Starting phenix.real_space_refine on Mon Jun 23 03:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eha_28145/06_2025/8eha_28145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eha_28145/06_2025/8eha_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_28145/06_2025/8eha_28145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eha_28145/06_2025/8eha_28145.map" model { file = "/net/cci-nas-00/data/ceres_data/8eha_28145/06_2025/8eha_28145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eha_28145/06_2025/8eha_28145.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: 13 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: 16.17, per 1000 atoms: 0.62 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: 6.45 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 11.29 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: 13.35 Time building geometry restraints manager: 7.64 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: 35927 2.08 - 4.16: 447 4.16 - 6.24: 50 6.24 - 8.32: 16 8.32 - 10.40: 2 Bond angle restraints: 36442 Sorted by residual: 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=" N ARG J 764 " pdb=" CA ARG J 764 " pdb=" C ARG J 764 " ideal model delta sigma weight residual 113.18 107.24 5.94 1.33e+00 5.65e-01 2.00e+01 angle pdb=" C VAL J 518 " pdb=" N ASN J 519 " pdb=" CA ASN J 519 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N GLN I 46 " pdb=" CA GLN I 46 " pdb=" C GLN I 46 " ideal model delta sigma weight residual 114.75 110.27 4.48 1.26e+00 6.30e-01 1.27e+01 angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 125.02 131.26 -6.24 1.76e+00 3.23e-01 1.26e+01 ... (remaining 36437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 15853 35.26 - 70.51: 518 70.51 - 105.77: 27 105.77 - 141.03: 2 141.03 - 176.29: 2 Dihedral angle restraints: 16402 sinusoidal: 7251 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 16399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3863 0.082 - 0.163: 308 0.163 - 0.245: 3 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: 1.430 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: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 78.320 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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= 0.228 Angle : 0.616 10.396 36454 Z= 0.340 Chirality : 0.043 0.409 4176 Planarity : 0.004 0.085 4545 Dihedral : 15.479 176.286 10518 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (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 TRP 0.009 0.001 TRP J 580 HIS 0.005 0.001 HIS G 23 PHE 0.013 0.001 PHE I 514 TYR 0.013 0.001 TYR J 723 ARG 0.005 0.000 ARG J 709 Details of bonding type rmsd hydrogen bonds : bond 0.17953 ( 1034) hydrogen bonds : angle 6.63642 ( 2879) metal coordination : bond 0.00632 ( 8) metal coordination : angle 1.69266 ( 12) covalent geometry : bond 0.00480 (26773) covalent geometry : angle 0.61532 (36442) *********************** 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 : 2.845 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: 0.8289 (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: 0.3819 time to fit residues: 307.9500 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 : 3.006 ------------------------------------------------------------------------------- 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 271 optimal weight: 30.0000 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 187 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS H 103 ASN ** I 494 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097557 restraints weight = 42384.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097816 restraints weight = 25865.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098289 restraints weight = 22154.998| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26781 Z= 0.126 Angle : 0.561 8.574 36454 Z= 0.291 Chirality : 0.042 0.209 4176 Planarity : 0.004 0.083 4545 Dihedral : 15.036 176.440 4391 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.44 % Allowed : 12.79 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3174 helix: 0.63 (0.16), residues: 1119 sheet: -1.38 (0.27), residues: 384 loop : -1.73 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.009 0.001 HIS I1023 PHE 0.013 0.001 PHE I 405 TYR 0.014 0.001 TYR G 152 ARG 0.008 0.000 ARG I 272 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1034) hydrogen bonds : angle 4.74796 ( 2879) metal coordination : bond 0.01366 ( 8) metal coordination : angle 3.33609 ( 12) covalent geometry : bond 0.00276 (26773) covalent geometry : angle 0.55801 (36442) *********************** 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 478 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 385 time to evaluate : 3.172 Fit side-chains revert: symmetry clash REVERT: G 50 SER cc_start: 0.9243 (m) cc_final: 0.8860 (p) REVERT: G 111 THR cc_start: 0.9186 (p) cc_final: 0.8933 (p) REVERT: G 202 VAL cc_start: 0.9495 (t) cc_final: 0.9248 (p) REVERT: H 102 LEU cc_start: 0.8429 (tp) cc_final: 0.8201 (tp) REVERT: H 150 ARG cc_start: 0.6545 (mpt180) cc_final: 0.5833 (mtm180) REVERT: I 39 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9085 (tp) REVERT: I 195 PHE cc_start: 0.8181 (m-10) cc_final: 0.7810 (m-10) REVERT: I 369 MET cc_start: 0.8254 (tmm) cc_final: 0.7977 (tmm) REVERT: I 423 ASP cc_start: 0.7525 (p0) cc_final: 0.7109 (p0) REVERT: I 434 ASP cc_start: 0.8179 (m-30) cc_final: 0.7705 (m-30) REVERT: I 459 MET cc_start: 0.8906 (mtp) cc_final: 0.8514 (mtp) REVERT: I 463 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: I 488 MET cc_start: 0.8305 (mmp) cc_final: 0.7572 (mmm) REVERT: I 930 ASP cc_start: 0.6974 (m-30) cc_final: 0.6734 (m-30) REVERT: I 997 TRP cc_start: 0.6752 (m100) cc_final: 0.5961 (m100) REVERT: I 1085 MET cc_start: 0.8955 (mmm) cc_final: 0.8503 (mmp) REVERT: I 1240 ASP cc_start: 0.8097 (p0) cc_final: 0.7846 (p0) REVERT: I 1290 MET cc_start: 0.8855 (mmt) cc_final: 0.8510 (mmp) REVERT: J 49 PHE cc_start: 0.7806 (m-80) cc_final: 0.7600 (m-10) REVERT: J 227 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: J 299 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8877 (tp) REVERT: J 644 MET cc_start: 0.8754 (mtt) cc_final: 0.8132 (mtt) REVERT: J 697 MET cc_start: 0.8643 (ttp) cc_final: 0.8336 (ttp) REVERT: J 698 MET cc_start: 0.7830 (tpt) cc_final: 0.7138 (tpt) REVERT: J 706 VAL cc_start: 0.8086 (m) cc_final: 0.7824 (m) REVERT: J 743 MET cc_start: 0.8953 (ptm) cc_final: 0.8725 (ptp) REVERT: J 806 ASP cc_start: 0.7732 (p0) cc_final: 0.7502 (p0) REVERT: J 822 MET cc_start: 0.8978 (mmt) cc_final: 0.8642 (mmt) REVERT: J 1158 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6593 (tm-30) REVERT: J 1159 ILE cc_start: 0.9212 (tp) cc_final: 0.8947 (tp) outliers start: 93 outliers final: 66 residues processed: 457 average time/residue: 0.3599 time to fit residues: 266.0751 Evaluate side-chains 408 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 3.041 ------------------------------------------------------------------------------- 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 192 VAL 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 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 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 319 LEU 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 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 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1178 LYS 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 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 728 SER 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 909 ILE Chi-restraints excluded: chain J residue 980 THR 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 229 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN I1023 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095496 restraints weight = 42406.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097048 restraints weight = 30851.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097079 restraints weight = 23721.632| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26781 Z= 0.165 Angle : 0.565 9.486 36454 Z= 0.292 Chirality : 0.042 0.176 4176 Planarity : 0.004 0.089 4545 Dihedral : 14.728 176.400 4364 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.58 % Allowed : 13.53 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3174 helix: 0.77 (0.16), residues: 1123 sheet: -1.44 (0.26), residues: 402 loop : -1.68 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.006 0.001 HIS I1023 PHE 0.015 0.001 PHE I 405 TYR 0.018 0.001 TYR G 152 ARG 0.006 0.000 ARG I 779 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1034) hydrogen bonds : angle 4.47958 ( 2879) metal coordination : bond 0.01090 ( 8) metal coordination : angle 2.89235 ( 12) covalent geometry : bond 0.00377 (26773) covalent geometry : angle 0.56305 (36442) *********************** 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 482 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 358 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9077 (m-80) cc_final: 0.8753 (m-10) REVERT: G 111 THR cc_start: 0.9142 (p) cc_final: 0.8886 (p) REVERT: G 120 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6324 (p0) REVERT: G 202 VAL cc_start: 0.9468 (t) cc_final: 0.9190 (p) REVERT: G 212 ASP cc_start: 0.8086 (t70) cc_final: 0.7830 (t70) REVERT: H 79 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8387 (mm) REVERT: H 102 LEU cc_start: 0.8144 (tp) cc_final: 0.7900 (tp) REVERT: I 68 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (tp) REVERT: I 184 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9081 (tt) REVERT: I 195 PHE cc_start: 0.8255 (m-10) cc_final: 0.7981 (m-10) REVERT: I 423 ASP cc_start: 0.7419 (p0) cc_final: 0.7063 (p0) REVERT: I 434 ASP cc_start: 0.8120 (m-30) cc_final: 0.7646 (m-30) REVERT: I 459 MET cc_start: 0.8913 (mtp) cc_final: 0.8510 (mtp) REVERT: I 463 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: I 488 MET cc_start: 0.8343 (mmp) cc_final: 0.7359 (tpt) REVERT: I 930 ASP cc_start: 0.7030 (m-30) cc_final: 0.6781 (m-30) REVERT: I 976 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7777 (ttm-80) REVERT: I 1085 MET cc_start: 0.9188 (mmm) cc_final: 0.8973 (mmm) REVERT: I 1107 MET cc_start: 0.7751 (mtm) cc_final: 0.7492 (mtm) REVERT: I 1240 ASP cc_start: 0.8254 (p0) cc_final: 0.7946 (p0) REVERT: I 1265 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7836 (t80) REVERT: I 1290 MET cc_start: 0.8860 (mmt) cc_final: 0.8515 (mmt) REVERT: J 49 PHE cc_start: 0.7704 (m-80) cc_final: 0.7500 (m-10) REVERT: J 227 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: J 560 ASN cc_start: 0.6543 (p0) cc_final: 0.6341 (p0) REVERT: J 644 MET cc_start: 0.8822 (mtt) cc_final: 0.8316 (mtt) REVERT: J 698 MET cc_start: 0.7891 (tpt) cc_final: 0.7155 (tpt) REVERT: J 706 VAL cc_start: 0.8150 (m) cc_final: 0.7922 (m) REVERT: J 806 ASP cc_start: 0.7772 (p0) cc_final: 0.7568 (p0) REVERT: J 822 MET cc_start: 0.8974 (mmt) cc_final: 0.8624 (mmt) REVERT: J 832 LYS cc_start: 0.6673 (mmtm) cc_final: 0.6372 (mmtt) REVERT: J 1158 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6611 (tm-30) REVERT: J 1159 ILE cc_start: 0.9129 (tp) cc_final: 0.8784 (tp) outliers start: 124 outliers final: 87 residues processed: 450 average time/residue: 0.3644 time to fit residues: 265.2266 Evaluate side-chains 420 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 326 time to evaluate : 3.087 ------------------------------------------------------------------------------- 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 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 27 THR 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 181 GLU 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 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 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 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 782 VAL 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 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 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 526 VAL 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 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 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 46 THR Chi-restraints excluded: chain K residue 55 GLU 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 234 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN G 93 GLN G 128 HIS I 673 HIS I1017 GLN I1023 HIS J 424 ASN ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.095159 restraints weight = 42611.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096869 restraints weight = 31027.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097333 restraints weight = 20612.496| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26781 Z= 0.173 Angle : 0.575 9.664 36454 Z= 0.296 Chirality : 0.042 0.172 4176 Planarity : 0.004 0.088 4545 Dihedral : 14.708 177.435 4364 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.92 % Allowed : 15.08 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3174 helix: 0.79 (0.16), residues: 1129 sheet: -1.37 (0.27), residues: 402 loop : -1.66 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.006 0.001 HIS I1023 PHE 0.015 0.001 PHE I 405 TYR 0.020 0.001 TYR G 152 ARG 0.006 0.000 ARG I 779 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1034) hydrogen bonds : angle 4.40304 ( 2879) metal coordination : bond 0.01054 ( 8) metal coordination : angle 2.53338 ( 12) covalent geometry : bond 0.00398 (26773) covalent geometry : angle 0.57350 (36442) *********************** 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: 133 poor density : 344 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9099 (mtmm) cc_final: 0.8821 (ptpp) REVERT: G 68 TYR cc_start: 0.9094 (m-80) cc_final: 0.8817 (m-10) REVERT: G 111 THR cc_start: 0.9129 (p) cc_final: 0.8876 (p) REVERT: G 120 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6252 (p0) REVERT: G 202 VAL cc_start: 0.9469 (t) cc_final: 0.9218 (p) REVERT: H 28 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8950 (pt) REVERT: H 79 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8378 (mm) REVERT: H 80 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8130 (mt-10) REVERT: H 102 LEU cc_start: 0.7839 (tp) cc_final: 0.7590 (tp) REVERT: I 184 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9087 (tt) REVERT: I 423 ASP cc_start: 0.7420 (p0) cc_final: 0.7041 (p0) REVERT: I 434 ASP cc_start: 0.8115 (m-30) cc_final: 0.7661 (m-30) REVERT: I 459 MET cc_start: 0.8852 (mtp) cc_final: 0.8449 (mtp) REVERT: I 463 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: I 488 MET cc_start: 0.8409 (mmp) cc_final: 0.7412 (tpt) REVERT: I 930 ASP cc_start: 0.7032 (m-30) cc_final: 0.6795 (m-30) REVERT: I 976 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7772 (ttm-80) REVERT: I 1085 MET cc_start: 0.9181 (mmm) cc_final: 0.8892 (mmm) REVERT: I 1107 MET cc_start: 0.7753 (mtm) cc_final: 0.7519 (mtm) REVERT: I 1230 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8903 (ttp) REVERT: I 1240 ASP cc_start: 0.8227 (p0) cc_final: 0.7944 (p0) REVERT: I 1265 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7988 (t80) REVERT: I 1290 MET cc_start: 0.8830 (mmt) cc_final: 0.8597 (mmt) REVERT: J 227 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: J 560 ASN cc_start: 0.6717 (p0) cc_final: 0.6514 (p0) REVERT: J 644 MET cc_start: 0.8828 (mtt) cc_final: 0.8392 (mtt) REVERT: J 697 MET cc_start: 0.8798 (ttp) cc_final: 0.8271 (ttp) REVERT: J 698 MET cc_start: 0.7871 (tpt) cc_final: 0.7007 (tpt) REVERT: J 702 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.6357 (pp30) REVERT: J 706 VAL cc_start: 0.8138 (m) cc_final: 0.7909 (m) REVERT: J 822 MET cc_start: 0.8972 (mmt) cc_final: 0.8600 (mmt) REVERT: J 1158 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6286 (tm-30) REVERT: J 1159 ILE cc_start: 0.9170 (tp) cc_final: 0.8554 (tp) REVERT: J 1188 GLU cc_start: 0.6179 (tp30) cc_final: 0.5637 (tm-30) outliers start: 133 outliers final: 103 residues processed: 443 average time/residue: 0.3785 time to fit residues: 274.3972 Evaluate side-chains 445 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 333 time to evaluate : 3.199 ------------------------------------------------------------------------------- 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 192 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU 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 181 GLU 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 144 VAL 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 221 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 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 561 ILE 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 802 VAL 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 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1230 MET 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 22 ILE 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 151 MET 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 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 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 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 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 46 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 110 optimal weight: 5.9990 chunk 232 optimal weight: 0.0470 chunk 174 optimal weight: 0.9980 chunk 297 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS J1098 GLN ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096897 restraints weight = 42399.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095893 restraints weight = 29170.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096515 restraints weight = 26271.380| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26781 Z= 0.139 Angle : 0.550 12.056 36454 Z= 0.284 Chirality : 0.042 0.180 4176 Planarity : 0.004 0.085 4545 Dihedral : 14.644 177.327 4364 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.73 % Allowed : 15.67 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3174 helix: 0.97 (0.16), residues: 1118 sheet: -1.20 (0.28), residues: 376 loop : -1.62 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.007 0.001 HIS I1023 PHE 0.013 0.001 PHE I 405 TYR 0.021 0.001 TYR G 152 ARG 0.004 0.000 ARG J1174 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 1034) hydrogen bonds : angle 4.26838 ( 2879) metal coordination : bond 0.00855 ( 8) metal coordination : angle 2.25803 ( 12) covalent geometry : bond 0.00319 (26773) covalent geometry : angle 0.54848 (36442) *********************** 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 495 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 367 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8839 (ptpp) REVERT: G 68 TYR cc_start: 0.9117 (m-80) cc_final: 0.8863 (m-10) REVERT: G 111 THR cc_start: 0.9120 (p) cc_final: 0.8867 (p) REVERT: G 120 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6398 (p0) REVERT: G 202 VAL cc_start: 0.9457 (t) cc_final: 0.9190 (p) REVERT: G 212 ASP cc_start: 0.8096 (t70) cc_final: 0.7814 (t70) REVERT: H 79 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8372 (mm) REVERT: H 80 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8196 (mt-10) REVERT: I 184 LEU cc_start: 0.9450 (tp) cc_final: 0.9065 (tt) REVERT: I 387 ASN cc_start: 0.8364 (m110) cc_final: 0.7955 (p0) REVERT: I 434 ASP cc_start: 0.8158 (m-30) cc_final: 0.7678 (m-30) REVERT: I 459 MET cc_start: 0.8851 (mtp) cc_final: 0.8513 (mtp) REVERT: I 463 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: I 488 MET cc_start: 0.8391 (mmp) cc_final: 0.7404 (tpt) REVERT: I 930 ASP cc_start: 0.7017 (m-30) cc_final: 0.6798 (m-30) REVERT: I 976 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7764 (ttm-80) REVERT: I 1085 MET cc_start: 0.9166 (mmm) cc_final: 0.8857 (mmm) REVERT: I 1230 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8919 (ttp) REVERT: I 1240 ASP cc_start: 0.8283 (p0) cc_final: 0.8025 (p0) REVERT: I 1265 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.8003 (t80) REVERT: I 1290 MET cc_start: 0.8712 (mmt) cc_final: 0.8435 (mmt) REVERT: J 227 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: J 643 ASP cc_start: 0.8595 (m-30) cc_final: 0.8260 (m-30) REVERT: J 644 MET cc_start: 0.8767 (mtt) cc_final: 0.8308 (mtt) REVERT: J 697 MET cc_start: 0.8790 (ttp) cc_final: 0.8256 (ttp) REVERT: J 698 MET cc_start: 0.7931 (tpt) cc_final: 0.7060 (tpt) REVERT: J 702 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.6334 (pp30) REVERT: J 706 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (m) REVERT: J 822 MET cc_start: 0.8962 (mmt) cc_final: 0.8570 (mmt) REVERT: J 1158 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6559 (tm-30) REVERT: J 1159 ILE cc_start: 0.9193 (tp) cc_final: 0.8852 (tp) outliers start: 128 outliers final: 96 residues processed: 458 average time/residue: 0.3897 time to fit residues: 288.4032 Evaluate side-chains 441 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 337 time to evaluate : 3.253 ------------------------------------------------------------------------------- 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 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 181 GLU 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 103 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 144 VAL 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 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 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 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 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 802 VAL 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 1230 MET 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 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 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 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 807 LEU Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 825 VAL 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 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 162 optimal weight: 0.0070 chunk 251 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 224 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 chunk 196 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN I1023 HIS ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100158 restraints weight = 42053.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100355 restraints weight = 31303.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100912 restraints weight = 24152.417| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26781 Z= 0.099 Angle : 0.538 9.614 36454 Z= 0.276 Chirality : 0.041 0.211 4176 Planarity : 0.004 0.081 4545 Dihedral : 14.534 177.075 4362 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.21 % Allowed : 16.67 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3174 helix: 1.14 (0.16), residues: 1117 sheet: -1.00 (0.29), residues: 365 loop : -1.52 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 33 HIS 0.008 0.001 HIS I1023 PHE 0.016 0.001 PHE I 385 TYR 0.017 0.001 TYR G 152 ARG 0.006 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 1034) hydrogen bonds : angle 4.06359 ( 2879) metal coordination : bond 0.00984 ( 8) metal coordination : angle 2.20006 ( 12) covalent geometry : bond 0.00217 (26773) covalent geometry : angle 0.53623 (36442) *********************** 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 510 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 396 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9049 (mtmm) cc_final: 0.8824 (ptpp) REVERT: G 68 TYR cc_start: 0.9071 (m-80) cc_final: 0.8751 (m-10) REVERT: G 111 THR cc_start: 0.9067 (p) cc_final: 0.8816 (p) REVERT: G 202 VAL cc_start: 0.9399 (t) cc_final: 0.9123 (p) REVERT: H 79 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8329 (mm) REVERT: H 150 ARG cc_start: 0.6374 (mpt180) cc_final: 0.6149 (ptp90) REVERT: I 197 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7417 (mtp180) REVERT: I 434 ASP cc_start: 0.7985 (m-30) cc_final: 0.7527 (m-30) REVERT: I 463 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: I 488 MET cc_start: 0.8190 (mmp) cc_final: 0.7330 (tpt) REVERT: I 766 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8152 (p0) REVERT: I 1085 MET cc_start: 0.9047 (mmm) cc_final: 0.8769 (mmm) REVERT: I 1188 ASP cc_start: 0.8003 (t70) cc_final: 0.7566 (t70) REVERT: I 1240 ASP cc_start: 0.8260 (p0) cc_final: 0.7947 (p0) REVERT: I 1265 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7688 (t80) REVERT: I 1290 MET cc_start: 0.8862 (mmt) cc_final: 0.8463 (mmp) REVERT: J 180 MET cc_start: 0.7289 (ttm) cc_final: 0.6853 (ttm) REVERT: J 219 LYS cc_start: 0.8429 (tppt) cc_final: 0.8049 (mmtp) REVERT: J 227 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: J 560 ASN cc_start: 0.6810 (p0) cc_final: 0.6185 (p0) REVERT: J 644 MET cc_start: 0.8648 (mtt) cc_final: 0.8135 (mtt) REVERT: J 698 MET cc_start: 0.8208 (tpt) cc_final: 0.7150 (tpt) REVERT: J 702 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.6264 (pp30) REVERT: J 706 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8112 (m) REVERT: J 822 MET cc_start: 0.8974 (mmt) cc_final: 0.8643 (mmt) REVERT: J 832 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6346 (mmtm) REVERT: J 936 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6341 (m90) REVERT: J 1158 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6576 (tm-30) REVERT: J 1159 ILE cc_start: 0.9087 (tp) cc_final: 0.8724 (tp) REVERT: J 1188 GLU cc_start: 0.6015 (tp30) cc_final: 0.5473 (tm-30) outliers start: 114 outliers final: 75 residues processed: 479 average time/residue: 0.4629 time to fit residues: 357.8469 Evaluate side-chains 431 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 348 time to evaluate : 3.756 ------------------------------------------------------------------------------- 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 176 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR 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 103 VAL 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 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 538 LEU 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 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 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 1101 LEU Chi-restraints excluded: chain I residue 1178 LYS 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 J residue 90 VAL 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 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 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 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 728 SER 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 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 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 85 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 134 optimal weight: 0.0570 chunk 93 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN H 227 GLN I1023 HIS ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099006 restraints weight = 42269.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099636 restraints weight = 25664.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099810 restraints weight = 20854.023| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26781 Z= 0.115 Angle : 0.560 12.027 36454 Z= 0.284 Chirality : 0.042 0.234 4176 Planarity : 0.004 0.096 4545 Dihedral : 14.466 177.590 4350 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.14 % Allowed : 17.49 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3174 helix: 1.20 (0.16), residues: 1119 sheet: -0.93 (0.29), residues: 353 loop : -1.43 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 PHE 0.017 0.001 PHE H 8 TYR 0.022 0.001 TYR G 152 ARG 0.007 0.000 ARG I 976 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 1034) hydrogen bonds : angle 4.02629 ( 2879) metal coordination : bond 0.00721 ( 8) metal coordination : angle 2.97636 ( 12) covalent geometry : bond 0.00262 (26773) covalent geometry : angle 0.55744 (36442) *********************** 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 463 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 351 time to evaluate : 7.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8844 (ptpp) REVERT: G 68 TYR cc_start: 0.9170 (m-80) cc_final: 0.8907 (m-10) REVERT: G 111 THR cc_start: 0.9067 (p) cc_final: 0.8805 (p) REVERT: G 120 ASP cc_start: 0.6959 (p0) cc_final: 0.6480 (p0) REVERT: G 202 VAL cc_start: 0.9411 (t) cc_final: 0.9131 (p) REVERT: H 79 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8330 (mm) REVERT: H 95 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6631 (mtmt) REVERT: H 150 ARG cc_start: 0.6218 (mpt180) cc_final: 0.5977 (ptp90) REVERT: I 197 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7445 (mtp85) REVERT: I 357 ASN cc_start: 0.7781 (t0) cc_final: 0.7483 (t0) REVERT: I 434 ASP cc_start: 0.8170 (m-30) cc_final: 0.7661 (m-30) REVERT: I 463 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: I 488 MET cc_start: 0.8212 (mmp) cc_final: 0.7259 (tpt) REVERT: I 997 TRP cc_start: 0.7270 (m100) cc_final: 0.6216 (m100) REVERT: I 1085 MET cc_start: 0.9129 (mmm) cc_final: 0.8830 (mmm) REVERT: I 1240 ASP cc_start: 0.8288 (p0) cc_final: 0.7986 (p0) REVERT: I 1265 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7765 (t80) REVERT: J 219 LYS cc_start: 0.8517 (tppt) cc_final: 0.8172 (mmtp) REVERT: J 227 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: J 560 ASN cc_start: 0.6886 (p0) cc_final: 0.6531 (p0) REVERT: J 644 MET cc_start: 0.8661 (mtt) cc_final: 0.8176 (mtt) REVERT: J 698 MET cc_start: 0.8163 (tpt) cc_final: 0.7100 (tpt) REVERT: J 702 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.6333 (pp30) REVERT: J 706 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (m) REVERT: J 822 MET cc_start: 0.8992 (mmt) cc_final: 0.8650 (mmt) REVERT: J 936 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6249 (m90) REVERT: J 1158 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6608 (tm-30) REVERT: J 1159 ILE cc_start: 0.9127 (tp) cc_final: 0.8746 (tp) REVERT: K 35 LYS cc_start: 0.8071 (mttp) cc_final: 0.7724 (mttp) outliers start: 112 outliers final: 88 residues processed: 435 average time/residue: 0.5187 time to fit residues: 372.0006 Evaluate side-chains 433 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 338 time to evaluate : 4.891 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR 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 91 THR Chi-restraints excluded: chain I residue 103 VAL 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 356 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN 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 641 GLU 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 765 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 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 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 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 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 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 491 LEU 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 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 728 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 286 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN I 554 HIS ** I 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093604 restraints weight = 42795.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.093619 restraints weight = 30029.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.094234 restraints weight = 24553.246| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26781 Z= 0.257 Angle : 0.665 14.336 36454 Z= 0.338 Chirality : 0.045 0.209 4176 Planarity : 0.005 0.095 4545 Dihedral : 14.705 179.621 4348 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.55 % Allowed : 17.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3174 helix: 0.93 (0.16), residues: 1125 sheet: -1.18 (0.28), residues: 385 loop : -1.51 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 183 HIS 0.008 0.001 HIS I 554 PHE 0.016 0.002 PHE H 8 TYR 0.030 0.002 TYR J 723 ARG 0.009 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1034) hydrogen bonds : angle 4.36447 ( 2879) metal coordination : bond 0.01680 ( 8) metal coordination : angle 3.08978 ( 12) covalent geometry : bond 0.00599 (26773) covalent geometry : angle 0.66316 (36442) *********************** 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 449 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 326 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 111 THR cc_start: 0.9168 (p) cc_final: 0.8914 (p) REVERT: G 202 VAL cc_start: 0.9475 (t) cc_final: 0.9233 (p) REVERT: H 79 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8412 (mm) REVERT: H 95 LYS cc_start: 0.7019 (mtpt) cc_final: 0.6779 (mtmt) REVERT: I 184 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9096 (tt) REVERT: I 357 ASN cc_start: 0.7898 (t0) cc_final: 0.7633 (t0) REVERT: I 434 ASP cc_start: 0.8113 (m-30) cc_final: 0.7691 (m-30) REVERT: I 463 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: I 488 MET cc_start: 0.8352 (mmp) cc_final: 0.7355 (tpt) REVERT: I 997 TRP cc_start: 0.7539 (m100) cc_final: 0.6360 (m100) REVERT: I 1085 MET cc_start: 0.9071 (mmm) cc_final: 0.8656 (mmm) REVERT: I 1230 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8826 (ttp) REVERT: I 1240 ASP cc_start: 0.8280 (p0) cc_final: 0.8046 (p0) REVERT: J 180 MET cc_start: 0.7685 (ttm) cc_final: 0.7137 (ttm) REVERT: J 227 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: J 560 ASN cc_start: 0.6755 (p0) cc_final: 0.6378 (p0) REVERT: J 644 MET cc_start: 0.8807 (mtt) cc_final: 0.8386 (mtt) REVERT: J 698 MET cc_start: 0.7908 (tpt) cc_final: 0.7060 (tpt) REVERT: J 702 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.6598 (pp30) REVERT: J 783 LEU cc_start: 0.9436 (mt) cc_final: 0.9014 (mp) REVERT: J 822 MET cc_start: 0.8916 (mmt) cc_final: 0.8605 (mmt) REVERT: J 936 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6415 (m90) REVERT: J 1158 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6363 (tm-30) REVERT: J 1159 ILE cc_start: 0.9124 (tp) cc_final: 0.8581 (tp) outliers start: 123 outliers final: 92 residues processed: 421 average time/residue: 0.3682 time to fit residues: 249.4958 Evaluate side-chains 415 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 316 time to evaluate : 3.152 ------------------------------------------------------------------------------- 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 101 THR 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 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR 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 211 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 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 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 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 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 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 802 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 72 CYS 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 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 414 GLU 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 573 THR 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 728 SER 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 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 46 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 249 optimal weight: 0.0170 chunk 317 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN I1023 HIS J1098 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097075 restraints weight = 42297.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096966 restraints weight = 27179.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097336 restraints weight = 23109.878| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2008 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= 0.126 Angle : 0.584 10.796 36454 Z= 0.295 Chirality : 0.042 0.333 4176 Planarity : 0.004 0.093 4545 Dihedral : 14.584 178.053 4342 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.55 % Allowed : 18.45 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3174 helix: 1.10 (0.16), residues: 1130 sheet: -1.02 (0.29), residues: 367 loop : -1.45 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.009 0.001 HIS I1023 PHE 0.014 0.001 PHE I 812 TYR 0.026 0.001 TYR J 723 ARG 0.008 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 1034) hydrogen bonds : angle 4.16799 ( 2879) metal coordination : bond 0.00843 ( 8) metal coordination : angle 2.80901 ( 12) covalent geometry : bond 0.00291 (26773) covalent geometry : angle 0.58192 (36442) *********************** 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 434 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 338 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8871 (ptpp) REVERT: G 111 THR cc_start: 0.9101 (p) cc_final: 0.8865 (p) REVERT: G 120 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6371 (p0) REVERT: G 202 VAL cc_start: 0.9450 (t) cc_final: 0.9181 (p) REVERT: H 79 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8349 (mm) REVERT: H 95 LYS cc_start: 0.7119 (mtpt) cc_final: 0.6847 (mtmt) REVERT: H 150 ARG cc_start: 0.6430 (mpt180) cc_final: 0.6129 (ptp90) REVERT: I 357 ASN cc_start: 0.8032 (t0) cc_final: 0.7735 (t0) REVERT: I 434 ASP cc_start: 0.8092 (m-30) cc_final: 0.7801 (m-30) REVERT: I 463 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: I 488 MET cc_start: 0.8335 (mmp) cc_final: 0.7326 (tpt) REVERT: I 997 TRP cc_start: 0.7608 (m100) cc_final: 0.6405 (m100) REVERT: I 1085 MET cc_start: 0.9117 (mmm) cc_final: 0.8774 (mmm) REVERT: I 1240 ASP cc_start: 0.8280 (p0) cc_final: 0.8027 (p0) REVERT: J 180 MET cc_start: 0.7614 (ttm) cc_final: 0.7041 (ttm) REVERT: J 227 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: J 474 LEU cc_start: 0.9266 (tp) cc_final: 0.9027 (tp) REVERT: J 560 ASN cc_start: 0.6797 (p0) cc_final: 0.6144 (p0) REVERT: J 644 MET cc_start: 0.8627 (mtt) cc_final: 0.8158 (mtt) REVERT: J 698 MET cc_start: 0.8185 (tpt) cc_final: 0.7268 (tpt) REVERT: J 702 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6247 (pp30) REVERT: J 822 MET cc_start: 0.8984 (mmt) cc_final: 0.8657 (mmt) REVERT: J 936 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6363 (m90) REVERT: J 1158 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6564 (tm-30) REVERT: J 1159 ILE cc_start: 0.9184 (tp) cc_final: 0.8770 (tp) outliers start: 96 outliers final: 82 residues processed: 406 average time/residue: 0.4766 time to fit residues: 318.3950 Evaluate side-chains 407 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 319 time to evaluate : 3.445 ------------------------------------------------------------------------------- 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 H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR 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 211 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 103 VAL 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 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 336 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 547 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 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 802 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1178 LYS Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1264 GLN 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 227 PHE 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 573 THR 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 728 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 211 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 210 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 277 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097305 restraints weight = 42215.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098205 restraints weight = 25052.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098627 restraints weight = 19986.611| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2067 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= 0.128 Angle : 0.594 14.563 36454 Z= 0.299 Chirality : 0.042 0.278 4176 Planarity : 0.004 0.093 4545 Dihedral : 14.542 178.030 4340 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.51 % Allowed : 18.82 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3174 helix: 1.15 (0.16), residues: 1130 sheet: -0.93 (0.29), residues: 364 loop : -1.41 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.009 0.001 HIS I1023 PHE 0.020 0.001 PHE I 812 TYR 0.025 0.001 TYR G 152 ARG 0.008 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1034) hydrogen bonds : angle 4.13768 ( 2879) metal coordination : bond 0.00808 ( 8) metal coordination : angle 2.56368 ( 12) covalent geometry : bond 0.00297 (26773) covalent geometry : angle 0.59216 (36442) ********************** 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 423 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 328 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8855 (ptpp) REVERT: G 111 THR cc_start: 0.9091 (p) cc_final: 0.8848 (p) REVERT: G 120 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6380 (p0) REVERT: G 202 VAL cc_start: 0.9430 (t) cc_final: 0.9158 (p) REVERT: H 79 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8261 (mm) REVERT: H 150 ARG cc_start: 0.6433 (mpt180) cc_final: 0.6130 (ptp90) REVERT: I 197 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7449 (mtp180) REVERT: I 357 ASN cc_start: 0.7949 (t0) cc_final: 0.7706 (t0) REVERT: I 434 ASP cc_start: 0.8133 (m-30) cc_final: 0.7845 (m-30) REVERT: I 463 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: I 488 MET cc_start: 0.8279 (mmp) cc_final: 0.7236 (tpt) REVERT: I 997 TRP cc_start: 0.7588 (m100) cc_final: 0.6361 (m100) REVERT: I 1085 MET cc_start: 0.9119 (mmm) cc_final: 0.8786 (mmm) REVERT: I 1188 ASP cc_start: 0.8164 (t70) cc_final: 0.7667 (t70) REVERT: I 1240 ASP cc_start: 0.8279 (p0) cc_final: 0.8007 (p0) REVERT: J 180 MET cc_start: 0.7584 (ttm) cc_final: 0.7016 (ttm) REVERT: J 227 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: J 474 LEU cc_start: 0.9353 (tp) cc_final: 0.9087 (tp) REVERT: J 560 ASN cc_start: 0.6791 (p0) cc_final: 0.6125 (p0) REVERT: J 698 MET cc_start: 0.8245 (tpt) cc_final: 0.7401 (tpt) REVERT: J 702 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.6373 (pp30) REVERT: J 822 MET cc_start: 0.9009 (mmt) cc_final: 0.8672 (mmt) REVERT: J 936 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6322 (m90) REVERT: J 1158 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6196 (tm-30) REVERT: J 1159 ILE cc_start: 0.9175 (tp) cc_final: 0.8517 (tp) REVERT: J 1283 SER cc_start: 0.8929 (m) cc_final: 0.8707 (p) outliers start: 95 outliers final: 82 residues processed: 399 average time/residue: 0.4498 time to fit residues: 293.4335 Evaluate side-chains 415 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 327 time to evaluate : 3.560 ------------------------------------------------------------------------------- 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 101 THR 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 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 211 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 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 184 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 336 LEU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 547 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 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 920 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1178 LYS Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1264 GLN 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 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 573 THR 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 728 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 112 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 263 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 314 ASN I 658 GLN I1023 HIS J1023 HIS J1098 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099435 restraints weight = 42632.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101203 restraints weight = 31099.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101539 restraints weight = 21210.640| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26781 Z= 0.109 Angle : 0.569 12.289 36454 Z= 0.287 Chirality : 0.042 0.258 4176 Planarity : 0.004 0.093 4545 Dihedral : 14.478 177.629 4340 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.11 % Allowed : 19.22 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3174 helix: 1.24 (0.16), residues: 1125 sheet: -0.87 (0.29), residues: 354 loop : -1.35 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.009 0.001 HIS I1023 PHE 0.012 0.001 PHE I 405 TYR 0.025 0.001 TYR G 152 ARG 0.008 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 1034) hydrogen bonds : angle 4.02755 ( 2879) metal coordination : bond 0.00571 ( 8) metal coordination : angle 2.27850 ( 12) covalent geometry : bond 0.00248 (26773) covalent geometry : angle 0.56745 (36442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9336.72 seconds wall clock time: 168 minutes 44.78 seconds (10124.78 seconds total)