Starting phenix.real_space_refine on Tue Sep 15 06:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x2n_22012/09_2026/6x2n_22012.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2n_22012/09_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_22012/09_2026/6x2n_22012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2n_22012/09_2026/6x2n_22012.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2n_22012/09_2026/6x2n_22012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2n_22012/09_2026/6x2n_22012.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x2n_22012/09_2026/6x2n_22012.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x2n_22012/09_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): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 7.77, per 1000 atoms: 0.22 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: 3.35 Conformation dependent library (CDL) restraints added in 1.6 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: 5.11 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: 11.90 Time building geometry restraints manager: 4.42 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=" C1' DT Q 48 " pdb=" N1 DT Q 48 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.96e+01 ... (remaining 36893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 49824 4.27 - 8.54: 520 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: 21318 34.14 - 68.28: 891 68.28 - 102.42: 67 102.42 - 136.56: 4 136.56 - 170.70: 2 Dihedral angle restraints: 22282 sinusoidal: 9853 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 22279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5124 0.103 - 0.206: 558 0.206 - 0.309: 51 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 46.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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= 0.540 Angle : 1.234 21.339 50402 Z= 0.736 Chirality : 0.068 0.516 5745 Planarity : 0.007 0.088 6199 Dihedral : 17.474 170.696 14270 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/Z covalent geometry : bond 0.00926 / 0.50 (36898) covalent geometry : angle 1.22301 / 0.74 (50390) hydrogen bonds : bond 0.16085 / 10.70 ( 1492) hydrogen bonds : angle 7.36265 / 5.07 ( 4037) metal coordination : bond 0.40235 / 25.42 ( 8) metal coordination : angle 10.81226 / 7.44 ( 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 : 1.327 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: 0.2182 time to fit residues: 169.2576 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 : 1.336 ------------------------------------------------------------------------------- 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: 20.0000 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... A 115 GLN 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** A 909 GLN H 18 GLN H 186 ASN I 69 GLN ** I 273 HIS ** 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090285 restraints weight = 132256.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091089 restraints weight = 76604.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091866 restraints weight = 48082.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091944 restraints weight = 42130.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092639 restraints weight = 38353.256| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36906 Z= 0.154 Angle : 0.753 12.852 50402 Z= 0.389 Chirality : 0.049 0.345 5745 Planarity : 0.005 0.067 6199 Dihedral : 16.518 168.046 5949 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 1.10 % Allowed : 8.20 % 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: -2.18 (0.12), residues: 4294 helix: -0.69 (0.13), residues: 1529 sheet: -1.42 (0.21), residues: 575 loop : -2.01 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 783 TYR 0.017 0.001 TYR G 177 PHE 0.034 0.001 PHE I 514 TRP 0.017 0.001 TRP J1193 HIS 0.010 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (36898) covalent geometry : angle 0.74463 / 0.39 (50390) hydrogen bonds : bond 0.05269 / 3.52 ( 1492) hydrogen bonds : angle 5.81907 / 3.99 ( 4037) metal coordination : bond 0.01196 / 0.61 ( 8) metal coordination : angle 7.50589 / 5.21 ( 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 459 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 419 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8133 (tpt) REVERT: A 639 MET cc_start: 0.7637 (mtp) cc_final: 0.6744 (mtp) REVERT: A 821 ASN cc_start: 0.8213 (t0) cc_final: 0.7649 (t0) REVERT: A 915 LEU cc_start: 0.8272 (mm) cc_final: 0.8055 (mm) REVERT: G 47 LEU cc_start: 0.9091 (mp) cc_final: 0.8880 (mp) REVERT: I 130 MET cc_start: 0.9014 (ttm) cc_final: 0.8807 (ttp) REVERT: I 187 GLU cc_start: 0.7540 (pm20) cc_final: 0.7305 (pm20) REVERT: I 195 PHE cc_start: 0.7499 (m-80) cc_final: 0.6818 (m-80) REVERT: I 472 GLU cc_start: 0.8387 (pp20) cc_final: 0.8177 (pp20) REVERT: I 654 ASP cc_start: 0.7937 (m-30) cc_final: 0.7710 (m-30) REVERT: I 741 MET cc_start: 0.8043 (tpp) cc_final: 0.7754 (tpp) REVERT: I 810 TYR cc_start: 0.8698 (m-80) cc_final: 0.8400 (m-80) REVERT: I 964 LEU cc_start: 0.8189 (tp) cc_final: 0.7902 (mt) REVERT: I 1079 ILE cc_start: 0.9061 (mm) cc_final: 0.8802 (mm) REVERT: I 1220 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (tp40) REVERT: I 1296 ASP cc_start: 0.7956 (t70) cc_final: 0.7570 (t0) REVERT: J 140 TYR cc_start: 0.8649 (m-10) cc_final: 0.8207 (m-10) REVERT: J 236 TRP cc_start: 0.8787 (m-10) cc_final: 0.7538 (m-90) REVERT: J 500 ILE cc_start: 0.9401 (mm) cc_final: 0.8961 (pt) REVERT: J 724 MET cc_start: 0.9008 (mtm) cc_final: 0.8712 (mtm) REVERT: J 821 MET cc_start: 0.7797 (tpp) cc_final: 0.7478 (tpp) REVERT: J 822 MET cc_start: 0.7233 (tpp) cc_final: 0.6847 (tpp) REVERT: J 913 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7499 (mt-10) REVERT: J 988 PHE cc_start: 0.6658 (t80) cc_final: 0.6203 (m-10) REVERT: J 1143 ASP cc_start: 0.8267 (t0) cc_final: 0.7959 (t0) REVERT: J 1189 MET cc_start: 0.8278 (tmm) cc_final: 0.8060 (tmm) REVERT: K 3 ARG cc_start: 0.7212 (mmp80) cc_final: 0.6801 (mmp-170) REVERT: K 44 ASP cc_start: 0.7430 (m-30) cc_final: 0.6943 (m-30) REVERT: K 67 ARG cc_start: 0.7189 (tpt90) cc_final: 0.6979 (tpt90) REVERT: K 68 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7388 (tm-30) REVERT: K 75 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6980 (tm-30) outliers start: 40 outliers final: 21 residues processed: 444 average time/residue: 0.2037 time to fit residues: 153.0937 Evaluate side-chains 368 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 966 SER 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 199 ASP Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1090 ASN 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 624 ILE Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 839 VAL 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: 0.9990 chunk 197 optimal weight: 6.9990 chunk 349 optimal weight: 6.9990 chunk 311 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 231 optimal weight: 0.0770 chunk 338 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 chunk 400 optimal weight: 6.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 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 232 ASN J 495 ASN ** J 951 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.112276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090859 restraints weight = 132696.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.092056 restraints weight = 75520.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092726 restraints weight = 47513.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092908 restraints weight = 41932.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092983 restraints weight = 37759.847| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36906 Z= 0.130 Angle : 0.695 13.254 50402 Z= 0.354 Chirality : 0.046 0.327 5745 Planarity : 0.005 0.062 6199 Dihedral : 16.201 167.378 5947 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 1.24 % Allowed : 12.15 % Favored : 86.60 % 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: -1.72 (0.12), residues: 4294 helix: -0.16 (0.13), residues: 1507 sheet: -1.32 (0.21), residues: 571 loop : -1.81 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 741 TYR 0.030 0.001 TYR G 185 PHE 0.022 0.001 PHE I 514 TRP 0.017 0.001 TRP J1193 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (36898) covalent geometry : angle 0.68906 / 0.35 (50390) hydrogen bonds : bond 0.04682 / 3.13 ( 1492) hydrogen bonds : angle 5.35652 / 3.69 ( 4037) metal coordination : bond 0.01266 / 0.67 ( 8) metal coordination : angle 5.76323 / 3.52 ( 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 433 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 388 time to evaluate : 1.248 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: 0.6575 (tpp) cc_final: 0.5901 (tpp) REVERT: A 157 MET cc_start: 0.5779 (tpt) cc_final: 0.4875 (pmm) REVERT: A 765 MET cc_start: 0.7220 (ttt) cc_final: 0.6820 (tmm) REVERT: A 1008 MET cc_start: 0.7941 (mmp) cc_final: 0.6978 (mmm) REVERT: G 35 PHE cc_start: 0.7483 (m-80) cc_final: 0.7205 (m-80) REVERT: G 47 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8802 (mt) REVERT: I 187 GLU cc_start: 0.7507 (pm20) cc_final: 0.7297 (pm20) REVERT: I 195 PHE cc_start: 0.7475 (m-80) cc_final: 0.6557 (m-80) REVERT: I 654 ASP cc_start: 0.7824 (m-30) cc_final: 0.7613 (m-30) REVERT: I 741 MET cc_start: 0.8044 (tpp) cc_final: 0.7751 (tpp) REVERT: I 964 LEU cc_start: 0.8175 (tp) cc_final: 0.7904 (mt) REVERT: I 1090 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8945 (t0) REVERT: I 1220 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8591 (tp40) REVERT: I 1296 ASP cc_start: 0.7945 (t70) cc_final: 0.7686 (t0) REVERT: J 130 MET cc_start: 0.8202 (ttp) cc_final: 0.7969 (ttp) REVERT: J 140 TYR cc_start: 0.8687 (m-10) cc_final: 0.8299 (m-10) REVERT: J 232 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7570 (m110) REVERT: J 236 TRP cc_start: 0.8858 (m-10) cc_final: 0.7731 (m-90) REVERT: J 821 MET cc_start: 0.7776 (tpp) cc_final: 0.7393 (tpp) REVERT: J 822 MET cc_start: 0.7340 (tpp) cc_final: 0.6832 (tpp) REVERT: J 913 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7360 (mt-10) REVERT: J 988 PHE cc_start: 0.6605 (t80) cc_final: 0.6235 (m-10) REVERT: J 1143 ASP cc_start: 0.8340 (t0) cc_final: 0.8085 (t0) REVERT: J 1189 MET cc_start: 0.8277 (tmm) cc_final: 0.8059 (tmm) REVERT: J 1193 TRP cc_start: 0.7084 (p90) cc_final: 0.6617 (p90) REVERT: K 3 ARG cc_start: 0.7183 (mmp80) cc_final: 0.6784 (mmp-170) REVERT: K 44 ASP cc_start: 0.7521 (m-30) cc_final: 0.6798 (m-30) outliers start: 45 outliers final: 20 residues processed: 418 average time/residue: 0.2021 time to fit residues: 144.1129 Evaluate side-chains 366 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 342 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 G residue 18 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 85 LEU 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 1090 ASN 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 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1120 THR 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: 20.0000 chunk 411 optimal weight: 0.0050 chunk 316 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 308 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 318 optimal weight: 7.9990 chunk 426 optimal weight: 0.4980 chunk 428 optimal weight: 40.0000 chunk 433 optimal weight: 50.0000 chunk 226 optimal weight: 8.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 663 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 519 ASN I 808 ASN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1236 ASN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN J 951 GLN ** 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 = 0.3840 r_free = 0.3840 target = 0.112697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091275 restraints weight = 131513.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092375 restraints weight = 80431.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093042 restraints weight = 47879.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093230 restraints weight = 42287.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093309 restraints weight = 39497.686| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 36906 Z= 0.121 Angle : 0.665 11.468 50402 Z= 0.338 Chirality : 0.046 0.308 5745 Planarity : 0.004 0.071 6199 Dihedral : 16.082 167.305 5947 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.57 % Allowed : 14.34 % Favored : 84.09 % 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: -1.46 (0.13), residues: 4294 helix: 0.12 (0.13), residues: 1510 sheet: -1.20 (0.21), residues: 574 loop : -1.70 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 542 TYR 0.018 0.001 TYR G 185 PHE 0.016 0.001 PHE I 514 TRP 0.018 0.001 TRP A1134 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (36898) covalent geometry : angle 0.65869 / 0.34 (50390) hydrogen bonds : bond 0.04300 / 2.89 ( 1492) hydrogen bonds : angle 5.16103 / 3.55 ( 4037) metal coordination : bond 0.01519 / 0.96 ( 8) metal coordination : angle 6.15942 / 3.80 ( 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 436 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 379 time to evaluate : 1.314 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 114 MET cc_start: 0.6426 (tpp) cc_final: 0.5823 (tpp) REVERT: A 157 MET cc_start: 0.5671 (tpt) cc_final: 0.4799 (pmm) REVERT: A 765 MET cc_start: 0.7493 (ttt) cc_final: 0.6409 (ptm) REVERT: A 967 MET cc_start: 0.8838 (pmm) cc_final: 0.8499 (pmm) REVERT: A 1008 MET cc_start: 0.7977 (mmp) cc_final: 0.6900 (mmm) REVERT: G 35 PHE cc_start: 0.7442 (m-80) cc_final: 0.7030 (m-80) REVERT: G 185 TYR cc_start: 0.8826 (p90) cc_final: 0.8305 (p90) REVERT: I 187 GLU cc_start: 0.7537 (pm20) cc_final: 0.7252 (pm20) REVERT: I 195 PHE cc_start: 0.7485 (m-80) cc_final: 0.6466 (m-80) REVERT: I 368 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.7649 (tpp-160) REVERT: I 654 ASP cc_start: 0.7886 (m-30) cc_final: 0.7673 (m-30) REVERT: I 741 MET cc_start: 0.8031 (tpp) cc_final: 0.7739 (tpp) REVERT: I 964 LEU cc_start: 0.8037 (tp) cc_final: 0.7772 (mt) REVERT: I 1090 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8966 (t0) REVERT: I 1220 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8584 (tp40) REVERT: I 1232 MET cc_start: 0.8988 (mmt) cc_final: 0.8394 (mmt) REVERT: I 1296 ASP cc_start: 0.7960 (t70) cc_final: 0.7628 (t0) REVERT: J 140 TYR cc_start: 0.8754 (m-10) cc_final: 0.8447 (m-10) REVERT: J 236 TRP cc_start: 0.8896 (m-10) cc_final: 0.7863 (m-10) REVERT: J 697 MET cc_start: 0.8709 (ttp) cc_final: 0.8344 (ttp) REVERT: J 747 MET cc_start: 0.7720 (mtp) cc_final: 0.7428 (mmt) REVERT: J 821 MET cc_start: 0.7758 (tpp) cc_final: 0.7375 (tpp) REVERT: J 822 MET cc_start: 0.7294 (tpp) cc_final: 0.6924 (tpp) REVERT: J 913 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7283 (mt-10) REVERT: J 988 PHE cc_start: 0.6564 (t80) cc_final: 0.6352 (m-10) REVERT: J 1017 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (p) REVERT: J 1143 ASP cc_start: 0.8291 (t0) cc_final: 0.8028 (t0) REVERT: J 1188 GLU cc_start: 0.7052 (pm20) cc_final: 0.6823 (pm20) REVERT: J 1193 TRP cc_start: 0.7062 (p90) cc_final: 0.6642 (p90) REVERT: K 3 ARG cc_start: 0.7172 (mmp80) cc_final: 0.6817 (mmp-170) REVERT: K 44 ASP cc_start: 0.7588 (m-30) cc_final: 0.6980 (m-30) REVERT: K 71 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8068 (tm-30) REVERT: K 79 GLU cc_start: 0.4667 (pt0) cc_final: 0.4458 (pt0) outliers start: 57 outliers final: 30 residues processed: 415 average time/residue: 0.2007 time to fit residues: 140.6863 Evaluate side-chains 381 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 142 MET 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 H residue 141 SER 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 946 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1090 ASN 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 357 VAL Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 60 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 256 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 432 HIS A 585 HIS A1094 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1010 GLN I1134 GLN I1157 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084565 restraints weight = 134241.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085593 restraints weight = 78109.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085584 restraints weight = 50167.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085915 restraints weight = 47616.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085980 restraints weight = 42445.717| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 36906 Z= 0.321 Angle : 0.801 12.326 50402 Z= 0.411 Chirality : 0.049 0.310 5745 Planarity : 0.005 0.072 6199 Dihedral : 16.181 165.448 5947 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 2.24 % Allowed : 15.19 % Favored : 82.57 % 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: -1.55 (0.13), residues: 4294 helix: 0.01 (0.13), residues: 1534 sheet: -1.25 (0.22), residues: 558 loop : -1.73 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 165 TYR 0.016 0.002 TYR G 177 PHE 0.021 0.002 PHE J1325 TRP 0.014 0.002 TRP A 913 HIS 0.009 0.002 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.32 (36898) covalent geometry : angle 0.79524 / 0.41 (50390) hydrogen bonds : bond 0.05526 / 3.66 ( 1492) hydrogen bonds : angle 5.46345 / 3.78 ( 4037) metal coordination : bond 0.02481 / 1.26 ( 8) metal coordination : angle 6.49211 / 3.60 ( 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 420 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 339 time to evaluate : 1.419 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: A 114 MET cc_start: 0.6794 (tpp) cc_final: 0.6051 (tpp) REVERT: A 157 MET cc_start: 0.5918 (tpt) cc_final: 0.5026 (pmm) REVERT: A 796 MET cc_start: 0.8154 (tmm) cc_final: 0.7889 (tmm) REVERT: A 967 MET cc_start: 0.8973 (pmm) cc_final: 0.8524 (pmm) REVERT: G 35 PHE cc_start: 0.7623 (m-80) cc_final: 0.7123 (m-80) REVERT: G 185 TYR cc_start: 0.8917 (p90) cc_final: 0.8616 (p90) REVERT: I 86 GLN cc_start: 0.8528 (tp40) cc_final: 0.8276 (tp40) REVERT: I 102 LEU cc_start: 0.8541 (tp) cc_final: 0.8276 (pt) REVERT: I 187 GLU cc_start: 0.7705 (pm20) cc_final: 0.7412 (pm20) REVERT: I 195 PHE cc_start: 0.7831 (m-80) cc_final: 0.6910 (m-80) REVERT: I 426 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8605 (pt) REVERT: I 654 ASP cc_start: 0.8126 (m-30) cc_final: 0.7870 (m-30) REVERT: I 741 MET cc_start: 0.8150 (tpp) cc_final: 0.7854 (tpp) REVERT: I 1220 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: I 1296 ASP cc_start: 0.8122 (t70) cc_final: 0.7728 (t0) REVERT: J 236 TRP cc_start: 0.8891 (m-10) cc_final: 0.7647 (m-90) REVERT: J 697 MET cc_start: 0.8963 (ttp) cc_final: 0.8433 (ttp) REVERT: J 747 MET cc_start: 0.7980 (mtp) cc_final: 0.7720 (mmt) REVERT: J 822 MET cc_start: 0.7736 (tpp) cc_final: 0.7343 (tpp) REVERT: J 913 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7450 (mt-10) REVERT: J 1143 ASP cc_start: 0.8331 (t0) cc_final: 0.8097 (t0) REVERT: J 1193 TRP cc_start: 0.6848 (p90) cc_final: 0.6352 (p90) REVERT: K 3 ARG cc_start: 0.7290 (mmp80) cc_final: 0.6809 (mmp-170) REVERT: K 41 GLU cc_start: 0.7513 (pm20) cc_final: 0.7241 (pm20) REVERT: K 44 ASP cc_start: 0.7557 (m-30) cc_final: 0.6823 (m-30) REVERT: K 71 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8257 (tm-30) outliers start: 81 outliers final: 52 residues processed: 393 average time/residue: 0.1933 time to fit residues: 130.5130 Evaluate side-chains 369 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU 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 435 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 568 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 966 SER 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 G residue 142 MET 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 199 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 426 ILE 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 714 VAL Chi-restraints excluded: chain I residue 777 VAL 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 1066 MET Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 473 THR 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 853 THR Chi-restraints excluded: chain J residue 932 MET 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: 7.9990 chunk 189 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 413 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 395 optimal weight: 6.9990 chunk 284 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J 495 ASN J 504 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086254 restraints weight = 132908.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087140 restraints weight = 73547.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087406 restraints weight = 47308.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087565 restraints weight = 46071.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087638 restraints weight = 41991.209| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36906 Z= 0.214 Angle : 0.715 12.414 50402 Z= 0.365 Chirality : 0.047 0.338 5745 Planarity : 0.005 0.097 6199 Dihedral : 16.143 162.572 5947 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer: Outliers : 1.99 % Allowed : 16.66 % Favored : 81.35 % 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: -1.43 (0.13), residues: 4294 helix: 0.17 (0.13), residues: 1523 sheet: -1.18 (0.22), residues: 534 loop : -1.71 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 67 TYR 0.015 0.001 TYR G 177 PHE 0.016 0.002 PHE I 514 TRP 0.017 0.001 TRP A1134 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (36898) covalent geometry : angle 0.70960 / 0.36 (50390) hydrogen bonds : bond 0.04686 / 3.12 ( 1492) hydrogen bonds : angle 5.27747 / 3.64 ( 4037) metal coordination : bond 0.01680 / 0.89 ( 8) metal coordination : angle 5.93346 / 3.47 ( 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 412 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 340 time to evaluate : 1.440 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: A 114 MET cc_start: 0.6724 (tpp) cc_final: 0.6010 (tpp) REVERT: A 157 MET cc_start: 0.5703 (tpt) cc_final: 0.4813 (pmm) REVERT: A 967 MET cc_start: 0.8911 (pmm) cc_final: 0.8454 (pmm) REVERT: G 185 TYR cc_start: 0.8885 (p90) cc_final: 0.8503 (p90) REVERT: I 86 GLN cc_start: 0.8500 (tp40) cc_final: 0.8227 (tp40) REVERT: I 187 GLU cc_start: 0.7702 (pm20) cc_final: 0.7371 (pm20) REVERT: I 195 PHE cc_start: 0.7877 (m-80) cc_final: 0.7027 (m-80) REVERT: I 429 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8484 (mtm) REVERT: I 492 MET cc_start: 0.7716 (ptp) cc_final: 0.7008 (mmt) REVERT: I 741 MET cc_start: 0.8038 (tpp) cc_final: 0.7714 (tpp) REVERT: I 810 TYR cc_start: 0.8754 (m-80) cc_final: 0.8509 (m-80) REVERT: I 1220 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8651 (tp40) REVERT: I 1296 ASP cc_start: 0.8082 (t70) cc_final: 0.7697 (t0) REVERT: J 161 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8054 (p) REVERT: J 236 TRP cc_start: 0.8841 (m-10) cc_final: 0.7827 (m-10) REVERT: J 698 MET cc_start: 0.8662 (mmm) cc_final: 0.8204 (mmm) REVERT: J 821 MET cc_start: 0.7950 (tpp) cc_final: 0.7672 (tpp) REVERT: J 822 MET cc_start: 0.7833 (tpp) cc_final: 0.7411 (tpp) REVERT: J 913 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7310 (mt-10) REVERT: J 1143 ASP cc_start: 0.8339 (t0) cc_final: 0.8090 (t0) REVERT: J 1188 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6561 (pm20) REVERT: J 1189 MET cc_start: 0.8547 (tmm) cc_final: 0.8203 (tmm) REVERT: J 1193 TRP cc_start: 0.6986 (p90) cc_final: 0.6474 (p90) REVERT: K 3 ARG cc_start: 0.7247 (mmp80) cc_final: 0.6811 (mmp-170) REVERT: K 44 ASP cc_start: 0.7592 (m-30) cc_final: 0.6834 (m-30) outliers start: 72 outliers final: 48 residues processed: 384 average time/residue: 0.2200 time to fit residues: 144.3410 Evaluate side-chains 383 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 435 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 742 ILE 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 966 SER 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 G residue 142 MET Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 51 MET 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 429 MET Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 820 GLU 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 1066 MET Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 466 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 853 THR Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 46 optimal weight: 30.0000 chunk 88 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 192 optimal weight: 0.0370 chunk 178 optimal weight: 4.9990 chunk 428 optimal weight: 40.0000 chunk 370 optimal weight: 10.0000 chunk 385 optimal weight: 20.0000 overall best weight: 3.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3767 r_free = 0.3767 target = 0.108212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.087253 restraints weight = 133500.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087995 restraints weight = 75812.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088125 restraints weight = 50759.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088387 restraints weight = 49488.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088429 restraints weight = 42648.917| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 36906 Z= 0.217 Angle : 0.719 12.504 50402 Z= 0.366 Chirality : 0.047 0.298 5745 Planarity : 0.005 0.089 6199 Dihedral : 16.124 162.769 5947 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 2.46 % Allowed : 17.24 % Favored : 80.30 % 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: -1.40 (0.13), residues: 4294 helix: 0.23 (0.13), residues: 1523 sheet: -1.20 (0.22), residues: 540 loop : -1.71 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 542 TYR 0.015 0.001 TYR G 177 PHE 0.014 0.002 PHE I 514 TRP 0.017 0.001 TRP A1134 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (36898) covalent geometry : angle 0.71384 / 0.37 (50390) hydrogen bonds : bond 0.04716 / 3.14 ( 1492) hydrogen bonds : angle 5.27244 / 3.65 ( 4037) metal coordination : bond 0.01679 / 0.89 ( 8) metal coordination : angle 5.71021 / 3.30 ( 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 430 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 341 time to evaluate : 1.499 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: 0.7330 (mtm) cc_final: 0.6914 (mtm) REVERT: A 114 MET cc_start: 0.6544 (tpp) cc_final: 0.5865 (tpp) REVERT: A 157 MET cc_start: 0.5431 (tpt) cc_final: 0.4758 (pmm) REVERT: G 35 PHE cc_start: 0.7414 (m-80) cc_final: 0.7016 (m-80) REVERT: G 185 TYR cc_start: 0.8918 (p90) cc_final: 0.8596 (p90) REVERT: I 187 GLU cc_start: 0.7699 (pm20) cc_final: 0.7358 (pm20) REVERT: I 195 PHE cc_start: 0.7983 (m-80) cc_final: 0.7140 (m-80) REVERT: I 429 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: I 492 MET cc_start: 0.7738 (ptp) cc_final: 0.6876 (mmt) REVERT: I 741 MET cc_start: 0.8055 (tpp) cc_final: 0.7733 (tpp) REVERT: I 810 TYR cc_start: 0.8780 (m-80) cc_final: 0.8513 (m-80) REVERT: I 1220 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8541 (tp40) REVERT: I 1274 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: I 1296 ASP cc_start: 0.8092 (t70) cc_final: 0.7682 (t0) REVERT: J 236 TRP cc_start: 0.8850 (m-10) cc_final: 0.7841 (m-10) REVERT: J 698 MET cc_start: 0.8798 (mmm) cc_final: 0.8555 (tpp) REVERT: J 821 MET cc_start: 0.7879 (tpp) cc_final: 0.7653 (tpp) REVERT: J 822 MET cc_start: 0.7802 (tpp) cc_final: 0.7387 (tpp) REVERT: J 1188 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6638 (pm20) REVERT: J 1189 MET cc_start: 0.8625 (tmm) cc_final: 0.8280 (tmm) REVERT: J 1193 TRP cc_start: 0.7207 (p90) cc_final: 0.6715 (p90) REVERT: K 3 ARG cc_start: 0.7256 (mmp80) cc_final: 0.6774 (mmp-170) REVERT: K 41 GLU cc_start: 0.7508 (pm20) cc_final: 0.7304 (pm20) REVERT: K 44 ASP cc_start: 0.7581 (m-30) cc_final: 0.6948 (m-30) REVERT: K 71 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 89 outliers final: 60 residues processed: 402 average time/residue: 0.2044 time to fit residues: 141.5399 Evaluate side-chains 387 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 324 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 450 LEU Chi-restraints excluded: chain A residue 723 LEU 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 966 SER 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 G residue 142 MET Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 51 MET 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 429 MET Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 820 GLU 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 1066 MET Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE 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 78 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 473 THR 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 737 ILE 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 932 MET Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 4 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 209 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 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 673 HIS ** 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** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3814 r_free = 0.3814 target = 0.109933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088731 restraints weight = 131788.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089706 restraints weight = 72660.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089985 restraints weight = 45513.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090131 restraints weight = 43383.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090200 restraints weight = 39905.883| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36906 Z= 0.126 Angle : 0.689 13.734 50402 Z= 0.346 Chirality : 0.046 0.399 5745 Planarity : 0.004 0.090 6199 Dihedral : 15.986 162.571 5947 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 1.66 % Allowed : 18.37 % Favored : 79.97 % 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: -1.20 (0.13), residues: 4294 helix: 0.42 (0.13), residues: 1522 sheet: -1.12 (0.21), residues: 583 loop : -1.59 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 67 TYR 0.016 0.001 TYR G 185 PHE 0.015 0.001 PHE I 514 TRP 0.020 0.001 TRP A1134 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (36898) covalent geometry : angle 0.68468 / 0.35 (50390) hydrogen bonds : bond 0.04111 / 2.75 ( 1492) hydrogen bonds : angle 5.04303 / 3.47 ( 4037) metal coordination : bond 0.00934 / 0.52 ( 8) metal coordination : angle 4.93446 / 2.93 ( 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 426 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 366 time to evaluate : 1.024 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: A 157 MET cc_start: 0.5344 (tpt) cc_final: 0.4669 (pmm) REVERT: A 821 ASN cc_start: 0.8720 (t0) cc_final: 0.8168 (t0) REVERT: A 967 MET cc_start: 0.8760 (pmm) cc_final: 0.8513 (pmm) REVERT: G 25 LYS cc_start: 0.8662 (tttp) cc_final: 0.7981 (tmtt) REVERT: G 35 PHE cc_start: 0.7239 (m-80) cc_final: 0.6860 (m-80) REVERT: G 185 TYR cc_start: 0.8889 (p90) cc_final: 0.8381 (p90) REVERT: I 187 GLU cc_start: 0.7630 (pm20) cc_final: 0.7269 (pm20) REVERT: I 195 PHE cc_start: 0.7832 (m-80) cc_final: 0.6817 (m-80) REVERT: I 368 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.8293 (tpp-160) REVERT: I 429 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: I 741 MET cc_start: 0.7995 (tpp) cc_final: 0.7667 (tpp) REVERT: I 1090 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8884 (t0) REVERT: I 1220 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8598 (tp40) REVERT: I 1274 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: I 1279 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7670 (mt-10) REVERT: I 1296 ASP cc_start: 0.7918 (t70) cc_final: 0.7669 (t0) REVERT: J 140 TYR cc_start: 0.8812 (m-10) cc_final: 0.8318 (m-10) REVERT: J 236 TRP cc_start: 0.8837 (m-10) cc_final: 0.7912 (m-10) REVERT: J 312 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.7012 (mmm-85) REVERT: J 643 ASP cc_start: 0.8898 (m-30) cc_final: 0.8567 (m-30) REVERT: J 822 MET cc_start: 0.7533 (tpp) cc_final: 0.7002 (tpp) REVERT: J 988 PHE cc_start: 0.6734 (t80) cc_final: 0.6457 (m-10) REVERT: J 1189 MET cc_start: 0.8582 (tmm) cc_final: 0.8329 (tmm) REVERT: J 1193 TRP cc_start: 0.7206 (p90) cc_final: 0.6720 (p90) REVERT: K 3 ARG cc_start: 0.7057 (mmp80) cc_final: 0.6712 (mmp-170) REVERT: K 44 ASP cc_start: 0.7587 (m-30) cc_final: 0.6819 (m-30) outliers start: 60 outliers final: 37 residues processed: 403 average time/residue: 0.2065 time to fit residues: 140.9114 Evaluate side-chains 378 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 337 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ARG 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 699 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 966 SER Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 19 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 30 ILE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE 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 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 1120 THR 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 72 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 180 optimal weight: 9.9990 chunk 416 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 392 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A1145 ASN H 103 ASN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS I 513 GLN ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN J 424 ASN J 495 ASN J 720 ASN ** 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 = 0.3717 r_free = 0.3717 target = 0.104089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082644 restraints weight = 134518.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083352 restraints weight = 88019.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.083863 restraints weight = 52759.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084113 restraints weight = 45725.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084256 restraints weight = 42470.115| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 36906 Z= 0.386 Angle : 0.887 12.948 50402 Z= 0.452 Chirality : 0.051 0.490 5745 Planarity : 0.006 0.091 6199 Dihedral : 16.202 162.618 5947 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.91 % Allowed : 18.73 % Favored : 79.36 % 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: -1.59 (0.13), residues: 4294 helix: 0.02 (0.13), residues: 1521 sheet: -1.37 (0.21), residues: 587 loop : -1.75 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 67 TYR 0.022 0.002 TYR I 810 PHE 0.019 0.003 PHE A 891 TRP 0.020 0.002 TRP A 913 HIS 0.014 0.002 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.39 (36898) covalent geometry : angle 0.88299 / 0.45 (50390) hydrogen bonds : bond 0.05975 / 3.92 ( 1492) hydrogen bonds : angle 5.59444 / 3.87 ( 4037) metal coordination : bond 0.02647 / 1.33 ( 8) metal coordination : angle 5.71023 / 3.13 ( 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 392 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 323 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.5338 (tpt) cc_final: 0.4739 (pmm) REVERT: A 158 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: I 187 GLU cc_start: 0.7704 (pm20) cc_final: 0.7320 (pm20) REVERT: I 195 PHE cc_start: 0.8034 (m-80) cc_final: 0.6962 (m-80) REVERT: I 368 ARG cc_start: 0.8482 (tpp-160) cc_final: 0.8178 (tpt170) REVERT: I 429 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: I 492 MET cc_start: 0.7924 (ptp) cc_final: 0.6939 (mmt) REVERT: I 741 MET cc_start: 0.8130 (tpp) cc_final: 0.7819 (tpp) REVERT: I 781 ASP cc_start: 0.8197 (t0) cc_final: 0.7789 (t0) REVERT: I 1274 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: I 1279 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7734 (mp0) REVERT: I 1296 ASP cc_start: 0.8300 (t70) cc_final: 0.7775 (t0) REVERT: J 238 ILE cc_start: 0.9259 (mm) cc_final: 0.9024 (mm) REVERT: J 709 ARG cc_start: 0.7105 (ptt-90) cc_final: 0.6896 (ptt-90) REVERT: J 822 MET cc_start: 0.7919 (tpp) cc_final: 0.7385 (tpp) REVERT: J 1193 TRP cc_start: 0.6997 (p90) cc_final: 0.6507 (p90) REVERT: J 1334 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7643 (tp30) REVERT: K 3 ARG cc_start: 0.7310 (mmp80) cc_final: 0.6830 (mmp-170) REVERT: K 44 ASP cc_start: 0.7679 (m-30) cc_final: 0.6916 (m-30) REVERT: K 71 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8345 (tm-30) outliers start: 69 outliers final: 54 residues processed: 372 average time/residue: 0.2093 time to fit residues: 132.5355 Evaluate side-chains 365 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 158 GLU 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 678 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 902 ARG 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 966 SER 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 G residue 19 VAL Chi-restraints excluded: chain G residue 85 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 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 429 MET 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 777 VAL Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE 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 1322 SER 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 708 ASN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 20 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 308 optimal weight: 9.9990 chunk 429 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 322 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 433 optimal weight: 50.0000 chunk 291 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN H 103 ASN ** H 132 HIS ** 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 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I1010 GLN I1257 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084707 restraints weight = 133498.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085820 restraints weight = 74015.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086057 restraints weight = 46318.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086255 restraints weight = 43962.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086319 restraints weight = 39810.724| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 36906 Z= 0.209 Angle : 0.762 12.926 50402 Z= 0.383 Chirality : 0.047 0.433 5745 Planarity : 0.005 0.087 6199 Dihedral : 16.142 159.524 5947 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.52 % Allowed : 19.61 % Favored : 78.87 % 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: -1.46 (0.13), residues: 4294 helix: 0.15 (0.13), residues: 1522 sheet: -1.36 (0.22), residues: 569 loop : -1.68 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 67 TYR 0.032 0.002 TYR G 185 PHE 0.024 0.002 PHE I1025 TRP 0.020 0.002 TRP A1134 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (36898) covalent geometry : angle 0.75704 / 0.38 (50390) hydrogen bonds : bond 0.04731 / 3.14 ( 1492) hydrogen bonds : angle 5.34166 / 3.68 ( 4037) metal coordination : bond 0.01592 / 0.85 ( 8) metal coordination : angle 5.62596 / 3.26 ( 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 383 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 328 time to evaluate : 1.396 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: 0.4980 (tpt) cc_final: 0.4569 (pmm) REVERT: G 25 LYS cc_start: 0.8786 (tttp) cc_final: 0.8325 (tptp) REVERT: H 25 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8707 (ttmm) REVERT: I 187 GLU cc_start: 0.7679 (pm20) cc_final: 0.7302 (pm20) REVERT: I 195 PHE cc_start: 0.8018 (m-80) cc_final: 0.7177 (m-80) REVERT: I 429 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8451 (mtm) REVERT: I 492 MET cc_start: 0.7609 (ptp) cc_final: 0.6834 (mmt) REVERT: I 515 MET cc_start: 0.8606 (ttp) cc_final: 0.8128 (ttt) REVERT: I 741 MET cc_start: 0.8054 (tpp) cc_final: 0.7741 (tpp) REVERT: I 781 ASP cc_start: 0.8134 (t0) cc_final: 0.7702 (t0) REVERT: I 1274 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: I 1296 ASP cc_start: 0.8199 (t70) cc_final: 0.7752 (t0) REVERT: J 236 TRP cc_start: 0.8883 (m-10) cc_final: 0.7895 (m-10) REVERT: J 238 ILE cc_start: 0.9241 (mm) cc_final: 0.9022 (mm) REVERT: J 643 ASP cc_start: 0.9026 (m-30) cc_final: 0.8696 (m-30) REVERT: J 822 MET cc_start: 0.7826 (tpp) cc_final: 0.7270 (tpp) REVERT: J 1193 TRP cc_start: 0.7062 (p90) cc_final: 0.6824 (p90) REVERT: K 3 ARG cc_start: 0.7241 (mmp80) cc_final: 0.6829 (mmp-170) REVERT: K 44 ASP cc_start: 0.7631 (m-30) cc_final: 0.6868 (m-30) outliers start: 55 outliers final: 46 residues processed: 364 average time/residue: 0.2176 time to fit residues: 134.1108 Evaluate side-chains 383 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ARG 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 678 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 902 ARG 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 966 SER Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain G residue 19 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 210 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1090 ASN Chi-restraints excluded: chain I residue 1096 ILE 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 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 776 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 72 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 89 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** 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 513 GLN ** 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** I1313 HIS J 424 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 = 0.3805 r_free = 0.3805 target = 0.109450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088594 restraints weight = 132082.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089251 restraints weight = 71004.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089462 restraints weight = 48619.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089629 restraints weight = 48643.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.089723 restraints weight = 41055.571| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.003 0.070 36906 Z= 0.130 Angle : 0.726 13.762 50402 Z= 0.360 Chirality : 0.046 0.409 5745 Planarity : 0.005 0.098 6199 Dihedral : 15.949 160.445 5947 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.35 % Allowed : 19.89 % Favored : 78.76 % 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: -1.23 (0.13), residues: 4294 helix: 0.38 (0.13), residues: 1519 sheet: -1.25 (0.21), residues: 578 loop : -1.55 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 67 TYR 0.028 0.001 TYR G 185 PHE 0.034 0.001 PHE I1025 TRP 0.024 0.002 TRP A1134 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (36898) covalent geometry : angle 0.72238 / 0.36 (50390) hydrogen bonds : bond 0.04094 / 2.73 ( 1492) hydrogen bonds : angle 5.09871 / 3.51 ( 4037) metal coordination : bond 0.00899 / 0.51 ( 8) metal coordination : angle 4.86355 / 2.87 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5665.08 seconds wall clock time: 99 minutes 10.21 seconds (5950.21 seconds total)