outlier: 4.292A pdb=" N VAL A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 4.028A pdb=" N ALA A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.704A pdb=" N GLN A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 746 removed outlier: 4.963A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 794 through 809 Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.661A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 removed outlier: 3.573A pdb=" N ARG A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.242A pdb=" N HIS A 890 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 891 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 891' Processing helix chain 'A' and resid 892 through 902 Processing helix chain 'A' and resid 923 through 936 Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 971 through 990 removed outlier: 4.317A pdb=" N GLY A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1019 through 1032 Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1074 Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1145 Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.745A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.509A pdb=" N THR G 157 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 158' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.768A pdb=" N ASN H 41 " --> pdb=" O HIS H 37 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.565A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.622A pdb=" N THR H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.624A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 216 through 225 removed outlier: 3.761A pdb=" N PHE I 225 " --> pdb=" O LEU I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.867A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.552A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.959A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.553A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 removed outlier: 3.568A pdb=" N LEU I 409 " --> pdb=" O PHE I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.842A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.561A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.943A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.992A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.069A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 676 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 978 Processing helix chain 'I' and resid 987 through 992 removed outlier: 4.398A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 4.338A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.365A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1108 through 1134 removed outlier: 4.091A pdb=" N ILE I1112 " --> pdb=" O ASN I1108 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.565A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.857A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.529A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.592A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.053A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.635A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.591A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 230 removed outlier: 3.519A pdb=" N VAL J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 237 removed outlier: 3.841A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.793A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.652A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.900A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.817A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.685A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.610A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.585A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 802 removed outlier: 3.916A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.605A pdb=" N GLY J1071 " --> pdb=" O THR J1068 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1068 through 1072' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.565A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU J1221 " --> pdb=" O PRO J1217 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG J1222 " --> pdb=" O HIS J1218 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.216A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.565A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1310 through 1315 Processing helix chain 'J' and resid 1327 through 1337 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 4.115A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.669A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.270A pdb=" N VAL A 42 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 108 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 44 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG A 17 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 removed outlier: 5.980A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 194 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 386 removed outlier: 5.702A pdb=" N VAL A 385 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN A 410 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.578A pdb=" N TYR A 493 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A 512 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 495 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 680 through 683 removed outlier: 3.532A pdb=" N LEU A 707 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 653 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A 729 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 655 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 726 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU A 754 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL A 728 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG A 624 " --> pdb=" O THR A 753 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 787 through 792 removed outlier: 5.953A pdb=" N LYS A 787 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 914 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 789 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A 916 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG A 791 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 883 " --> pdb=" O TYR A 911 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AB1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.579A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 97 through 104 removed outlier: 5.541A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.639A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 15 through 18 removed outlier: 6.673A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.966A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB9, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.680A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AC2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.272A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC4, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.196A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER I 574 " --> pdb=" O CYS I 559 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.933A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.959A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.032A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.958A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AD1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.346A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AD3, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AD4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.392A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.649A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.526A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 830 through 838 removed outlier: 3.762A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 842 through 843 removed outlier: 3.772A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.994A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AE3, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.542A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE6, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE7, first strand: chain 'J' and resid 34 through 37 removed outlier: 4.625A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AF1, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AF2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AF3, first strand: chain 'J' and resid 820 through 822 removed outlier: 7.408A pdb=" N LYS J 881 " --> pdb=" O ALA J 845 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.666A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 991 through 996 removed outlier: 6.463A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF7, first strand: chain 'J' and resid 1025 through 1026 Processing sheet with id=AF8, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.676A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.988A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 5.837A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY J1161 " --> pdb=" O VAL J1204 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.649A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1364 hydrogen bonds defined for protein. 3777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 134 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 10.42 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7627 1.32 - 1.45: 8548 1.45 - 1.57: 20252 1.57 - 1.70: 224 1.70 - 1.82: 247 Bond restraints: 36898 Sorted by residual: bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.39e+01 bond pdb=" C CYS J 898 " pdb=" N TYR J 899 " ideal model delta sigma weight residual 1.334 1.232 0.102 1.30e-02 5.92e+03 6.13e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" CA PHE J 116 " pdb=" C PHE J 116 " ideal model delta sigma weight residual 1.522 1.439 0.083 1.37e-02 5.33e+03 3.70e+01 bond pdb=" C5 ATP A2000 " pdb=" N7 ATP A2000 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.36e+01 ... (remaining 36893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 49832 4.27 - 8.54: 512 8.54 - 12.80: 36 12.80 - 17.07: 8 17.07 - 21.34: 2 Bond angle restraints: 50390 Sorted by residual: angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 119.06 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" O CYS J 898 " pdb=" C CYS J 898 " pdb=" N TYR J 899 " ideal model delta sigma weight residual 122.22 137.33 -15.11 1.17e+00 7.31e-01 1.67e+02 angle pdb=" CA CYS J 898 " pdb=" C CYS J 898 " pdb=" N TYR J 899 " ideal model delta sigma weight residual 117.63 101.84 15.79 1.25e+00 6.40e-01 1.59e+02 angle pdb=" C CYS J 898 " pdb=" N TYR J 899 " pdb=" CA TYR J 899 " ideal model delta sigma weight residual 120.88 104.06 16.82 1.62e+00 3.81e-01 1.08e+02 ... (remaining 50385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 21362 34.14 - 68.28: 910 68.28 - 102.42: 69 102.42 - 136.56: 4 136.56 - 170.70: 2 Dihedral angle restraints: 22347 sinusoidal: 9918 harmonic: 12429 Sorted by residual: dihedral pdb=" CA SER I 512 " pdb=" C SER I 512 " pdb=" N GLN I 513 " pdb=" CA GLN I 513 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO A 310 " pdb=" C PRO A 310 " pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER J 263 " pdb=" C SER J 263 " pdb=" N ASP J 264 " pdb=" CA ASP J 264 " ideal model delta harmonic sigma weight residual -180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 22344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5150 0.103 - 0.206: 541 0.206 - 0.309: 42 0.309 - 0.413: 9 0.413 - 0.516: 3 Chirality restraints: 5745 Sorted by residual: chirality pdb=" CA GLN J 504 " pdb=" N GLN J 504 " pdb=" C GLN J 504 " pdb=" CB GLN J 504 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CG LEU G 83 " pdb=" CB LEU G 83 " pdb=" CD1 LEU G 83 " pdb=" CD2 LEU G 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA SER J 503 " pdb=" N SER J 503 " pdb=" C SER J 503 " pdb=" CB SER J 503 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 5742 not shown) Planarity restraints: 6199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS J 814 " -0.041 2.00e-02 2.50e+03 7.78e-02 6.05e+01 pdb=" C CYS J 814 " 0.135 2.00e-02 2.50e+03 pdb=" O CYS J 814 " -0.049 2.00e-02 2.50e+03 pdb=" N GLY J 815 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 898 " -0.017 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C CYS J 898 " 0.077 2.00e-02 2.50e+03 pdb=" O CYS J 898 " -0.032 2.00e-02 2.50e+03 pdb=" N TYR J 899 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 128 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C LEU A 128 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 128 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL A 129 " 0.021 2.00e-02 2.50e+03 ... (remaining 6196 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 497 2.60 - 3.17: 30185 3.17 - 3.75: 59698 3.75 - 4.32: 79078 4.32 - 4.90: 125906 Nonbonded interactions: 295364 Sorted by model distance: nonbonded pdb=" O THR A 464 " pdb=" CG PRO A 467 " model vdw 2.024 3.440 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.056 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.084 2.170 nonbonded pdb=" CD2 LEU I1101 " pdb=" O GLN J 504 " model vdw 2.179 3.460 ... (remaining 295359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 42.980 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.011 0.917 36906 Z= 0.474 Angle : 1.220 21.339 50402 Z= 0.690 Chirality : 0.066 0.516 5745 Planarity : 0.007 0.088 6199 Dihedral : 17.593 170.696 14335 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.15 % Favored : 91.57 % Rotamer: Outliers : 0.28 % Allowed : 0.69 % Favored : 99.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.11), residues: 4294 helix: -1.65 (0.12), residues: 1470 sheet: -1.68 (0.21), residues: 561 loop : -2.16 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG A 902 TYR 0.037 0.003 TYR I 584 PHE 0.044 0.004 PHE I 514 TRP 0.030 0.003 TRP A 913 HIS 0.024 0.003 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00918 (36898) covalent geometry : angle 1.20827 (50390) hydrogen bonds : bond 0.16085 ( 1492) hydrogen bonds : angle 7.36265 ( 4037) metal coordination : bond 0.40235 ( 8) metal coordination : angle 10.81226 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 463 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5842 (tpp) cc_final: 0.5301 (tpp) REVERT: A 157 MET cc_start: 0.5961 (tpt) cc_final: 0.5758 (pmm) REVERT: A 873 THR cc_start: 0.8051 (p) cc_final: 0.7779 (p) REVERT: H 147 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7135 (tm-30) REVERT: H 185 TYR cc_start: 0.9406 (p90) cc_final: 0.9194 (p90) REVERT: I 102 LEU cc_start: 0.8845 (tp) cc_final: 0.8543 (pt) REVERT: I 195 PHE cc_start: 0.7808 (m-80) cc_final: 0.7039 (m-80) REVERT: I 654 ASP cc_start: 0.8119 (m-30) cc_final: 0.7737 (m-30) REVERT: I 741 MET cc_start: 0.8151 (tpp) cc_final: 0.7890 (tpp) REVERT: I 964 LEU cc_start: 0.8171 (tp) cc_final: 0.7869 (mt) REVERT: I 1079 ILE cc_start: 0.9093 (mm) cc_final: 0.8857 (mm) REVERT: I 1143 GLU cc_start: 0.8595 (pp20) cc_final: 0.8300 (pp20) REVERT: I 1296 ASP cc_start: 0.8089 (t70) cc_final: 0.7562 (t0) REVERT: J 29 MET cc_start: 0.8171 (tpp) cc_final: 0.7852 (tpt) REVERT: J 46 TYR cc_start: 0.7068 (m-10) cc_final: 0.6657 (m-80) REVERT: J 724 MET cc_start: 0.9048 (mtm) cc_final: 0.8699 (mtm) REVERT: J 868 TRP cc_start: 0.8174 (m100) cc_final: 0.7303 (m100) REVERT: J 1143 ASP cc_start: 0.8358 (t0) cc_final: 0.8056 (t0) REVERT: J 1281 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8355 (mt-10) REVERT: K 3 ARG cc_start: 0.7267 (mmp80) cc_final: 0.6408 (mmm160) REVERT: K 44 ASP cc_start: 0.7598 (m-30) cc_final: 0.6724 (m-30) outliers start: 10 outliers final: 2 residues processed: 470 average time/residue: 0.2225 time to fit residues: 171.9818 Evaluate side-chains 353 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 351 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 1090 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.0170 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 651 GLN A 665 HIS ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 186 ASN I 69 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1236 ASN J 266 ASN J 424 ASN J 495 ASN ** J 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN J1197 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.111863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090621 restraints weight = 132373.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.091434 restraints weight = 79088.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091973 restraints weight = 49755.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092295 restraints weight = 43618.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092357 restraints weight = 40461.908| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36906 Z= 0.143 Angle : 0.696 11.996 50402 Z= 0.360 Chirality : 0.045 0.249 5745 Planarity : 0.005 0.068 6199 Dihedral : 16.725 169.679 6014 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 1.13 % Allowed : 8.18 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 4294 helix: -0.56 (0.13), residues: 1518 sheet: -1.30 (0.21), residues: 557 loop : -1.95 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 368 TYR 0.016 0.001 TYR G 177 PHE 0.030 0.001 PHE I 514 TRP 0.019 0.001 TRP J1193 HIS 0.009 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00306 (36898) covalent geometry : angle 0.68756 (50390) hydrogen bonds : bond 0.04876 ( 1492) hydrogen bonds : angle 5.61555 ( 4037) metal coordination : bond 0.02545 ( 8) metal coordination : angle 6.91446 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 421 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6997 (ttt) cc_final: 0.6632 (ttt) REVERT: A 771 ARG cc_start: 0.6999 (ptp-170) cc_final: 0.5990 (ptp-170) REVERT: A 821 ASN cc_start: 0.8193 (t0) cc_final: 0.7551 (t0) REVERT: I 102 LEU cc_start: 0.8756 (tp) cc_final: 0.8524 (pt) REVERT: I 187 GLU cc_start: 0.7581 (pm20) cc_final: 0.7352 (pm20) REVERT: I 195 PHE cc_start: 0.7441 (m-80) cc_final: 0.6765 (m-80) REVERT: I 370 MET cc_start: 0.7891 (mmm) cc_final: 0.7676 (mmm) REVERT: I 654 ASP cc_start: 0.7920 (m-30) cc_final: 0.7659 (m-30) REVERT: I 741 MET cc_start: 0.8070 (tpp) cc_final: 0.7771 (tpp) REVERT: I 810 TYR cc_start: 0.8639 (m-80) cc_final: 0.8428 (m-80) REVERT: I 964 LEU cc_start: 0.8168 (tp) cc_final: 0.7895 (mt) REVERT: I 1079 ILE cc_start: 0.9042 (mm) cc_final: 0.8811 (mm) REVERT: I 1220 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8589 (tp40) REVERT: I 1296 ASP cc_start: 0.7995 (t70) cc_final: 0.7577 (t0) REVERT: J 140 TYR cc_start: 0.8698 (m-10) cc_final: 0.8294 (m-10) REVERT: J 236 TRP cc_start: 0.8801 (m-10) cc_final: 0.7566 (m-90) REVERT: J 500 ILE cc_start: 0.9394 (mm) cc_final: 0.8988 (pt) REVERT: J 724 MET cc_start: 0.8937 (mtm) cc_final: 0.8462 (mtm) REVERT: J 821 MET cc_start: 0.7767 (tpp) cc_final: 0.7393 (tpp) REVERT: J 822 MET cc_start: 0.7292 (tpp) cc_final: 0.6846 (tpp) REVERT: J 913 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7385 (mt-10) REVERT: J 1143 ASP cc_start: 0.8241 (t0) cc_final: 0.7996 (t0) REVERT: J 1189 MET cc_start: 0.8269 (tmm) cc_final: 0.8060 (tmm) REVERT: K 3 ARG cc_start: 0.7143 (mmp80) cc_final: 0.6733 (mmp-170) REVERT: K 44 ASP cc_start: 0.7442 (m-30) cc_final: 0.6895 (m-30) REVERT: K 68 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7292 (tm-30) REVERT: K 75 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6836 (tm-30) outliers start: 41 outliers final: 19 residues processed: 446 average time/residue: 0.2070 time to fit residues: 155.9083 Evaluate side-chains 360 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 340 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 27 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 349 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 338 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 400 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 ASN A1094 HIS G 227 GLN I 69 GLN I 148 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1010 GLN I1236 ASN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 495 ASN ** J 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088699 restraints weight = 133142.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089374 restraints weight = 72713.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089621 restraints weight = 47448.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090197 restraints weight = 46553.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090120 restraints weight = 39571.099| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36906 Z= 0.195 Angle : 0.693 11.033 50402 Z= 0.356 Chirality : 0.044 0.258 5745 Planarity : 0.005 0.065 6199 Dihedral : 16.542 168.923 6010 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 1.44 % Allowed : 12.35 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 4294 helix: -0.06 (0.13), residues: 1519 sheet: -1.31 (0.21), residues: 568 loop : -1.80 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 741 TYR 0.025 0.001 TYR G 185 PHE 0.021 0.002 PHE I 514 TRP 0.023 0.002 TRP A1134 HIS 0.009 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00434 (36898) covalent geometry : angle 0.68709 (50390) hydrogen bonds : bond 0.04774 ( 1492) hydrogen bonds : angle 5.36732 ( 4037) metal coordination : bond 0.01707 ( 8) metal coordination : angle 5.81540 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.5814 (tpt) cc_final: 0.4835 (pmm) REVERT: A 915 LEU cc_start: 0.8270 (mm) cc_final: 0.8034 (mm) REVERT: G 35 PHE cc_start: 0.7479 (m-80) cc_final: 0.7138 (m-80) REVERT: I 102 LEU cc_start: 0.8743 (tp) cc_final: 0.8480 (pt) REVERT: I 187 GLU cc_start: 0.7587 (pm20) cc_final: 0.7343 (pm20) REVERT: I 195 PHE cc_start: 0.7494 (m-80) cc_final: 0.6478 (m-80) REVERT: I 542 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7798 (mmt-90) REVERT: I 741 MET cc_start: 0.8123 (tpp) cc_final: 0.7828 (tpp) REVERT: I 951 MET cc_start: 0.8116 (ptp) cc_final: 0.7771 (ptp) REVERT: I 964 LEU cc_start: 0.8324 (tp) cc_final: 0.8010 (mt) REVERT: I 1079 ILE cc_start: 0.9034 (mm) cc_final: 0.8800 (mm) REVERT: I 1220 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8743 (tp40) REVERT: I 1296 ASP cc_start: 0.8039 (t70) cc_final: 0.7723 (t0) REVERT: J 236 TRP cc_start: 0.8833 (m-10) cc_final: 0.7639 (m-90) REVERT: J 724 MET cc_start: 0.8891 (mtm) cc_final: 0.8451 (mtm) REVERT: J 747 MET cc_start: 0.7910 (mtp) cc_final: 0.7558 (mmt) REVERT: J 821 MET cc_start: 0.7840 (tpp) cc_final: 0.7476 (tpp) REVERT: J 822 MET cc_start: 0.7501 (tpp) cc_final: 0.7104 (tpp) REVERT: J 1143 ASP cc_start: 0.8355 (t0) cc_final: 0.8123 (t0) REVERT: J 1193 TRP cc_start: 0.7099 (p90) cc_final: 0.6584 (p90) REVERT: K 3 ARG cc_start: 0.7325 (mmp80) cc_final: 0.6841 (mmp-170) REVERT: K 44 ASP cc_start: 0.7492 (m-30) cc_final: 0.6814 (m-30) outliers start: 52 outliers final: 34 residues processed: 397 average time/residue: 0.2051 time to fit residues: 137.3050 Evaluate side-chains 371 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 336 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 124 optimal weight: 10.0000 chunk 411 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 343 optimal weight: 0.9980 chunk 318 optimal weight: 8.9990 chunk 426 optimal weight: 0.0010 chunk 428 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1236 ASN J 232 ASN J 504 GLN ** J 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.108630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087320 restraints weight = 131918.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088318 restraints weight = 74266.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088403 restraints weight = 48187.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088590 restraints weight = 45821.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088696 restraints weight = 41715.754| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36906 Z= 0.172 Angle : 0.665 11.234 50402 Z= 0.341 Chirality : 0.044 0.247 5745 Planarity : 0.005 0.071 6199 Dihedral : 16.413 167.500 6010 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 1.80 % Allowed : 14.28 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4294 helix: 0.16 (0.13), residues: 1520 sheet: -1.25 (0.21), residues: 562 loop : -1.69 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.018 0.001 TYR G 185 PHE 0.017 0.001 PHE I 514 TRP 0.018 0.001 TRP A1134 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00379 (36898) covalent geometry : angle 0.65773 (50390) hydrogen bonds : bond 0.04422 ( 1492) hydrogen bonds : angle 5.23283 ( 4037) metal coordination : bond 0.02119 ( 8) metal coordination : angle 6.21612 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 360 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6655 (tpp) cc_final: 0.5910 (tpp) REVERT: A 157 MET cc_start: 0.5526 (tpt) cc_final: 0.4752 (pmm) REVERT: A 765 MET cc_start: 0.7701 (ttt) cc_final: 0.7429 (ttt) REVERT: A 928 LYS cc_start: 0.9142 (pptt) cc_final: 0.8769 (pptt) REVERT: G 35 PHE cc_start: 0.7490 (m-80) cc_final: 0.7082 (m-80) REVERT: G 185 TYR cc_start: 0.8836 (p90) cc_final: 0.8232 (p90) REVERT: I 102 LEU cc_start: 0.8800 (tp) cc_final: 0.8550 (pt) REVERT: I 187 GLU cc_start: 0.7625 (pm20) cc_final: 0.7343 (pm20) REVERT: I 195 PHE cc_start: 0.7515 (m-80) cc_final: 0.6398 (m-80) REVERT: I 370 MET cc_start: 0.7581 (mmm) cc_final: 0.7356 (mmm) REVERT: I 488 MET cc_start: 0.8271 (mmt) cc_final: 0.7923 (mmt) REVERT: I 492 MET cc_start: 0.8152 (ptp) cc_final: 0.7131 (tpt) REVERT: I 542 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7897 (mmt-90) REVERT: I 741 MET cc_start: 0.8056 (tpp) cc_final: 0.7758 (tpp) REVERT: I 1079 ILE cc_start: 0.9036 (mm) cc_final: 0.8700 (mm) REVERT: I 1143 GLU cc_start: 0.8611 (pp20) cc_final: 0.8383 (tm-30) REVERT: I 1220 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8658 (tp40) REVERT: I 1296 ASP cc_start: 0.8053 (t70) cc_final: 0.7662 (t0) REVERT: J 232 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7616 (m110) REVERT: J 236 TRP cc_start: 0.8839 (m-10) cc_final: 0.7873 (m-10) REVERT: J 747 MET cc_start: 0.7953 (mtp) cc_final: 0.7691 (mmt) REVERT: J 821 MET cc_start: 0.7898 (tpp) cc_final: 0.7551 (tpp) REVERT: J 822 MET cc_start: 0.7676 (tpp) cc_final: 0.7275 (tpp) REVERT: J 1143 ASP cc_start: 0.8315 (t0) cc_final: 0.8074 (t0) REVERT: J 1193 TRP cc_start: 0.7142 (p90) cc_final: 0.6631 (p90) REVERT: K 3 ARG cc_start: 0.7213 (mmp80) cc_final: 0.6737 (mmp-170) REVERT: K 44 ASP cc_start: 0.7515 (m-30) cc_final: 0.6787 (m-30) outliers start: 65 outliers final: 42 residues processed: 401 average time/residue: 0.2035 time to fit residues: 139.4990 Evaluate side-chains 377 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 256 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 376 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN G 227 GLN H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1134 GLN I1157 GLN J 232 ASN J 341 ASN J 495 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.105885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084884 restraints weight = 133423.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085525 restraints weight = 72783.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085839 restraints weight = 48255.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085972 restraints weight = 46591.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086065 restraints weight = 42515.876| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 36906 Z= 0.279 Angle : 0.734 11.680 50402 Z= 0.378 Chirality : 0.046 0.256 5745 Planarity : 0.005 0.075 6199 Dihedral : 16.454 165.694 6010 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.85 % Favored : 92.13 % Rotamer: Outliers : 2.35 % Allowed : 16.02 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4294 helix: 0.11 (0.13), residues: 1524 sheet: -1.32 (0.22), residues: 560 loop : -1.72 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 67 TYR 0.017 0.002 TYR G 177 PHE 0.016 0.002 PHE I 514 TRP 0.016 0.002 TRP A 913 HIS 0.010 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00620 (36898) covalent geometry : angle 0.72768 (50390) hydrogen bonds : bond 0.05079 ( 1492) hydrogen bonds : angle 5.37175 ( 4037) metal coordination : bond 0.02151 ( 8) metal coordination : angle 6.11533 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6365 (tpp) cc_final: 0.5496 (tpp) REVERT: A 157 MET cc_start: 0.5835 (tpt) cc_final: 0.5096 (pmm) REVERT: A 765 MET cc_start: 0.7845 (ttt) cc_final: 0.7547 (ttt) REVERT: A 796 MET cc_start: 0.8114 (tmm) cc_final: 0.7849 (tmm) REVERT: G 185 TYR cc_start: 0.8886 (p90) cc_final: 0.8454 (p90) REVERT: I 102 LEU cc_start: 0.8819 (tp) cc_final: 0.8472 (pt) REVERT: I 187 GLU cc_start: 0.7719 (pm20) cc_final: 0.7407 (pm20) REVERT: I 195 PHE cc_start: 0.7978 (m-80) cc_final: 0.7179 (m-80) REVERT: I 370 MET cc_start: 0.7722 (mmm) cc_final: 0.7476 (mmm) REVERT: I 542 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7883 (mmt180) REVERT: I 741 MET cc_start: 0.8064 (tpp) cc_final: 0.7737 (tpp) REVERT: I 810 TYR cc_start: 0.8774 (m-80) cc_final: 0.8512 (m-80) REVERT: I 1143 GLU cc_start: 0.8672 (pp20) cc_final: 0.8416 (tm-30) REVERT: I 1220 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8530 (tp40) REVERT: I 1296 ASP cc_start: 0.8122 (t70) cc_final: 0.7725 (t0) REVERT: J 130 MET cc_start: 0.8284 (ttp) cc_final: 0.8065 (ttp) REVERT: J 236 TRP cc_start: 0.8886 (m-10) cc_final: 0.7731 (m-90) REVERT: J 238 ILE cc_start: 0.9236 (mm) cc_final: 0.9003 (mm) REVERT: J 697 MET cc_start: 0.8949 (ttp) cc_final: 0.8549 (ttp) REVERT: J 822 MET cc_start: 0.7851 (tpp) cc_final: 0.7374 (tpp) REVERT: J 1193 TRP cc_start: 0.7046 (p90) cc_final: 0.6519 (p90) REVERT: K 3 ARG cc_start: 0.7229 (mmp80) cc_final: 0.6736 (mmp-170) REVERT: K 44 ASP cc_start: 0.7548 (m-30) cc_final: 0.6781 (m-30) outliers start: 85 outliers final: 56 residues processed: 392 average time/residue: 0.2071 time to fit residues: 137.6484 Evaluate side-chains 379 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 229 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 413 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 395 optimal weight: 30.0000 chunk 284 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1257 GLN J 720 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.105293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083796 restraints weight = 132936.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084440 restraints weight = 86508.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084913 restraints weight = 52252.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085094 restraints weight = 45152.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085192 restraints weight = 42723.268| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 36906 Z= 0.273 Angle : 0.735 13.046 50402 Z= 0.376 Chirality : 0.046 0.394 5745 Planarity : 0.005 0.053 6199 Dihedral : 16.455 163.419 6010 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.64 % Favored : 92.34 % Rotamer: Outliers : 2.73 % Allowed : 17.46 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 4294 helix: 0.10 (0.13), residues: 1523 sheet: -1.34 (0.22), residues: 560 loop : -1.75 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 744 TYR 0.015 0.002 TYR G 177 PHE 0.015 0.002 PHE I 514 TRP 0.017 0.002 TRP A 913 HIS 0.009 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00607 (36898) covalent geometry : angle 0.72923 (50390) hydrogen bonds : bond 0.04968 ( 1492) hydrogen bonds : angle 5.37416 ( 4037) metal coordination : bond 0.01929 ( 8) metal coordination : angle 6.13483 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 327 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7280 (mtm) cc_final: 0.7069 (mtm) REVERT: A 114 MET cc_start: 0.6957 (tpp) cc_final: 0.6164 (tpp) REVERT: A 157 MET cc_start: 0.5209 (tpt) cc_final: 0.4778 (pmm) REVERT: A 496 MET cc_start: 0.8687 (mmm) cc_final: 0.8422 (mmm) REVERT: A 727 ILE cc_start: 0.8840 (mm) cc_final: 0.8562 (mm) REVERT: G 35 PHE cc_start: 0.7505 (m-80) cc_final: 0.7073 (m-80) REVERT: G 185 TYR cc_start: 0.8933 (p90) cc_final: 0.8546 (p90) REVERT: I 102 LEU cc_start: 0.8793 (tp) cc_final: 0.8537 (pt) REVERT: I 187 GLU cc_start: 0.7692 (pm20) cc_final: 0.7320 (pm20) REVERT: I 195 PHE cc_start: 0.8030 (m-80) cc_final: 0.7224 (m-80) REVERT: I 492 MET cc_start: 0.7854 (ptp) cc_final: 0.7015 (mmt) REVERT: I 542 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7682 (mmt-90) REVERT: I 741 MET cc_start: 0.8070 (tpp) cc_final: 0.7676 (tpp) REVERT: I 1143 GLU cc_start: 0.8701 (pp20) cc_final: 0.8424 (tm-30) REVERT: I 1274 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: I 1296 ASP cc_start: 0.8188 (t70) cc_final: 0.7754 (t0) REVERT: J 49 PHE cc_start: 0.8505 (m-80) cc_final: 0.8290 (m-80) REVERT: J 130 MET cc_start: 0.8281 (ttp) cc_final: 0.8041 (ttp) REVERT: J 238 ILE cc_start: 0.9299 (mm) cc_final: 0.9099 (mm) REVERT: J 697 MET cc_start: 0.8835 (ttp) cc_final: 0.8523 (ttp) REVERT: J 821 MET cc_start: 0.8047 (tpp) cc_final: 0.7805 (tpp) REVERT: J 822 MET cc_start: 0.7910 (tpp) cc_final: 0.7391 (tpp) REVERT: J 1189 MET cc_start: 0.8277 (tmm) cc_final: 0.8065 (tmm) REVERT: J 1193 TRP cc_start: 0.7066 (p90) cc_final: 0.6525 (p90) REVERT: K 3 ARG cc_start: 0.7227 (mmp80) cc_final: 0.6752 (mmp-170) REVERT: K 44 ASP cc_start: 0.7560 (m-30) cc_final: 0.6788 (m-30) outliers start: 99 outliers final: 70 residues processed: 402 average time/residue: 0.2056 time to fit residues: 140.4273 Evaluate side-chains 391 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 319 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 708 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 46 optimal weight: 40.0000 chunk 88 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 330 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 428 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086837 restraints weight = 132253.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087682 restraints weight = 73827.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088069 restraints weight = 46510.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088277 restraints weight = 44292.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088316 restraints weight = 40223.558| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36906 Z= 0.135 Angle : 0.660 13.678 50402 Z= 0.333 Chirality : 0.044 0.368 5745 Planarity : 0.004 0.053 6199 Dihedral : 16.301 164.033 6010 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.29 % Favored : 93.69 % Rotamer: Outliers : 2.18 % Allowed : 18.78 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 4294 helix: 0.40 (0.13), residues: 1520 sheet: -1.27 (0.22), residues: 559 loop : -1.61 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 67 TYR 0.017 0.001 TYR G 185 PHE 0.014 0.001 PHE I 514 TRP 0.016 0.001 TRP A1134 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00301 (36898) covalent geometry : angle 0.65520 (50390) hydrogen bonds : bond 0.04142 ( 1492) hydrogen bonds : angle 5.05764 ( 4037) metal coordination : bond 0.01125 ( 8) metal coordination : angle 5.24277 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 368 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6488 (tpp) cc_final: 0.6207 (tpp) REVERT: A 157 MET cc_start: 0.5465 (tpt) cc_final: 0.4902 (pmm) REVERT: A 727 ILE cc_start: 0.8759 (mm) cc_final: 0.8505 (mm) REVERT: A 821 ASN cc_start: 0.8452 (t0) cc_final: 0.7943 (t0) REVERT: A 967 MET cc_start: 0.9109 (pmm) cc_final: 0.8789 (pmm) REVERT: G 25 LYS cc_start: 0.8605 (tttp) cc_final: 0.8341 (tptp) REVERT: G 185 TYR cc_start: 0.8918 (p90) cc_final: 0.8404 (p90) REVERT: I 102 LEU cc_start: 0.8749 (tp) cc_final: 0.8531 (pt) REVERT: I 187 GLU cc_start: 0.7630 (pm20) cc_final: 0.7234 (pm20) REVERT: I 195 PHE cc_start: 0.7874 (m-80) cc_final: 0.6839 (m-80) REVERT: I 370 MET cc_start: 0.7583 (mmm) cc_final: 0.7367 (mmm) REVERT: I 492 MET cc_start: 0.7491 (ptp) cc_final: 0.6693 (mmt) REVERT: I 515 MET cc_start: 0.8536 (ttp) cc_final: 0.8031 (ttt) REVERT: I 542 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7515 (mmt-90) REVERT: I 741 MET cc_start: 0.8030 (tpp) cc_final: 0.7691 (tpp) REVERT: I 810 TYR cc_start: 0.8639 (m-80) cc_final: 0.8318 (m-80) REVERT: I 1143 GLU cc_start: 0.8585 (pp20) cc_final: 0.8311 (tm-30) REVERT: I 1274 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: I 1296 ASP cc_start: 0.7955 (t70) cc_final: 0.7662 (t0) REVERT: J 49 PHE cc_start: 0.8502 (m-80) cc_final: 0.8299 (m-80) REVERT: J 236 TRP cc_start: 0.8866 (m-10) cc_final: 0.7689 (m-90) REVERT: J 238 ILE cc_start: 0.9260 (mm) cc_final: 0.9052 (mm) REVERT: J 643 ASP cc_start: 0.9000 (m-30) cc_final: 0.8695 (m-30) REVERT: J 821 MET cc_start: 0.7910 (tpp) cc_final: 0.7693 (tpp) REVERT: J 822 MET cc_start: 0.7880 (tpp) cc_final: 0.7352 (tpp) REVERT: J 1193 TRP cc_start: 0.7208 (p90) cc_final: 0.6656 (p90) REVERT: K 3 ARG cc_start: 0.7230 (mmp80) cc_final: 0.6839 (mmp-170) REVERT: K 43 ASN cc_start: 0.8656 (t0) cc_final: 0.8394 (t0) REVERT: K 44 ASP cc_start: 0.7475 (m-30) cc_final: 0.6691 (m-30) outliers start: 79 outliers final: 50 residues processed: 426 average time/residue: 0.2119 time to fit residues: 152.4300 Evaluate side-chains 388 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 209 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 201 optimal weight: 0.0980 chunk 196 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN G 227 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.109189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088388 restraints weight = 132124.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088907 restraints weight = 71104.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089113 restraints weight = 48674.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089339 restraints weight = 48567.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089394 restraints weight = 41180.755| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36906 Z= 0.134 Angle : 0.667 16.368 50402 Z= 0.333 Chirality : 0.044 0.364 5745 Planarity : 0.004 0.079 6199 Dihedral : 16.206 166.432 6010 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 1.88 % Allowed : 19.53 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4294 helix: 0.49 (0.13), residues: 1523 sheet: -1.16 (0.21), residues: 579 loop : -1.54 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 67 TYR 0.015 0.001 TYR G 185 PHE 0.013 0.001 PHE I 514 TRP 0.042 0.002 TRP J1020 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00301 (36898) covalent geometry : angle 0.66340 (50390) hydrogen bonds : bond 0.04002 ( 1492) hydrogen bonds : angle 4.91859 ( 4037) metal coordination : bond 0.01018 ( 8) metal coordination : angle 4.39943 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6737 (tpp) cc_final: 0.6038 (tpp) REVERT: A 157 MET cc_start: 0.5164 (tpt) cc_final: 0.4734 (pmm) REVERT: A 821 ASN cc_start: 0.8468 (t0) cc_final: 0.7580 (t0) REVERT: A 967 MET cc_start: 0.9094 (pmm) cc_final: 0.8847 (pmm) REVERT: G 25 LYS cc_start: 0.8572 (tttp) cc_final: 0.8311 (tptp) REVERT: I 102 LEU cc_start: 0.8732 (tp) cc_final: 0.8519 (pt) REVERT: I 187 GLU cc_start: 0.7609 (pm20) cc_final: 0.7222 (pm20) REVERT: I 195 PHE cc_start: 0.7786 (m-80) cc_final: 0.6746 (m-80) REVERT: I 492 MET cc_start: 0.7407 (ptp) cc_final: 0.6596 (mmt) REVERT: I 515 MET cc_start: 0.8493 (ttp) cc_final: 0.7981 (ttt) REVERT: I 542 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7351 (mmt180) REVERT: I 741 MET cc_start: 0.8006 (tpp) cc_final: 0.7661 (tpp) REVERT: I 810 TYR cc_start: 0.8679 (m-80) cc_final: 0.8439 (m-80) REVERT: I 1066 MET cc_start: 0.8448 (ptp) cc_final: 0.8167 (ptm) REVERT: I 1143 GLU cc_start: 0.8573 (pp20) cc_final: 0.8306 (tm-30) REVERT: I 1220 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8512 (tp40) REVERT: I 1274 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: I 1296 ASP cc_start: 0.7905 (t70) cc_final: 0.7633 (t0) REVERT: J 236 TRP cc_start: 0.8868 (m-10) cc_final: 0.7718 (m-90) REVERT: J 643 ASP cc_start: 0.9001 (m-30) cc_final: 0.8693 (m-30) REVERT: J 822 MET cc_start: 0.7871 (tpp) cc_final: 0.7382 (tpp) REVERT: J 1193 TRP cc_start: 0.7211 (p90) cc_final: 0.6659 (p90) REVERT: K 3 ARG cc_start: 0.7096 (mmp80) cc_final: 0.6702 (mmp-170) REVERT: K 43 ASN cc_start: 0.8647 (t0) cc_final: 0.8394 (t0) REVERT: K 44 ASP cc_start: 0.7436 (m-30) cc_final: 0.6650 (m-30) outliers start: 68 outliers final: 54 residues processed: 409 average time/residue: 0.2078 time to fit residues: 144.1614 Evaluate side-chains 395 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 339 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 180 optimal weight: 0.0060 chunk 416 optimal weight: 1.9990 chunk 425 optimal weight: 9.9990 chunk 392 optimal weight: 2.9990 chunk 332 optimal weight: 0.7980 chunk 385 optimal weight: 6.9990 chunk 400 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 761 GLN I 808 ASN I1236 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087730 restraints weight = 132317.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088413 restraints weight = 72179.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088565 restraints weight = 49114.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088824 restraints weight = 48112.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088871 restraints weight = 41301.611| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36906 Z= 0.162 Angle : 0.688 14.855 50402 Z= 0.341 Chirality : 0.044 0.424 5745 Planarity : 0.004 0.054 6199 Dihedral : 16.191 166.375 6010 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.99 % Allowed : 20.00 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4294 helix: 0.49 (0.13), residues: 1523 sheet: -1.14 (0.21), residues: 580 loop : -1.54 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 634 TYR 0.016 0.001 TYR G 185 PHE 0.017 0.001 PHE J 988 TRP 0.030 0.001 TRP J1020 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00365 (36898) covalent geometry : angle 0.68475 (50390) hydrogen bonds : bond 0.04077 ( 1492) hydrogen bonds : angle 4.93057 ( 4037) metal coordination : bond 0.01218 ( 8) metal coordination : angle 4.09797 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 348 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7971 (mpp) cc_final: 0.7359 (mpp) REVERT: A 114 MET cc_start: 0.6826 (tpp) cc_final: 0.6278 (tpp) REVERT: A 157 MET cc_start: 0.5131 (tpt) cc_final: 0.4727 (pmm) REVERT: A 496 MET cc_start: 0.8596 (mmm) cc_final: 0.8369 (mmm) REVERT: A 821 ASN cc_start: 0.8507 (t0) cc_final: 0.8037 (t0) REVERT: A 967 MET cc_start: 0.9170 (pmm) cc_final: 0.8902 (pmm) REVERT: G 25 LYS cc_start: 0.8598 (tttp) cc_final: 0.8318 (tptp) REVERT: H 102 LEU cc_start: 0.8446 (tt) cc_final: 0.8216 (pp) REVERT: I 102 LEU cc_start: 0.8744 (tp) cc_final: 0.8524 (pt) REVERT: I 187 GLU cc_start: 0.7625 (pm20) cc_final: 0.7237 (pm20) REVERT: I 195 PHE cc_start: 0.7803 (m-80) cc_final: 0.6760 (m-80) REVERT: I 492 MET cc_start: 0.7454 (ptp) cc_final: 0.6593 (mmt) REVERT: I 515 MET cc_start: 0.8512 (ttp) cc_final: 0.8075 (ttt) REVERT: I 542 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7438 (mmt-90) REVERT: I 741 MET cc_start: 0.8030 (tpp) cc_final: 0.7684 (tpp) REVERT: I 761 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8475 (mm110) REVERT: I 1066 MET cc_start: 0.8514 (ptp) cc_final: 0.8158 (ptm) REVERT: I 1143 GLU cc_start: 0.8662 (pp20) cc_final: 0.8397 (tm-30) REVERT: I 1220 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8521 (tp40) REVERT: I 1274 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: I 1296 ASP cc_start: 0.7949 (t70) cc_final: 0.7657 (t0) REVERT: J 49 PHE cc_start: 0.8313 (m-80) cc_final: 0.8050 (m-10) REVERT: J 236 TRP cc_start: 0.8858 (m-10) cc_final: 0.7683 (m-90) REVERT: J 643 ASP cc_start: 0.9016 (m-30) cc_final: 0.8750 (m-30) REVERT: J 822 MET cc_start: 0.7945 (tpp) cc_final: 0.7449 (tpp) REVERT: J 973 LEU cc_start: 0.7525 (pp) cc_final: 0.7003 (tp) REVERT: J 1193 TRP cc_start: 0.7093 (p90) cc_final: 0.6514 (p90) REVERT: K 3 ARG cc_start: 0.7102 (mmp80) cc_final: 0.6715 (mmp-170) REVERT: K 43 ASN cc_start: 0.8660 (t0) cc_final: 0.8400 (t0) REVERT: K 44 ASP cc_start: 0.7448 (m-30) cc_final: 0.6670 (m-30) outliers start: 72 outliers final: 65 residues processed: 402 average time/residue: 0.2097 time to fit residues: 143.0532 Evaluate side-chains 404 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 336 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 185 ILE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 308 optimal weight: 8.9990 chunk 429 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 433 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087302 restraints weight = 133187.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088109 restraints weight = 77047.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088164 restraints weight = 51451.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088365 restraints weight = 49567.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088714 restraints weight = 43765.296| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 36906 Z= 0.200 Angle : 0.840 59.182 50402 Z= 0.454 Chirality : 0.045 0.652 5745 Planarity : 0.004 0.063 6199 Dihedral : 16.196 166.376 6010 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.99 % Allowed : 20.00 % Favored : 78.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4294 helix: 0.48 (0.13), residues: 1523 sheet: -1.14 (0.21), residues: 580 loop : -1.53 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 67 TYR 0.015 0.001 TYR G 185 PHE 0.029 0.001 PHE I1025 TRP 0.025 0.001 TRP J1020 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00450 (36898) covalent geometry : angle 0.83797 (50390) hydrogen bonds : bond 0.04115 ( 1492) hydrogen bonds : angle 4.94417 ( 4037) metal coordination : bond 0.01245 ( 8) metal coordination : angle 4.10357 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 336 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7958 (mpp) cc_final: 0.7340 (mpp) REVERT: A 114 MET cc_start: 0.6807 (tpp) cc_final: 0.6256 (tpp) REVERT: A 157 MET cc_start: 0.5130 (tpt) cc_final: 0.4727 (pmm) REVERT: A 496 MET cc_start: 0.8610 (mmm) cc_final: 0.8387 (mmm) REVERT: A 821 ASN cc_start: 0.8475 (t0) cc_final: 0.8029 (t0) REVERT: A 967 MET cc_start: 0.9163 (pmm) cc_final: 0.8890 (pmm) REVERT: G 25 LYS cc_start: 0.8596 (tttp) cc_final: 0.8320 (tptp) REVERT: H 102 LEU cc_start: 0.8478 (tt) cc_final: 0.8213 (pp) REVERT: I 102 LEU cc_start: 0.8735 (tp) cc_final: 0.8518 (pt) REVERT: I 187 GLU cc_start: 0.7636 (pm20) cc_final: 0.7248 (pm20) REVERT: I 195 PHE cc_start: 0.7811 (m-80) cc_final: 0.6763 (m-80) REVERT: I 492 MET cc_start: 0.7464 (ptp) cc_final: 0.6597 (mmt) REVERT: I 515 MET cc_start: 0.8453 (ttp) cc_final: 0.7967 (ttt) REVERT: I 542 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7431 (mmt-90) REVERT: I 741 MET cc_start: 0.8024 (tpp) cc_final: 0.7689 (tpp) REVERT: I 1025 PHE cc_start: 0.7692 (t80) cc_final: 0.6899 (m-80) REVERT: I 1066 MET cc_start: 0.8412 (ptp) cc_final: 0.8117 (ptm) REVERT: I 1143 GLU cc_start: 0.8658 (pp20) cc_final: 0.8396 (tm-30) REVERT: I 1220 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8527 (tp40) REVERT: I 1274 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: I 1296 ASP cc_start: 0.7951 (t70) cc_final: 0.7652 (t0) REVERT: J 49 PHE cc_start: 0.8315 (m-80) cc_final: 0.8046 (m-10) REVERT: J 236 TRP cc_start: 0.8862 (m-10) cc_final: 0.7690 (m-90) REVERT: J 643 ASP cc_start: 0.9023 (m-30) cc_final: 0.8757 (m-30) REVERT: J 822 MET cc_start: 0.7957 (tpp) cc_final: 0.7461 (tpp) REVERT: J 973 LEU cc_start: 0.7532 (pp) cc_final: 0.6989 (tp) REVERT: J 1193 TRP cc_start: 0.7083 (p90) cc_final: 0.6503 (p90) REVERT: K 3 ARG cc_start: 0.7100 (mmp80) cc_final: 0.6719 (mmp-170) REVERT: K 43 ASN cc_start: 0.8657 (t0) cc_final: 0.8395 (t0) REVERT: K 44 ASP cc_start: 0.7447 (m-30) cc_final: 0.6663 (m-30) outliers start: 72 outliers final: 67 residues processed: 391 average time/residue: 0.2012 time to fit residues: 133.2823 Evaluate side-chains 405 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 821 ARG Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 185 ILE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 120 optimal weight: 0.0030 chunk 211 optimal weight: 7.9990 chunk 424 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 167 optimal weight: 0.0020 chunk 88 optimal weight: 9.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087346 restraints weight = 132477.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088117 restraints weight = 76851.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088182 restraints weight = 51468.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088374 restraints weight = 49508.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088772 restraints weight = 43786.022| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 36906 Z= 0.200 Angle : 0.840 59.182 50402 Z= 0.454 Chirality : 0.045 0.652 5745 Planarity : 0.004 0.063 6199 Dihedral : 16.196 166.376 6010 Min Nonbonded Distance : 1.565 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.93 % Allowed : 20.06 % Favored : 78.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4294 helix: 0.48 (0.13), residues: 1523 sheet: -1.14 (0.21), residues: 580 loop : -1.53 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 67 TYR 0.015 0.001 TYR G 185 PHE 0.029 0.001 PHE I1025 TRP 0.025 0.001 TRP J1020 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00450 (36898) covalent geometry : angle 0.83797 (50390) hydrogen bonds : bond 0.04115 ( 1492) hydrogen bonds : angle 4.94417 ( 4037) metal coordination : bond 0.01245 ( 8) metal coordination : angle 4.10357 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5520.46 seconds wall clock time: 97 minutes 6.99 seconds (5826.99 seconds total)