Starting phenix.real_space_refine on Sun Jul 5 08:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.map" model { file = "/net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eha_28145/07_2026/8eha_28145.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16259 2.51 5 N 4641 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26250 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} 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: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10371 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} 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: "J" Number of atoms: 10541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10541 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15501 SG CYS J 70 105.714 101.302 89.302 1.00 86.03 S ATOM 15515 SG CYS J 72 106.137 105.046 89.685 1.00 93.36 S ATOM 15623 SG CYS J 85 107.825 102.735 92.115 1.00 92.75 S ATOM 15647 SG CYS J 88 104.079 102.968 92.255 1.00 90.67 S ATOM 21335 SG CYS J 814 87.623 36.796 85.517 1.00 51.34 S ATOM 21900 SG CYS J 888 86.076 40.281 86.040 1.00 45.23 S ATOM 21951 SG CYS J 895 87.068 39.081 82.561 1.00 43.74 S ATOM 21972 SG CYS J 898 84.093 37.581 84.308 1.00 42.91 S Time building chain proxies: 5.35, per 1000 atoms: 0.20 Number of scatterers: 26250 At special positions: 0 Unit cell: (139.1, 149.5, 162.5, 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 106 16.00 P 63 15.00 Mg 1 11.99 O 5178 8.00 N 4641 7.00 C 16259 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: 2.29 Conformation dependent library (CDL) restraints added in 940.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 48 sheets defined 36.5% alpha, 16.7% beta 30 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.617A 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 111 through 115 removed outlier: 3.616A pdb=" N ASP G 114 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.580A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 30 through 40 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.736A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.600A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.604A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.986A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.636A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.924A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.779A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.505A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.987A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.815A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.923A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.860A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 980 removed outlier: 3.767A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.629A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.785A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.847A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.733A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.680A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 removed outlier: 3.586A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY I1282 " --> pdb=" O LEU I1278 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1298 through 1309 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.702A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.645A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.729A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 100 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.688A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 285 removed outlier: 3.631A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.768A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) 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 416 removed outlier: 4.357A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (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 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.690A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 614 through 634 removed outlier: 3.522A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 670 Processing helix chain 'J' and resid 676 through 702 removed outlier: 4.111A pdb=" N GLN J 702 " --> pdb=" O MET J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 770 through 804 removed outlier: 3.790A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR J 797 " --> pdb=" O SER J 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 removed outlier: 4.193A pdb=" N GLU J 873 " --> pdb=" O CYS J 869 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 932 removed outlier: 3.609A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix removed outlier: 4.117A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 933 through 937 Processing helix chain 'J' and resid 1139 through 1147 Processing helix chain 'J' and resid 1218 through 1244 removed outlier: 3.541A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.331A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.640A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1310 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.777A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.636A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 79 removed outlier: 3.616A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.143A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.143A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 99 removed outlier: 6.891A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 147 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 55 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 53 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'G' and resid 102 through 104 removed outlier: 3.673A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.566A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.718A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 19 " --> pdb=" O HIS H 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.718A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.575A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.436A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 60 Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.461A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.746A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU I 204 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AC3, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC4, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.655A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 295 through 296 removed outlier: 4.547A pdb=" N LYS I 295 " --> pdb=" O LEU I 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AD1, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.649A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.545A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.591A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.870A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 830 through 841 removed outlier: 5.732A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.998A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.218A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.778A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.216A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AE3, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.518A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 707 through 708 Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.812A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 956 through 961 removed outlier: 3.959A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP J 986 " --> pdb=" O THR J 991 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR J 991 " --> pdb=" O ASP J 986 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.646A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.658A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.454A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 977 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8672 1.34 - 1.46: 4701 1.46 - 1.58: 13087 1.58 - 1.70: 126 1.70 - 1.82: 187 Bond restraints: 26773 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.822 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.727 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.705 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C19 1N7 I1401 " pdb=" C2 1N7 I1401 " ideal model delta sigma weight residual 1.551 1.398 0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C4 1N7 I1401 " pdb=" C5 1N7 I1401 " ideal model delta sigma weight residual 1.534 1.394 0.140 2.00e-02 2.50e+03 4.93e+01 ... (remaining 26768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 35870 2.08 - 4.16: 503 4.16 - 6.24: 51 6.24 - 8.32: 16 8.32 - 10.40: 2 Bond angle restraints: 36442 Sorted by residual: angle pdb=" O4' DC B 18 " pdb=" C4' DC B 18 " pdb=" C3' DC B 18 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.96e+01 angle pdb=" C ILE I1079 " pdb=" N ASN I1080 " pdb=" CA ASN I1080 " ideal model delta sigma weight residual 120.49 127.67 -7.18 1.42e+00 4.96e-01 2.56e+01 angle pdb=" O4' DA B 19 " pdb=" C4' DA B 19 " pdb=" C3' DA B 19 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4' DG B 17 " pdb=" C4' DG B 17 " pdb=" C3' DG B 17 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 36437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 15775 35.26 - 70.51: 486 70.51 - 105.77: 24 105.77 - 141.03: 2 141.03 - 176.29: 2 Dihedral angle restraints: 16289 sinusoidal: 7138 harmonic: 9151 Sorted by residual: dihedral pdb=" CA GLU J 925 " pdb=" C GLU J 925 " pdb=" N PRO J 926 " pdb=" CA PRO J 926 " ideal model delta harmonic sigma weight residual 180.00 144.14 35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" CA LEU J1138 " pdb=" C LEU J1138 " pdb=" N PRO J1139 " pdb=" CA PRO J1139 " ideal model delta harmonic sigma weight residual 180.00 146.93 33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA VAL I1309 " pdb=" C VAL I1309 " pdb=" N ASP I1310 " pdb=" CA ASP I1310 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 16286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3840 0.082 - 0.163: 330 0.163 - 0.245: 4 0.245 - 0.327: 1 0.327 - 0.409: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.94 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C15 1N7 I1401 " pdb=" C14 1N7 I1401 " pdb=" C16 1N7 I1401 " pdb=" C2 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C5 1N7 I1401 " pdb=" C4 1N7 I1401 " pdb=" C6 1N7 I1401 " pdb=" C9 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.61 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4173 not shown) Planarity restraints: 4545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 925 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO J 926 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO J 926 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 926 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO J1139 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO J 851 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.034 5.00e-02 4.00e+02 ... (remaining 4542 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 242 2.58 - 3.16: 20907 3.16 - 3.74: 41211 3.74 - 4.32: 54820 4.32 - 4.90: 92687 Nonbonded interactions: 209867 Sorted by model distance: nonbonded pdb=" O3' C R 18 " pdb="MG MG R 101 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R 101 " model vdw 2.038 2.170 nonbonded pdb=" O6 DG A 3 " pdb=" N6 DA B 29 " model vdw 2.077 3.120 nonbonded pdb=" NH2 ARG I 528 " pdb=" O SER I 576 " model vdw 2.196 3.120 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.216 3.040 ... (remaining 209862 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 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.300 Find NCS groups from input model: 0.280 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 : 0.005 0.290 26781 Z= 0.284 Angle : 0.633 10.396 36454 Z= 0.390 Chirality : 0.044 0.409 4176 Planarity : 0.004 0.085 4545 Dihedral : 15.146 176.286 10405 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.77 % Allowed : 9.69 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3174 helix: 0.23 (0.16), residues: 1071 sheet: -1.36 (0.28), residues: 369 loop : -1.75 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 709 TYR 0.013 0.001 TYR J 723 PHE 0.013 0.001 PHE I 514 TRP 0.009 0.001 TRP J 580 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.28 (26773) covalent geometry : angle 0.63215 / 0.39 (36442) hydrogen bonds : bond 0.17953 / 19.31 ( 1034) hydrogen bonds : angle 6.63642 / 6.44 ( 2879) metal coordination : bond 0.00632 / 0.58 ( 8) metal coordination : angle 1.69266 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 421 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 LEU cc_start: 0.8737 (tp) cc_final: 0.8396 (tp) REVERT: I 195 PHE cc_start: 0.8124 (m-10) cc_final: 0.7827 (m-10) REVERT: I 423 ASP cc_start: 0.7499 (p0) cc_final: 0.6937 (p0) REVERT: I 434 ASP cc_start: 0.8097 (m-30) cc_final: 0.7781 (m-30) REVERT: I 459 MET cc_start: 0.8914 (mtp) cc_final: 0.8683 (mtp) REVERT: I 704 MET cc_start: 0.8428 (tpp) cc_final: 0.8108 (tpp) REVERT: I 930 ASP cc_start: 0.7275 (m-30) cc_final: 0.6977 (m-30) REVERT: I 940 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: I 941 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7029 (mtmm) REVERT: I 997 TRP cc_start: 0.6652 (m100) cc_final: 0.6037 (m100) REVERT: I 1240 ASP cc_start: 0.8036 (p0) cc_final: 0.7786 (p0) REVERT: I 1290 MET cc_start: 0.8700 (mmt) cc_final: 0.8471 (mmt) REVERT: J 92 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (p) REVERT: J 227 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: J 308 ASP cc_start: 0.8710 (t0) cc_final: 0.8418 (t0) REVERT: J 644 MET cc_start: 0.8750 (mtt) cc_final: 0.8120 (mtt) REVERT: J 697 MET cc_start: 0.8671 (ttp) cc_final: 0.8415 (ttp) REVERT: J 698 MET cc_start: 0.7805 (tpt) cc_final: 0.7090 (tpt) REVERT: J 706 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7999 (m) REVERT: J 806 ASP cc_start: 0.7829 (p0) cc_final: 0.7514 (p0) REVERT: J 822 MET cc_start: 0.8978 (mmt) cc_final: 0.8660 (mmt) REVERT: J 831 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7383 (m) REVERT: J 1158 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6486 (tm-30) REVERT: J 1159 ILE cc_start: 0.9140 (tp) cc_final: 0.8890 (tp) outliers start: 102 outliers final: 49 residues processed: 502 average time/residue: 0.1543 time to fit residues: 124.9169 Evaluate side-chains 390 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 940 GLU Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 737 ASN I1023 HIS ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN J 968 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097073 restraints weight = 42668.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097391 restraints weight = 29742.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097858 restraints weight = 23917.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098207 restraints weight = 19825.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098333 restraints weight = 18440.092| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26781 Z= 0.138 Angle : 0.594 10.006 36454 Z= 0.310 Chirality : 0.044 0.226 4176 Planarity : 0.004 0.081 4545 Dihedral : 14.486 172.680 4278 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.44 % Allowed : 12.72 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.28 (0.15), residues: 3174 helix: 0.59 (0.16), residues: 1112 sheet: -1.44 (0.27), residues: 371 loop : -1.74 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 272 TYR 0.015 0.001 TYR G 152 PHE 0.015 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (26773) covalent geometry : angle 0.59015 / 0.31 (36442) hydrogen bonds : bond 0.04576 / 4.99 ( 1034) hydrogen bonds : angle 4.99762 / 5.10 ( 2879) metal coordination : bond 0.00971 / 0.92 ( 8) metal coordination : angle 3.65927 / 7.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 366 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 LEU cc_start: 0.8569 (tp) cc_final: 0.8236 (tp) REVERT: I 423 ASP cc_start: 0.7492 (p0) cc_final: 0.7136 (p0) REVERT: I 434 ASP cc_start: 0.8154 (m-30) cc_final: 0.7680 (m-30) REVERT: I 459 MET cc_start: 0.8943 (mtp) cc_final: 0.8537 (mtp) REVERT: I 463 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: I 488 MET cc_start: 0.8281 (mmp) cc_final: 0.7528 (mmm) REVERT: I 930 ASP cc_start: 0.7054 (m-30) cc_final: 0.6796 (m-30) REVERT: I 941 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7202 (mtmm) REVERT: I 997 TRP cc_start: 0.6682 (m100) cc_final: 0.5980 (m100) REVERT: I 1085 MET cc_start: 0.9011 (mmm) cc_final: 0.8610 (mmp) REVERT: I 1240 ASP cc_start: 0.8162 (p0) cc_final: 0.7932 (p0) REVERT: I 1290 MET cc_start: 0.8864 (mmt) cc_final: 0.8524 (mmp) REVERT: J 227 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: J 299 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8819 (tp) REVERT: J 308 ASP cc_start: 0.8709 (t0) cc_final: 0.8487 (t0) REVERT: J 644 MET cc_start: 0.8820 (mtt) cc_final: 0.8220 (mtt) REVERT: J 697 MET cc_start: 0.8667 (ttp) cc_final: 0.8332 (ttp) REVERT: J 698 MET cc_start: 0.7825 (tpt) cc_final: 0.7098 (tpt) REVERT: J 706 VAL cc_start: 0.8178 (m) cc_final: 0.7912 (m) REVERT: J 743 MET cc_start: 0.8885 (ptm) cc_final: 0.8608 (ptp) REVERT: J 806 ASP cc_start: 0.7739 (p0) cc_final: 0.7481 (p0) REVERT: J 822 MET cc_start: 0.8937 (mmt) cc_final: 0.8599 (mmt) REVERT: J 1158 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6629 (tm-30) REVERT: J 1159 ILE cc_start: 0.9123 (tp) cc_final: 0.8865 (tp) outliers start: 93 outliers final: 68 residues processed: 435 average time/residue: 0.1571 time to fit residues: 110.1394 Evaluate side-chains 400 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 328 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 139 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 288 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 191 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 ASN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094907 restraints weight = 42900.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095722 restraints weight = 31823.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096146 restraints weight = 23319.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096564 restraints weight = 20435.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096758 restraints weight = 18568.468| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26781 Z= 0.192 Angle : 0.593 9.754 36454 Z= 0.309 Chirality : 0.044 0.229 4176 Planarity : 0.004 0.087 4545 Dihedral : 14.525 174.568 4260 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.73 % Allowed : 13.05 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.22 (0.15), residues: 3174 helix: 0.73 (0.16), residues: 1109 sheet: -1.57 (0.26), residues: 389 loop : -1.73 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 779 TYR 0.022 0.001 TYR G 152 PHE 0.014 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (26773) covalent geometry : angle 0.59009 / 0.31 (36442) hydrogen bonds : bond 0.04205 / 4.60 ( 1034) hydrogen bonds : angle 4.73375 / 4.92 ( 2879) metal coordination : bond 0.01231 / 1.15 ( 8) metal coordination : angle 3.14266 / 5.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 339 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 202 VAL cc_start: 0.9449 (t) cc_final: 0.9179 (p) REVERT: H 79 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8441 (mm) REVERT: H 102 LEU cc_start: 0.8187 (tp) cc_final: 0.7955 (tp) REVERT: I 423 ASP cc_start: 0.7433 (p0) cc_final: 0.7110 (p0) REVERT: I 434 ASP cc_start: 0.8145 (m-30) cc_final: 0.7707 (m-30) REVERT: I 459 MET cc_start: 0.8926 (mtp) cc_final: 0.8520 (mtp) REVERT: I 463 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: I 488 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: I 930 ASP cc_start: 0.6986 (m-30) cc_final: 0.6746 (m-30) REVERT: I 1085 MET cc_start: 0.9228 (mmm) cc_final: 0.9021 (mmm) REVERT: I 1240 ASP cc_start: 0.8178 (p0) cc_final: 0.7940 (p0) REVERT: I 1265 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7837 (t80) REVERT: I 1290 MET cc_start: 0.8905 (mmt) cc_final: 0.8600 (mmt) REVERT: J 227 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8617 (m-80) REVERT: J 298 MET cc_start: 0.8077 (mmp) cc_final: 0.7716 (mmp) REVERT: J 532 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7502 (tm-30) REVERT: J 644 MET cc_start: 0.8855 (mtt) cc_final: 0.8354 (mtt) REVERT: J 698 MET cc_start: 0.7846 (tpt) cc_final: 0.7061 (tpt) REVERT: J 702 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6312 (pp30) REVERT: J 706 VAL cc_start: 0.8183 (m) cc_final: 0.7964 (m) REVERT: J 806 ASP cc_start: 0.7720 (p0) cc_final: 0.7499 (p0) REVERT: J 822 MET cc_start: 0.8929 (mmt) cc_final: 0.8569 (mmt) REVERT: J 832 LYS cc_start: 0.6327 (mmtm) cc_final: 0.6090 (mmtt) REVERT: J 1158 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6714 (tm-30) REVERT: J 1159 ILE cc_start: 0.9126 (tp) cc_final: 0.8786 (tp) REVERT: K 7 GLN cc_start: 0.8439 (tp40) cc_final: 0.8236 (tp40) outliers start: 128 outliers final: 92 residues processed: 436 average time/residue: 0.1427 time to fit residues: 101.3761 Evaluate side-chains 417 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 319 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 249 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 266 optimal weight: 0.0370 chunk 163 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 139 optimal weight: 0.0670 chunk 88 optimal weight: 4.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 ASN I1023 HIS ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097619 restraints weight = 42496.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096950 restraints weight = 27813.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097636 restraints weight = 25200.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097986 restraints weight = 20807.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098215 restraints weight = 18900.764| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26781 Z= 0.114 Angle : 0.554 8.597 36454 Z= 0.287 Chirality : 0.043 0.245 4176 Planarity : 0.004 0.080 4545 Dihedral : 14.391 174.314 4256 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.36 % Allowed : 14.38 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.08 (0.15), residues: 3174 helix: 0.86 (0.16), residues: 1114 sheet: -1.37 (0.27), residues: 379 loop : -1.70 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 779 TYR 0.020 0.001 TYR G 152 PHE 0.013 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (26773) covalent geometry : angle 0.55203 / 0.29 (36442) hydrogen bonds : bond 0.03739 / 4.06 ( 1034) hydrogen bonds : angle 4.48532 / 4.67 ( 2879) metal coordination : bond 0.00742 / 0.71 ( 8) metal coordination : angle 2.67200 / 4.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 359 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: H 79 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8364 (mm) REVERT: I 423 ASP cc_start: 0.7476 (p0) cc_final: 0.7153 (p0) REVERT: I 434 ASP cc_start: 0.8189 (m-30) cc_final: 0.7710 (m-30) REVERT: I 459 MET cc_start: 0.8842 (mtp) cc_final: 0.8481 (mtp) REVERT: I 463 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: I 488 MET cc_start: 0.8356 (mmp) cc_final: 0.7359 (tpt) REVERT: I 930 ASP cc_start: 0.6975 (m-30) cc_final: 0.6728 (m-30) REVERT: I 997 TRP cc_start: 0.6939 (m100) cc_final: 0.6078 (m100) REVERT: I 1085 MET cc_start: 0.9080 (mmm) cc_final: 0.8835 (mmm) REVERT: I 1107 MET cc_start: 0.7679 (mtm) cc_final: 0.7425 (mtm) REVERT: I 1240 ASP cc_start: 0.8124 (p0) cc_final: 0.7873 (p0) REVERT: I 1265 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7722 (t80) REVERT: I 1290 MET cc_start: 0.8823 (mmt) cc_final: 0.8445 (mmp) REVERT: J 227 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: J 285 LEU cc_start: 0.8612 (mp) cc_final: 0.8394 (mp) REVERT: J 298 MET cc_start: 0.8078 (mmp) cc_final: 0.7688 (mmp) REVERT: J 560 ASN cc_start: 0.6845 (p0) cc_final: 0.6205 (p0) REVERT: J 644 MET cc_start: 0.8704 (mtt) cc_final: 0.8170 (mtt) REVERT: J 697 MET cc_start: 0.8586 (ttp) cc_final: 0.8198 (ttp) REVERT: J 698 MET cc_start: 0.7915 (tpt) cc_final: 0.7172 (tpt) REVERT: J 706 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7876 (m) REVERT: J 822 MET cc_start: 0.8986 (mmt) cc_final: 0.8625 (mmt) REVERT: J 898 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7760 (m) REVERT: J 1158 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6652 (tm-30) REVERT: J 1159 ILE cc_start: 0.9092 (tp) cc_final: 0.8734 (tp) outliers start: 118 outliers final: 84 residues processed: 447 average time/residue: 0.1493 time to fit residues: 108.1924 Evaluate side-chains 418 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 328 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 145 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 128 HIS I1023 HIS ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096621 restraints weight = 42232.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.096602 restraints weight = 30861.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097182 restraints weight = 24486.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097617 restraints weight = 19945.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097703 restraints weight = 18232.610| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26781 Z= 0.161 Angle : 0.577 10.681 36454 Z= 0.299 Chirality : 0.043 0.227 4176 Planarity : 0.004 0.089 4545 Dihedral : 14.380 175.151 4254 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.03 % Allowed : 14.79 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.05 (0.15), residues: 3174 helix: 0.89 (0.16), residues: 1118 sheet: -1.37 (0.27), residues: 398 loop : -1.68 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 137 TYR 0.023 0.001 TYR G 185 PHE 0.013 0.001 PHE I 405 TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (26773) covalent geometry : angle 0.57550 / 0.30 (36442) hydrogen bonds : bond 0.03786 / 4.13 ( 1034) hydrogen bonds : angle 4.42716 / 4.68 ( 2879) metal coordination : bond 0.01017 / 0.96 ( 8) metal coordination : angle 2.66033 / 4.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 334 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9076 (m-80) cc_final: 0.8747 (m-10) REVERT: G 111 THR cc_start: 0.9144 (p) cc_final: 0.8894 (p) REVERT: H 28 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8958 (pt) REVERT: H 79 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8394 (mm) REVERT: I 423 ASP cc_start: 0.7463 (p0) cc_final: 0.7102 (p0) REVERT: I 434 ASP cc_start: 0.8142 (m-30) cc_final: 0.7667 (m-30) REVERT: I 459 MET cc_start: 0.8844 (mtp) cc_final: 0.8449 (mtp) REVERT: I 463 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: I 488 MET cc_start: 0.8392 (mmp) cc_final: 0.7414 (tpt) REVERT: I 930 ASP cc_start: 0.6999 (m-30) cc_final: 0.6763 (m-30) REVERT: I 976 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7745 (ttm-80) REVERT: I 1085 MET cc_start: 0.9126 (mmm) cc_final: 0.8816 (mmm) REVERT: I 1107 MET cc_start: 0.7790 (mtm) cc_final: 0.7540 (mtm) REVERT: I 1240 ASP cc_start: 0.8192 (p0) cc_final: 0.7911 (p0) REVERT: I 1265 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7888 (t80) REVERT: I 1290 MET cc_start: 0.8949 (mmt) cc_final: 0.8616 (mmt) REVERT: J 227 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: J 298 MET cc_start: 0.8054 (mmp) cc_final: 0.7670 (mmp) REVERT: J 560 ASN cc_start: 0.6758 (p0) cc_final: 0.6171 (p0) REVERT: J 644 MET cc_start: 0.8818 (mtt) cc_final: 0.8412 (mtt) REVERT: J 697 MET cc_start: 0.8653 (ttp) cc_final: 0.8287 (ttp) REVERT: J 698 MET cc_start: 0.7932 (tpt) cc_final: 0.7063 (tpt) REVERT: J 702 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6298 (pp30) REVERT: J 706 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7933 (m) REVERT: J 822 MET cc_start: 0.8967 (mmt) cc_final: 0.8596 (mmt) REVERT: J 898 CYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7849 (m) REVERT: J 1158 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6648 (tm-30) REVERT: J 1159 ILE cc_start: 0.9092 (tp) cc_final: 0.8729 (tp) outliers start: 136 outliers final: 103 residues processed: 434 average time/residue: 0.1547 time to fit residues: 109.8359 Evaluate side-chains 430 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 319 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 229 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 201 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN G 93 GLN I1023 HIS ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098198 restraints weight = 42104.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099226 restraints weight = 29404.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099617 restraints weight = 21831.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099995 restraints weight = 18672.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100031 restraints weight = 17193.965| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26781 Z= 0.111 Angle : 0.563 11.546 36454 Z= 0.288 Chirality : 0.043 0.230 4176 Planarity : 0.004 0.084 4545 Dihedral : 14.315 175.309 4254 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.99 % Allowed : 16.08 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3174 helix: 1.00 (0.16), residues: 1117 sheet: -1.19 (0.28), residues: 376 loop : -1.62 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 52 TYR 0.022 0.001 TYR G 185 PHE 0.012 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (26773) covalent geometry : angle 0.56197 / 0.29 (36442) hydrogen bonds : bond 0.03565 / 3.86 ( 1034) hydrogen bonds : angle 4.30604 / 4.54 ( 2879) metal coordination : bond 0.00667 / 0.63 ( 8) metal coordination : angle 2.31048 / 4.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 358 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9061 (m-80) cc_final: 0.8729 (m-10) REVERT: G 111 THR cc_start: 0.9128 (p) cc_final: 0.8870 (p) REVERT: H 28 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8931 (pt) REVERT: H 79 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8374 (mm) REVERT: H 80 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8177 (mt-10) REVERT: H 150 ARG cc_start: 0.6410 (mpt180) cc_final: 0.6006 (ptp90) REVERT: I 349 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8139 (mm-30) REVERT: I 434 ASP cc_start: 0.8070 (m-30) cc_final: 0.7571 (m-30) REVERT: I 459 MET cc_start: 0.8840 (mtp) cc_final: 0.8482 (mtp) REVERT: I 463 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: I 488 MET cc_start: 0.8396 (mmp) cc_final: 0.7427 (tpt) REVERT: I 930 ASP cc_start: 0.6973 (m-30) cc_final: 0.6749 (m-30) REVERT: I 976 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7772 (ttm-80) REVERT: I 1085 MET cc_start: 0.9150 (mmm) cc_final: 0.8846 (mmm) REVERT: I 1240 ASP cc_start: 0.8188 (p0) cc_final: 0.7897 (p0) REVERT: I 1265 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7706 (t80) REVERT: I 1290 MET cc_start: 0.8916 (mmt) cc_final: 0.8661 (mmt) REVERT: J 180 MET cc_start: 0.7536 (ttm) cc_final: 0.7105 (ttm) REVERT: J 219 LYS cc_start: 0.8518 (tppt) cc_final: 0.8250 (mmtp) REVERT: J 227 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: J 298 MET cc_start: 0.8017 (mmp) cc_final: 0.7648 (mmp) REVERT: J 560 ASN cc_start: 0.6863 (p0) cc_final: 0.6156 (p0) REVERT: J 644 MET cc_start: 0.8739 (mtt) cc_final: 0.8285 (mtt) REVERT: J 697 MET cc_start: 0.8541 (ttp) cc_final: 0.8197 (ttp) REVERT: J 698 MET cc_start: 0.7975 (tpt) cc_final: 0.7287 (tpt) REVERT: J 706 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7921 (m) REVERT: J 822 MET cc_start: 0.8970 (mmt) cc_final: 0.8608 (mmt) REVERT: J 1158 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6719 (tm-30) REVERT: J 1159 ILE cc_start: 0.9067 (tp) cc_final: 0.8733 (tp) outliers start: 108 outliers final: 83 residues processed: 438 average time/residue: 0.1593 time to fit residues: 113.5758 Evaluate side-chains 424 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 335 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 311 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 273 optimal weight: 2.9990 chunk 78 optimal weight: 0.0010 overall best weight: 2.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN I 673 HIS I1023 HIS J1098 GLN ** K 73 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 = 0.3525 r_free = 0.3525 target = 0.128393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.096306 restraints weight = 42207.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096163 restraints weight = 30083.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.096607 restraints weight = 24660.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097104 restraints weight = 20311.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097243 restraints weight = 18095.122| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26781 Z= 0.174 Angle : 0.593 13.632 36454 Z= 0.302 Chirality : 0.043 0.231 4176 Planarity : 0.004 0.099 4545 Dihedral : 14.359 175.813 4248 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.62 % Allowed : 16.30 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3174 helix: 0.99 (0.16), residues: 1111 sheet: -1.27 (0.27), residues: 403 loop : -1.60 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 779 TYR 0.022 0.001 TYR G 185 PHE 0.024 0.001 PHE I 230 TRP 0.004 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (26773) covalent geometry : angle 0.58962 / 0.30 (36442) hydrogen bonds : bond 0.03721 / 4.05 ( 1034) hydrogen bonds : angle 4.32748 / 4.61 ( 2879) metal coordination : bond 0.01698 / 1.37 ( 8) metal coordination : angle 3.51810 / 7.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 341 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9096 (m-80) cc_final: 0.8801 (m-10) REVERT: G 111 THR cc_start: 0.9140 (p) cc_final: 0.8883 (p) REVERT: H 28 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8967 (pt) REVERT: H 79 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8379 (mm) REVERT: I 357 ASN cc_start: 0.7851 (t0) cc_final: 0.7537 (t0) REVERT: I 434 ASP cc_start: 0.8187 (m-30) cc_final: 0.7693 (m-30) REVERT: I 459 MET cc_start: 0.8885 (mtp) cc_final: 0.8491 (mtp) REVERT: I 463 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: I 488 MET cc_start: 0.8464 (mmp) cc_final: 0.7464 (tpt) REVERT: I 930 ASP cc_start: 0.7014 (m-30) cc_final: 0.6793 (m-30) REVERT: I 976 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7647 (ttm-80) REVERT: I 1085 MET cc_start: 0.9127 (mmm) cc_final: 0.8789 (mmm) REVERT: I 1107 MET cc_start: 0.7792 (mtm) cc_final: 0.7558 (mtm) REVERT: I 1240 ASP cc_start: 0.8196 (p0) cc_final: 0.7903 (p0) REVERT: I 1265 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7842 (t80) REVERT: J 227 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: J 560 ASN cc_start: 0.6886 (p0) cc_final: 0.6189 (p0) REVERT: J 697 MET cc_start: 0.8612 (ttp) cc_final: 0.8237 (ttp) REVERT: J 698 MET cc_start: 0.7951 (tpt) cc_final: 0.7091 (tpt) REVERT: J 702 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6431 (pp30) REVERT: J 706 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (m) REVERT: J 822 MET cc_start: 0.8968 (mmt) cc_final: 0.8603 (mmt) REVERT: J 1158 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6779 (tm-30) REVERT: J 1159 ILE cc_start: 0.9120 (tp) cc_final: 0.8771 (tp) outliers start: 125 outliers final: 104 residues processed: 437 average time/residue: 0.1615 time to fit residues: 115.0960 Evaluate side-chains 439 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 328 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 211 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 185 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1023 HIS ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098309 restraints weight = 42457.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098627 restraints weight = 29775.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099279 restraints weight = 23607.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099675 restraints weight = 19187.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099750 restraints weight = 17739.303| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26781 Z= 0.112 Angle : 0.571 10.804 36454 Z= 0.291 Chirality : 0.043 0.290 4176 Planarity : 0.004 0.092 4545 Dihedral : 14.305 175.685 4248 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.14 % Allowed : 16.89 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3174 helix: 1.05 (0.16), residues: 1115 sheet: -1.16 (0.28), residues: 371 loop : -1.51 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 133 TYR 0.028 0.001 TYR J 723 PHE 0.014 0.001 PHE H 8 TRP 0.007 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (26773) covalent geometry : angle 0.56725 / 0.29 (36442) hydrogen bonds : bond 0.03490 / 3.77 ( 1034) hydrogen bonds : angle 4.22581 / 4.48 ( 2879) metal coordination : bond 0.00899 / 0.79 ( 8) metal coordination : angle 3.44915 / 7.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 362 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9113 (m-80) cc_final: 0.8831 (m-10) REVERT: G 111 THR cc_start: 0.9106 (p) cc_final: 0.8853 (p) REVERT: G 120 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6342 (p0) REVERT: G 212 ASP cc_start: 0.8107 (t70) cc_final: 0.7836 (t70) REVERT: H 28 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8919 (pt) REVERT: H 79 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8363 (mm) REVERT: H 150 ARG cc_start: 0.6287 (mpt180) cc_final: 0.5910 (ptp90) REVERT: I 357 ASN cc_start: 0.7834 (t0) cc_final: 0.7520 (t0) REVERT: I 434 ASP cc_start: 0.8060 (m-30) cc_final: 0.7568 (m-30) REVERT: I 463 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: I 488 MET cc_start: 0.8327 (mmp) cc_final: 0.7349 (tpt) REVERT: I 930 ASP cc_start: 0.6916 (m-30) cc_final: 0.6716 (m-30) REVERT: I 976 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7663 (ttm-80) REVERT: I 1085 MET cc_start: 0.9069 (mmm) cc_final: 0.8741 (mmm) REVERT: I 1240 ASP cc_start: 0.8207 (p0) cc_final: 0.7902 (p0) REVERT: I 1265 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7798 (t80) REVERT: J 180 MET cc_start: 0.7504 (ttm) cc_final: 0.6996 (ttm) REVERT: J 219 LYS cc_start: 0.8556 (tppt) cc_final: 0.8189 (mmtp) REVERT: J 227 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: J 560 ASN cc_start: 0.6785 (p0) cc_final: 0.6351 (p0) REVERT: J 643 ASP cc_start: 0.8522 (m-30) cc_final: 0.8213 (m-30) REVERT: J 697 MET cc_start: 0.8544 (ttp) cc_final: 0.8150 (ttp) REVERT: J 698 MET cc_start: 0.8256 (tpt) cc_final: 0.7294 (tpt) REVERT: J 702 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6182 (pp30) REVERT: J 706 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7944 (m) REVERT: J 822 MET cc_start: 0.8944 (mmt) cc_final: 0.8601 (mmt) REVERT: J 936 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6226 (m90) REVERT: J 1158 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6709 (tm-30) REVERT: J 1159 ILE cc_start: 0.9081 (tp) cc_final: 0.8754 (tp) outliers start: 112 outliers final: 88 residues processed: 445 average time/residue: 0.1634 time to fit residues: 118.1273 Evaluate side-chains 439 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 342 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 272 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1023 HIS K 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096231 restraints weight = 42473.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097797 restraints weight = 31810.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098265 restraints weight = 21872.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098585 restraints weight = 18335.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098658 restraints weight = 16660.850| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26781 Z= 0.150 Angle : 0.588 11.503 36454 Z= 0.299 Chirality : 0.043 0.230 4176 Planarity : 0.004 0.102 4545 Dihedral : 14.313 176.202 4244 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.33 % Allowed : 17.26 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3174 helix: 1.03 (0.16), residues: 1114 sheet: -1.16 (0.28), residues: 375 loop : -1.49 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 779 TYR 0.023 0.001 TYR G 185 PHE 0.019 0.001 PHE I 230 TRP 0.006 0.001 TRP J1193 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (26773) covalent geometry : angle 0.58495 / 0.30 (36442) hydrogen bonds : bond 0.03555 / 3.85 ( 1034) hydrogen bonds : angle 4.23160 / 4.51 ( 2879) metal coordination : bond 0.01014 / 0.90 ( 8) metal coordination : angle 3.13909 / 6.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 342 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9127 (m-80) cc_final: 0.8903 (m-10) REVERT: G 111 THR cc_start: 0.9112 (p) cc_final: 0.8860 (p) REVERT: G 120 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6373 (p0) REVERT: H 79 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8373 (mm) REVERT: H 150 ARG cc_start: 0.6311 (mpt180) cc_final: 0.5918 (ptp90) REVERT: I 357 ASN cc_start: 0.7819 (t0) cc_final: 0.7504 (t0) REVERT: I 434 ASP cc_start: 0.8063 (m-30) cc_final: 0.7590 (m-30) REVERT: I 463 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: I 488 MET cc_start: 0.8322 (mmp) cc_final: 0.7334 (tpt) REVERT: I 976 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7685 (ttm-80) REVERT: I 1085 MET cc_start: 0.9190 (mmm) cc_final: 0.8851 (mmm) REVERT: I 1240 ASP cc_start: 0.8238 (p0) cc_final: 0.7964 (p0) REVERT: I 1265 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7793 (t80) REVERT: J 180 MET cc_start: 0.7629 (ttm) cc_final: 0.7096 (ttm) REVERT: J 219 LYS cc_start: 0.8569 (tppt) cc_final: 0.8280 (mmtp) REVERT: J 227 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: J 560 ASN cc_start: 0.6750 (p0) cc_final: 0.6310 (p0) REVERT: J 643 ASP cc_start: 0.8566 (m-30) cc_final: 0.8237 (m-30) REVERT: J 697 MET cc_start: 0.8604 (ttp) cc_final: 0.8227 (ttp) REVERT: J 698 MET cc_start: 0.8014 (tpt) cc_final: 0.7089 (tpt) REVERT: J 702 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6383 (pp30) REVERT: J 706 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7920 (m) REVERT: J 822 MET cc_start: 0.8943 (mmt) cc_final: 0.8597 (mmt) REVERT: J 936 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6269 (m90) REVERT: J 1158 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6410 (tm-30) REVERT: J 1159 ILE cc_start: 0.9089 (tp) cc_final: 0.8514 (tp) outliers start: 117 outliers final: 97 residues processed: 430 average time/residue: 0.1673 time to fit residues: 116.4248 Evaluate side-chains 442 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 337 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 69 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 259 optimal weight: 0.0050 chunk 62 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1023 HIS K 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096852 restraints weight = 42385.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098723 restraints weight = 31436.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098876 restraints weight = 22317.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099276 restraints weight = 18641.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099309 restraints weight = 16609.752| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26781 Z= 0.134 Angle : 0.593 16.629 36454 Z= 0.301 Chirality : 0.043 0.229 4176 Planarity : 0.004 0.101 4545 Dihedral : 14.313 176.084 4244 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.03 % Allowed : 17.82 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3174 helix: 1.05 (0.16), residues: 1117 sheet: -1.17 (0.28), residues: 374 loop : -1.46 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 133 TYR 0.023 0.001 TYR G 185 PHE 0.018 0.001 PHE I 230 TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (26773) covalent geometry : angle 0.59057 / 0.30 (36442) hydrogen bonds : bond 0.03493 / 3.77 ( 1034) hydrogen bonds : angle 4.19563 / 4.47 ( 2879) metal coordination : bond 0.00885 / 0.79 ( 8) metal coordination : angle 3.00974 / 6.11 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 357 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9164 (m-80) cc_final: 0.8918 (m-10) REVERT: G 111 THR cc_start: 0.9092 (p) cc_final: 0.8842 (p) REVERT: G 120 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6377 (p0) REVERT: G 212 ASP cc_start: 0.8124 (t70) cc_final: 0.7836 (t70) REVERT: H 79 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8340 (mm) REVERT: H 142 MET cc_start: 0.7259 (pmm) cc_final: 0.6867 (ptp) REVERT: H 150 ARG cc_start: 0.6286 (mpt180) cc_final: 0.5912 (ptp90) REVERT: I 357 ASN cc_start: 0.7815 (t0) cc_final: 0.7503 (t0) REVERT: I 387 ASN cc_start: 0.8361 (m110) cc_final: 0.8072 (p0) REVERT: I 434 ASP cc_start: 0.8068 (m-30) cc_final: 0.7596 (m-30) REVERT: I 463 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: I 488 MET cc_start: 0.8317 (mmp) cc_final: 0.7306 (tpt) REVERT: I 976 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7665 (ttm-80) REVERT: I 1085 MET cc_start: 0.9188 (mmm) cc_final: 0.8861 (mmm) REVERT: I 1240 ASP cc_start: 0.8233 (p0) cc_final: 0.7959 (p0) REVERT: I 1265 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7852 (t80) REVERT: J 180 MET cc_start: 0.7613 (ttm) cc_final: 0.7100 (ttm) REVERT: J 219 LYS cc_start: 0.8566 (tppt) cc_final: 0.8277 (mmtp) REVERT: J 227 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: J 474 LEU cc_start: 0.9369 (tp) cc_final: 0.9106 (tp) REVERT: J 560 ASN cc_start: 0.6758 (p0) cc_final: 0.6323 (p0) REVERT: J 643 ASP cc_start: 0.8565 (m-30) cc_final: 0.8244 (m-30) REVERT: J 697 MET cc_start: 0.8588 (ttp) cc_final: 0.8195 (ttp) REVERT: J 698 MET cc_start: 0.8106 (tpt) cc_final: 0.7206 (tpt) REVERT: J 702 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.6347 (pp30) REVERT: J 706 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (m) REVERT: J 822 MET cc_start: 0.8932 (mmt) cc_final: 0.8558 (mmt) REVERT: J 936 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6273 (m90) REVERT: J 1158 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6735 (tm-30) REVERT: J 1159 ILE cc_start: 0.9087 (tp) cc_final: 0.8725 (tp) REVERT: J 1167 LYS cc_start: 0.5827 (tptt) cc_final: 0.5407 (mmmt) outliers start: 109 outliers final: 94 residues processed: 439 average time/residue: 0.1729 time to fit residues: 122.4029 Evaluate side-chains 438 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 336 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 311 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 268 optimal weight: 0.0040 chunk 2 optimal weight: 30.0000 chunk 148 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 132 HIS I1023 HIS K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096600 restraints weight = 42291.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098756 restraints weight = 31533.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098703 restraints weight = 22152.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099152 restraints weight = 18673.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.099131 restraints weight = 16578.684| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26781 Z= 0.144 Angle : 0.590 11.731 36454 Z= 0.301 Chirality : 0.043 0.307 4176 Planarity : 0.004 0.100 4545 Dihedral : 14.329 176.248 4243 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.18 % Allowed : 17.74 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3174 helix: 1.05 (0.16), residues: 1117 sheet: -1.15 (0.28), residues: 374 loop : -1.44 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 133 TYR 0.023 0.001 TYR G 185 PHE 0.018 0.001 PHE I 230 TRP 0.018 0.001 TRP J1193 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (26773) covalent geometry : angle 0.58810 / 0.30 (36442) hydrogen bonds : bond 0.03485 / 3.77 ( 1034) hydrogen bonds : angle 4.19659 / 4.49 ( 2879) metal coordination : bond 0.00971 / 0.87 ( 8) metal coordination : angle 2.97544 / 6.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.39 seconds wall clock time: 84 minutes 50.42 seconds (5090.42 seconds total)