Starting phenix.real_space_refine on Mon Aug 25 08:57:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eha_28145/08_2025/8eha_28145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eha_28145/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eha_28145/08_2025/8eha_28145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eha_28145/08_2025/8eha_28145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eha_28145/08_2025/8eha_28145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eha_28145/08_2025/8eha_28145.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16259 2.51 5 N 4641 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26250 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10371 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 10541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10541 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 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: 5.57, per 1000 atoms: 0.21 Number of scatterers: 26250 At special positions: 0 Unit cell: (139.1, 149.5, 162.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 63 15.00 Mg 1 11.99 O 5178 8.00 N 4641 7.00 C 16259 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 877.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 48 sheets defined 36.5% alpha, 16.7% beta 30 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.617A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.616A pdb=" N ASP G 114 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.580A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 30 through 40 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.736A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.600A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.604A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.986A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.636A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.924A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.779A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.505A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.987A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.815A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.923A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.860A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 980 removed outlier: 3.767A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.629A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.785A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.847A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.733A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.680A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 removed outlier: 3.586A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY I1282 " --> pdb=" O LEU I1278 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1298 through 1309 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.702A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.645A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.729A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 100 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.688A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 285 removed outlier: 3.631A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.768A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 removed outlier: 4.357A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.690A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 614 through 634 removed outlier: 3.522A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 670 Processing helix chain 'J' and resid 676 through 702 removed outlier: 4.111A pdb=" N GLN J 702 " --> pdb=" O MET J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 770 through 804 removed outlier: 3.790A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR J 797 " --> pdb=" O SER J 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 removed outlier: 4.193A pdb=" N GLU J 873 " --> pdb=" O CYS J 869 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 932 removed outlier: 3.609A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix removed outlier: 4.117A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 933 through 937 Processing helix chain 'J' and resid 1139 through 1147 Processing helix chain 'J' and resid 1218 through 1244 removed outlier: 3.541A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.331A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.640A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1310 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.777A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.636A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 79 removed outlier: 3.616A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.143A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.143A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 99 removed outlier: 6.891A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 147 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 55 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 53 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'G' and resid 102 through 104 removed outlier: 3.673A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.566A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.718A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 19 " --> pdb=" O HIS H 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 15 removed outlier: 5.718A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.575A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.436A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 60 Processing sheet with id=AB7, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.461A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.746A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU I 204 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AC3, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC4, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.655A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 295 through 296 removed outlier: 4.547A pdb=" N LYS I 295 " --> pdb=" O LEU I 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.518A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AD1, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.649A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.545A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.591A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.870A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 830 through 841 removed outlier: 5.732A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.998A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.218A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.778A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.216A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AE3, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.518A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 707 through 708 Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.812A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 956 through 961 removed outlier: 3.959A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP J 986 " --> pdb=" O THR J 991 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR J 991 " --> pdb=" O ASP J 986 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.646A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.658A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.454A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 977 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 2.73 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.870 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.14), residues: 3174 helix: 0.23 (0.16), residues: 1071 sheet: -1.36 (0.28), residues: 369 loop : -1.75 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 709 TYR 0.013 0.001 TYR J 723 PHE 0.013 0.001 PHE I 514 TRP 0.009 0.001 TRP J 580 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00480 (26773) covalent geometry : angle 0.61532 (36442) hydrogen bonds : bond 0.17953 ( 1034) hydrogen bonds : angle 6.63642 ( 2879) metal coordination : bond 0.00632 ( 8) metal coordination : angle 1.69266 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 421 time to evaluate : 0.961 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: 0.7228 (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: 0.1668 time to fit residues: 134.9289 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 940 GLU Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS H 103 ASN I 494 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097270 restraints weight = 42630.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097954 restraints weight = 26864.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098084 restraints weight = 23444.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.098599 restraints weight = 19239.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098723 restraints weight = 17114.246| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0974 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= 0.131 Angle : 0.568 8.796 36454 Z= 0.294 Chirality : 0.042 0.216 4176 Planarity : 0.004 0.083 4545 Dihedral : 15.065 176.304 4391 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.55 % Allowed : 12.64 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3174 helix: 0.62 (0.16), residues: 1119 sheet: -1.39 (0.27), residues: 384 loop : -1.74 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 272 TYR 0.014 0.001 TYR G 152 PHE 0.014 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00293 (26773) covalent geometry : angle 0.56455 (36442) hydrogen bonds : bond 0.03954 ( 1034) hydrogen bonds : angle 4.77224 ( 2879) metal coordination : bond 0.00940 ( 8) metal coordination : angle 3.33209 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 379 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: G 202 VAL cc_start: 0.9500 (t) cc_final: 0.9253 (p) REVERT: H 102 LEU cc_start: 0.8408 (tp) cc_final: 0.8164 (tp) REVERT: H 150 ARG cc_start: 0.6559 (mpt180) cc_final: 0.5844 (mtm180) REVERT: I 39 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9094 (tp) REVERT: I 195 PHE cc_start: 0.8183 (m-10) cc_final: 0.7819 (m-10) REVERT: I 423 ASP cc_start: 0.7532 (p0) cc_final: 0.7129 (p0) REVERT: I 434 ASP cc_start: 0.8162 (m-30) cc_final: 0.7691 (m-30) REVERT: I 459 MET cc_start: 0.8898 (mtp) cc_final: 0.8494 (mtp) REVERT: I 463 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: I 488 MET cc_start: 0.8291 (mmp) cc_final: 0.7541 (mmm) REVERT: I 930 ASP cc_start: 0.6943 (m-30) cc_final: 0.6699 (m-30) REVERT: I 997 TRP cc_start: 0.6729 (m100) cc_final: 0.5970 (m100) REVERT: I 1085 MET cc_start: 0.8962 (mmm) cc_final: 0.8514 (mmp) REVERT: I 1240 ASP cc_start: 0.8129 (p0) cc_final: 0.7880 (p0) REVERT: I 1290 MET cc_start: 0.8890 (mmt) cc_final: 0.8556 (mmp) REVERT: J 49 PHE cc_start: 0.7815 (m-80) cc_final: 0.7614 (m-10) REVERT: J 227 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: J 299 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8873 (tp) REVERT: J 644 MET cc_start: 0.8808 (mtt) cc_final: 0.8223 (mtt) REVERT: J 697 MET cc_start: 0.8651 (ttp) cc_final: 0.8337 (ttp) REVERT: J 698 MET cc_start: 0.7830 (tpt) cc_final: 0.7106 (tpt) REVERT: J 706 VAL cc_start: 0.8147 (m) cc_final: 0.7895 (m) REVERT: J 743 MET cc_start: 0.8978 (ptm) cc_final: 0.8732 (ptp) REVERT: J 806 ASP cc_start: 0.7726 (p0) cc_final: 0.7497 (p0) REVERT: J 822 MET cc_start: 0.8979 (mmt) cc_final: 0.8640 (mmt) REVERT: J 1158 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6600 (tm-30) REVERT: J 1159 ILE cc_start: 0.9214 (tp) cc_final: 0.8948 (tp) outliers start: 96 outliers final: 68 residues processed: 452 average time/residue: 0.1787 time to fit residues: 129.9517 Evaluate side-chains 409 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 337 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 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 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 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 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 1225 VAL 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 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 139 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 268 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN G 128 HIS I1023 HIS J 424 ASN ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.093994 restraints weight = 42827.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.095531 restraints weight = 31813.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.095923 restraints weight = 21516.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096266 restraints weight = 18707.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096293 restraints weight = 17232.374| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26781 Z= 0.222 Angle : 0.609 9.591 36454 Z= 0.313 Chirality : 0.043 0.176 4176 Planarity : 0.004 0.083 4545 Dihedral : 14.857 177.628 4365 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.84 % Allowed : 13.79 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 3174 helix: 0.64 (0.16), residues: 1133 sheet: -1.51 (0.26), residues: 394 loop : -1.71 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 709 TYR 0.017 0.001 TYR G 152 PHE 0.016 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00514 (26773) covalent geometry : angle 0.60635 (36442) hydrogen bonds : bond 0.04021 ( 1034) hydrogen bonds : angle 4.61889 ( 2879) metal coordination : bond 0.01432 ( 8) metal coordination : angle 3.10456 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 351 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 111 THR cc_start: 0.9159 (p) cc_final: 0.8912 (p) REVERT: G 202 VAL cc_start: 0.9485 (t) cc_final: 0.9248 (p) REVERT: G 212 ASP cc_start: 0.8205 (t70) cc_final: 0.7940 (t70) REVERT: H 79 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8416 (mm) REVERT: H 102 LEU cc_start: 0.8300 (tp) cc_final: 0.8023 (tp) REVERT: I 68 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8046 (tp) REVERT: I 184 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9103 (tt) REVERT: I 423 ASP cc_start: 0.7412 (p0) cc_final: 0.7062 (p0) REVERT: I 434 ASP cc_start: 0.8149 (m-30) cc_final: 0.7688 (m-30) REVERT: I 459 MET cc_start: 0.8907 (mtp) cc_final: 0.8479 (mtp) REVERT: I 463 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: I 488 MET cc_start: 0.8421 (mmp) cc_final: 0.7456 (tpt) REVERT: I 930 ASP cc_start: 0.6984 (m-30) cc_final: 0.6740 (m-30) REVERT: I 976 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7730 (ttm-80) REVERT: I 1085 MET cc_start: 0.9147 (mmm) cc_final: 0.8903 (mmm) REVERT: I 1107 MET cc_start: 0.7826 (mtm) cc_final: 0.7596 (mtm) REVERT: I 1240 ASP cc_start: 0.8258 (p0) cc_final: 0.7978 (p0) REVERT: I 1265 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7927 (t80) REVERT: I 1290 MET cc_start: 0.8923 (mmt) cc_final: 0.8643 (mmt) REVERT: J 227 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: J 560 ASN cc_start: 0.6602 (p0) cc_final: 0.6400 (p0) REVERT: J 644 MET cc_start: 0.8832 (mtt) cc_final: 0.8369 (mtt) REVERT: J 698 MET cc_start: 0.7857 (tpt) cc_final: 0.7066 (tpt) REVERT: J 702 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6502 (pp30) REVERT: J 706 VAL cc_start: 0.8160 (m) cc_final: 0.7948 (m) REVERT: J 822 MET cc_start: 0.8965 (mmt) cc_final: 0.8612 (mmt) REVERT: J 832 LYS cc_start: 0.6684 (mmtm) cc_final: 0.6442 (mmtt) REVERT: J 1158 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6361 (tm-30) REVERT: J 1159 ILE cc_start: 0.9157 (tp) cc_final: 0.8829 (tp) outliers start: 131 outliers final: 93 residues processed: 447 average time/residue: 0.1570 time to fit residues: 114.3583 Evaluate side-chains 422 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 322 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 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 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 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 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 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 135 ILE 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 507 VAL Chi-restraints excluded: chain J residue 526 VAL 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 707 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 249 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN I 673 HIS I1023 HIS J1098 GLN ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.095959 restraints weight = 42497.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095253 restraints weight = 27634.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095889 restraints weight = 24885.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096242 restraints weight = 20669.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096418 restraints weight = 18712.092| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26781 Z= 0.164 Angle : 0.567 8.507 36454 Z= 0.293 Chirality : 0.042 0.189 4176 Planarity : 0.004 0.084 4545 Dihedral : 14.712 177.533 4363 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.88 % Allowed : 15.64 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.15), residues: 3174 helix: 0.74 (0.16), residues: 1134 sheet: -1.42 (0.27), residues: 388 loop : -1.69 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 779 TYR 0.020 0.001 TYR G 152 PHE 0.015 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00377 (26773) covalent geometry : angle 0.56501 (36442) hydrogen bonds : bond 0.03661 ( 1034) hydrogen bonds : angle 4.42897 ( 2879) metal coordination : bond 0.01017 ( 8) metal coordination : angle 2.67108 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 344 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9102 (mtmm) cc_final: 0.8828 (ptpp) REVERT: G 68 TYR cc_start: 0.9098 (m-80) cc_final: 0.8824 (m-10) REVERT: G 111 THR cc_start: 0.9126 (p) cc_final: 0.8869 (p) REVERT: G 202 VAL cc_start: 0.9475 (t) cc_final: 0.9223 (p) REVERT: H 28 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8959 (pt) REVERT: H 79 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8389 (mm) REVERT: H 80 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8195 (mt-10) REVERT: H 200 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9009 (tttt) REVERT: I 423 ASP cc_start: 0.7439 (p0) cc_final: 0.7060 (p0) REVERT: I 434 ASP cc_start: 0.8203 (m-30) cc_final: 0.7717 (m-30) REVERT: I 459 MET cc_start: 0.8847 (mtp) cc_final: 0.8457 (mtp) REVERT: I 463 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: I 488 MET cc_start: 0.8413 (mmp) cc_final: 0.7486 (tpt) REVERT: I 930 ASP cc_start: 0.7010 (m-30) cc_final: 0.6772 (m-30) REVERT: I 976 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7722 (ttm-80) REVERT: I 997 TRP cc_start: 0.6988 (m100) cc_final: 0.6141 (m100) REVERT: I 1085 MET cc_start: 0.9080 (mmm) cc_final: 0.8760 (mmm) REVERT: I 1240 ASP cc_start: 0.8207 (p0) cc_final: 0.7911 (p0) REVERT: I 1265 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7991 (t80) REVERT: I 1290 MET cc_start: 0.8738 (mmt) cc_final: 0.8450 (mmt) REVERT: J 227 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: J 644 MET cc_start: 0.8794 (mtt) cc_final: 0.8332 (mtt) REVERT: J 698 MET cc_start: 0.7836 (tpt) cc_final: 0.6930 (tpt) REVERT: J 702 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.6431 (pp30) REVERT: J 706 VAL cc_start: 0.8198 (m) cc_final: 0.7993 (m) REVERT: J 822 MET cc_start: 0.8975 (mmt) cc_final: 0.8606 (mmt) REVERT: J 1158 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6339 (tm-30) REVERT: J 1159 ILE cc_start: 0.9190 (tp) cc_final: 0.8934 (tp) outliers start: 132 outliers final: 102 residues processed: 442 average time/residue: 0.1409 time to fit residues: 100.6833 Evaluate side-chains 442 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 333 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 176 CYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 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 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 H residue 200 LYS 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 138 ILE 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 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 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 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 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 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 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 728 SER Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 145 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I1023 HIS ** 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 = 0.3534 r_free = 0.3534 target = 0.129224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097585 restraints weight = 42126.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097394 restraints weight = 29641.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097903 restraints weight = 24996.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098309 restraints weight = 21735.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098490 restraints weight = 18465.293| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26781 Z= 0.128 Angle : 0.547 12.132 36454 Z= 0.282 Chirality : 0.042 0.230 4176 Planarity : 0.004 0.092 4545 Dihedral : 14.614 177.205 4363 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.58 % Allowed : 16.16 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 3174 helix: 0.96 (0.16), residues: 1124 sheet: -1.19 (0.28), residues: 376 loop : -1.64 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 133 TYR 0.015 0.001 TYR G 152 PHE 0.013 0.001 PHE I 405 TRP 0.006 0.001 TRP J 580 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00293 (26773) covalent geometry : angle 0.54596 (36442) hydrogen bonds : bond 0.03408 ( 1034) hydrogen bonds : angle 4.26489 ( 2879) metal coordination : bond 0.00775 ( 8) metal coordination : angle 2.22825 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 369 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8844 (ptpp) REVERT: G 68 TYR cc_start: 0.9054 (m-80) cc_final: 0.8796 (m-10) REVERT: G 111 THR cc_start: 0.9113 (p) cc_final: 0.8857 (p) REVERT: G 202 VAL cc_start: 0.9446 (t) cc_final: 0.9180 (p) REVERT: G 212 ASP cc_start: 0.8123 (t70) cc_final: 0.7858 (t70) REVERT: H 28 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8941 (pt) REVERT: H 79 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8369 (mm) REVERT: H 80 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8143 (mt-10) REVERT: I 423 ASP cc_start: 0.7448 (p0) cc_final: 0.7247 (p0) REVERT: I 434 ASP cc_start: 0.8048 (m-30) cc_final: 0.7584 (m-30) REVERT: I 459 MET cc_start: 0.8829 (mtp) cc_final: 0.8496 (mtp) REVERT: I 463 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: I 488 MET cc_start: 0.8346 (mmp) cc_final: 0.7356 (tpt) REVERT: I 930 ASP cc_start: 0.6962 (m-30) cc_final: 0.6756 (m-30) REVERT: I 976 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7791 (ttm-80) REVERT: I 1085 MET cc_start: 0.9112 (mmm) cc_final: 0.8782 (mmm) REVERT: I 1240 ASP cc_start: 0.8222 (p0) cc_final: 0.7959 (p0) REVERT: I 1265 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7893 (t80) REVERT: I 1290 MET cc_start: 0.8704 (mmt) cc_final: 0.8449 (mmt) REVERT: J 227 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: J 560 ASN cc_start: 0.6863 (p0) cc_final: 0.6285 (p0) REVERT: J 644 MET cc_start: 0.8756 (mtt) cc_final: 0.8293 (mtt) REVERT: J 697 MET cc_start: 0.8792 (ttp) cc_final: 0.8231 (ttp) REVERT: J 698 MET cc_start: 0.7980 (tpt) cc_final: 0.7284 (tpt) REVERT: J 822 MET cc_start: 0.8958 (mmt) cc_final: 0.8577 (mmt) REVERT: J 936 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6355 (m90) REVERT: J 1158 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6241 (tm-30) REVERT: J 1159 ILE cc_start: 0.9184 (tp) cc_final: 0.8919 (tp) REVERT: K 31 GLN cc_start: 0.8827 (tt0) cc_final: 0.8537 (tt0) outliers start: 124 outliers final: 95 residues processed: 457 average time/residue: 0.1523 time to fit residues: 112.6237 Evaluate side-chains 441 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 340 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 28 LEU 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 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 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 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 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 680 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 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 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 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 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 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 728 SER 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 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 1134 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 229 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 201 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 165 optimal weight: 0.0470 chunk 320 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN G 93 GLN I1023 HIS K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099890 restraints weight = 41988.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098744 restraints weight = 27265.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099413 restraints weight = 25386.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099794 restraints weight = 21676.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099999 restraints weight = 19057.815| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26781 Z= 0.102 Angle : 0.543 11.320 36454 Z= 0.277 Chirality : 0.041 0.278 4176 Planarity : 0.004 0.083 4545 Dihedral : 14.529 176.751 4358 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.36 % Allowed : 17.15 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.15), residues: 3174 helix: 1.13 (0.16), residues: 1116 sheet: -1.04 (0.28), residues: 376 loop : -1.51 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 133 TYR 0.014 0.001 TYR G 152 PHE 0.012 0.001 PHE I 405 TRP 0.006 0.001 TRP J 33 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00227 (26773) covalent geometry : angle 0.54049 (36442) hydrogen bonds : bond 0.03224 ( 1034) hydrogen bonds : angle 4.10233 ( 2879) metal coordination : bond 0.00970 ( 8) metal coordination : angle 2.69104 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 380 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8852 (ptpp) REVERT: G 68 TYR cc_start: 0.9113 (m-80) cc_final: 0.8878 (m-10) REVERT: G 111 THR cc_start: 0.9068 (p) cc_final: 0.8813 (p) REVERT: G 202 VAL cc_start: 0.9406 (t) cc_final: 0.9131 (p) REVERT: H 79 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8352 (mm) REVERT: H 150 ARG cc_start: 0.6356 (mpt180) cc_final: 0.6111 (ptp90) REVERT: I 423 ASP cc_start: 0.7414 (p0) cc_final: 0.7212 (p0) REVERT: I 434 ASP cc_start: 0.8043 (m-30) cc_final: 0.7563 (m-30) REVERT: I 463 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: I 488 MET cc_start: 0.8311 (mmp) cc_final: 0.7386 (tpt) REVERT: I 997 TRP cc_start: 0.7125 (m100) cc_final: 0.6212 (m100) REVERT: I 1085 MET cc_start: 0.9053 (mmm) cc_final: 0.8760 (mmm) REVERT: I 1240 ASP cc_start: 0.8188 (p0) cc_final: 0.7898 (p0) REVERT: I 1265 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7791 (t80) REVERT: I 1290 MET cc_start: 0.8866 (mmt) cc_final: 0.8538 (mmt) REVERT: J 137 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8566 (mtm110) REVERT: J 180 MET cc_start: 0.7394 (ttm) cc_final: 0.6964 (ttm) REVERT: J 219 LYS cc_start: 0.8457 (tppt) cc_final: 0.8087 (mmtp) REVERT: J 227 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: J 560 ASN cc_start: 0.6904 (p0) cc_final: 0.6292 (p0) REVERT: J 643 ASP cc_start: 0.8513 (m-30) cc_final: 0.8312 (m-30) REVERT: J 644 MET cc_start: 0.8677 (mtt) cc_final: 0.8176 (mtt) REVERT: J 698 MET cc_start: 0.8220 (tpt) cc_final: 0.7637 (tpt) REVERT: J 743 MET cc_start: 0.8815 (ptm) cc_final: 0.8583 (ptp) REVERT: J 822 MET cc_start: 0.8951 (mmt) cc_final: 0.8598 (mmt) REVERT: J 832 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6419 (mmtm) REVERT: J 936 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6388 (m90) REVERT: J 1158 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6355 (tm-30) outliers start: 118 outliers final: 84 residues processed: 465 average time/residue: 0.1722 time to fit residues: 129.7263 Evaluate side-chains 435 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 346 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU 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 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 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 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 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 1178 LYS Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 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 324 LEU Chi-restraints excluded: chain J residue 354 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 639 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 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 910 ASN 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 59 ILE Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 311 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 chunk 210 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 78 optimal weight: 0.0370 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097870 restraints weight = 42218.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098353 restraints weight = 25508.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098766 restraints weight = 21017.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.099355 restraints weight = 17697.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.099388 restraints weight = 16218.252| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26781 Z= 0.120 Angle : 0.562 10.950 36454 Z= 0.284 Chirality : 0.041 0.218 4176 Planarity : 0.004 0.093 4545 Dihedral : 14.475 177.201 4349 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.33 % Allowed : 17.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3174 helix: 1.13 (0.16), residues: 1125 sheet: -0.94 (0.29), residues: 353 loop : -1.44 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 311 TYR 0.023 0.001 TYR G 152 PHE 0.017 0.001 PHE H 8 TRP 0.004 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00275 (26773) covalent geometry : angle 0.55914 (36442) hydrogen bonds : bond 0.03260 ( 1034) hydrogen bonds : angle 4.09005 ( 2879) metal coordination : bond 0.00846 ( 8) metal coordination : angle 2.96559 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 360 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8855 (ptpp) REVERT: G 111 THR cc_start: 0.9072 (p) cc_final: 0.8808 (p) REVERT: G 120 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6454 (p0) REVERT: G 202 VAL cc_start: 0.9418 (t) cc_final: 0.9137 (p) REVERT: H 79 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8336 (mm) REVERT: H 95 LYS cc_start: 0.7042 (mtpt) cc_final: 0.6668 (mtmt) REVERT: H 150 ARG cc_start: 0.6312 (mpt180) cc_final: 0.6064 (ptp90) REVERT: I 357 ASN cc_start: 0.7902 (t0) cc_final: 0.7610 (t0) REVERT: I 434 ASP cc_start: 0.8226 (m-30) cc_final: 0.7717 (m-30) REVERT: I 463 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: I 488 MET cc_start: 0.8235 (mmp) cc_final: 0.7297 (tpt) REVERT: I 997 TRP cc_start: 0.7386 (m100) cc_final: 0.6180 (m100) REVERT: I 1085 MET cc_start: 0.9144 (mmm) cc_final: 0.8801 (mmm) REVERT: I 1188 ASP cc_start: 0.8118 (t70) cc_final: 0.7662 (t70) REVERT: I 1240 ASP cc_start: 0.8261 (p0) cc_final: 0.7937 (p0) REVERT: I 1265 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7784 (t80) REVERT: J 219 LYS cc_start: 0.8515 (tppt) cc_final: 0.8232 (mmtp) REVERT: J 227 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: J 560 ASN cc_start: 0.6851 (p0) cc_final: 0.6236 (p0) REVERT: J 643 ASP cc_start: 0.8573 (m-30) cc_final: 0.8236 (m-30) REVERT: J 644 MET cc_start: 0.8749 (mtt) cc_final: 0.8309 (mtt) REVERT: J 698 MET cc_start: 0.8220 (tpt) cc_final: 0.7166 (tpt) REVERT: J 702 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.6335 (pp30) REVERT: J 822 MET cc_start: 0.8967 (mmt) cc_final: 0.8580 (mmt) REVERT: J 832 LYS cc_start: 0.7168 (mmtt) cc_final: 0.6370 (mmtm) REVERT: J 1158 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6182 (tm-30) REVERT: J 1169 THR cc_start: 0.7968 (m) cc_final: 0.7653 (m) outliers start: 117 outliers final: 92 residues processed: 448 average time/residue: 0.1701 time to fit residues: 122.6860 Evaluate side-chains 433 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 335 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 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 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 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 941 LYS 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 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 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 728 SER Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 211 optimal weight: 0.0470 chunk 54 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 6 optimal weight: 0.0030 chunk 216 optimal weight: 7.9990 chunk 185 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 296 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 overall best weight: 0.3088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 227 GLN I1023 HIS ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100932 restraints weight = 42328.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101125 restraints weight = 25706.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101710 restraints weight = 21327.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102190 restraints weight = 18363.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102265 restraints weight = 16053.043| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26781 Z= 0.101 Angle : 0.565 12.084 36454 Z= 0.285 Chirality : 0.042 0.286 4176 Planarity : 0.004 0.091 4545 Dihedral : 14.433 177.935 4348 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.66 % Allowed : 18.30 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3174 helix: 1.24 (0.16), residues: 1130 sheet: -0.85 (0.30), residues: 348 loop : -1.40 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 976 TYR 0.024 0.001 TYR J 723 PHE 0.026 0.001 PHE I 230 TRP 0.006 0.001 TRP J 33 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00224 (26773) covalent geometry : angle 0.56373 (36442) hydrogen bonds : bond 0.03111 ( 1034) hydrogen bonds : angle 3.98045 ( 2879) metal coordination : bond 0.00453 ( 8) metal coordination : angle 2.38383 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 382 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 111 THR cc_start: 0.8951 (p) cc_final: 0.8681 (p) REVERT: G 202 VAL cc_start: 0.9371 (t) cc_final: 0.9108 (p) REVERT: H 79 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8269 (mm) REVERT: H 95 LYS cc_start: 0.7087 (mtpt) cc_final: 0.6702 (mtmt) REVERT: I 357 ASN cc_start: 0.7899 (t0) cc_final: 0.7601 (t0) REVERT: I 434 ASP cc_start: 0.8164 (m-30) cc_final: 0.7662 (m-30) REVERT: I 463 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: I 488 MET cc_start: 0.8141 (mmp) cc_final: 0.7117 (tpt) REVERT: I 766 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8233 (p0) REVERT: I 997 TRP cc_start: 0.7384 (m100) cc_final: 0.6284 (m100) REVERT: I 1085 MET cc_start: 0.9099 (mmm) cc_final: 0.8826 (mmm) REVERT: I 1188 ASP cc_start: 0.7970 (t70) cc_final: 0.7546 (t70) REVERT: I 1231 TYR cc_start: 0.9370 (t80) cc_final: 0.9136 (t80) REVERT: I 1240 ASP cc_start: 0.8268 (p0) cc_final: 0.7925 (p0) REVERT: I 1265 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7477 (t80) REVERT: I 1290 MET cc_start: 0.8935 (mmt) cc_final: 0.8697 (mmt) REVERT: J 180 MET cc_start: 0.7354 (ttm) cc_final: 0.6802 (ttm) REVERT: J 219 LYS cc_start: 0.8458 (tppt) cc_final: 0.8177 (mmtp) REVERT: J 227 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: J 311 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8418 (ttm-80) REVERT: J 395 LYS cc_start: 0.8483 (ttpp) cc_final: 0.7934 (tptt) REVERT: J 485 MET cc_start: 0.8478 (ttm) cc_final: 0.8136 (ttt) REVERT: J 560 ASN cc_start: 0.6811 (p0) cc_final: 0.6172 (p0) REVERT: J 644 MET cc_start: 0.8640 (mtt) cc_final: 0.8131 (mtt) REVERT: J 697 MET cc_start: 0.8741 (ttp) cc_final: 0.7944 (ttp) REVERT: J 698 MET cc_start: 0.8132 (tpt) cc_final: 0.7164 (tpt) REVERT: J 702 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6007 (pp30) REVERT: J 822 MET cc_start: 0.9003 (mmt) cc_final: 0.8657 (mmt) REVERT: J 936 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6198 (m90) REVERT: J 1158 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6209 (tm-30) REVERT: J 1169 THR cc_start: 0.7967 (m) cc_final: 0.7755 (m) REVERT: J 1283 SER cc_start: 0.8945 (m) cc_final: 0.8667 (p) REVERT: K 29 GLN cc_start: 0.8216 (mt0) cc_final: 0.7917 (mt0) outliers start: 99 outliers final: 65 residues processed: 458 average time/residue: 0.1561 time to fit residues: 115.3474 Evaluate side-chains 427 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 355 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS 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 228 LEU 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 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU 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 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU 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 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 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 999 GLU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 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 491 LEU 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 710 ASP Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 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 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 272 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN I 494 ASN I 554 HIS I1023 HIS J 929 GLN ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094137 restraints weight = 42737.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094031 restraints weight = 29579.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094608 restraints weight = 24725.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.094994 restraints weight = 20649.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095041 restraints weight = 19166.347| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26781 Z= 0.247 Angle : 0.665 15.958 36454 Z= 0.336 Chirality : 0.045 0.249 4176 Planarity : 0.005 0.100 4545 Dihedral : 14.600 179.621 4342 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.25 % Allowed : 18.04 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.15), residues: 3174 helix: 0.96 (0.16), residues: 1137 sheet: -1.04 (0.28), residues: 380 loop : -1.47 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 54 TYR 0.025 0.002 TYR J 723 PHE 0.015 0.002 PHE I 230 TRP 0.006 0.001 TRP I 183 HIS 0.008 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00578 (26773) covalent geometry : angle 0.66287 (36442) hydrogen bonds : bond 0.03769 ( 1034) hydrogen bonds : angle 4.28261 ( 2879) metal coordination : bond 0.01576 ( 8) metal coordination : angle 2.92705 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 329 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 111 THR cc_start: 0.9152 (p) cc_final: 0.8903 (p) REVERT: G 202 VAL cc_start: 0.9483 (t) cc_final: 0.9232 (p) REVERT: H 79 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8323 (mm) REVERT: H 82 LEU cc_start: 0.8902 (mt) cc_final: 0.8641 (mt) REVERT: H 95 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6853 (mtmt) REVERT: I 184 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9121 (tt) REVERT: I 357 ASN cc_start: 0.7907 (t0) cc_final: 0.7620 (t0) REVERT: I 434 ASP cc_start: 0.8127 (m-30) cc_final: 0.7679 (m-30) REVERT: I 463 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: I 488 MET cc_start: 0.8329 (mmp) cc_final: 0.7270 (tpt) REVERT: I 976 ARG cc_start: 0.6852 (ttm-80) cc_final: 0.6485 (ttm-80) REVERT: I 997 TRP cc_start: 0.7505 (m100) cc_final: 0.6365 (m100) REVERT: I 1085 MET cc_start: 0.9089 (mmm) cc_final: 0.8692 (mmm) REVERT: I 1188 ASP cc_start: 0.8252 (t70) cc_final: 0.7877 (t70) REVERT: I 1240 ASP cc_start: 0.8316 (p0) cc_final: 0.8066 (p0) REVERT: I 1322 SER cc_start: 0.8390 (t) cc_final: 0.8092 (m) REVERT: J 180 MET cc_start: 0.7732 (ttm) cc_final: 0.7176 (ttm) REVERT: J 227 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: J 330 MET cc_start: 0.8127 (ptp) cc_final: 0.7840 (ptp) REVERT: J 560 ASN cc_start: 0.6802 (p0) cc_final: 0.6228 (p0) REVERT: J 644 MET cc_start: 0.8767 (mtt) cc_final: 0.8348 (mtt) REVERT: J 698 MET cc_start: 0.8154 (tpt) cc_final: 0.7279 (tpt) REVERT: J 702 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6496 (pp30) REVERT: J 822 MET cc_start: 0.8975 (mmt) cc_final: 0.8600 (mmt) REVERT: J 936 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6363 (m90) REVERT: J 1158 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6423 (tm-30) REVERT: K 55 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7810 (tt0) outliers start: 115 outliers final: 89 residues processed: 414 average time/residue: 0.1695 time to fit residues: 113.3183 Evaluate side-chains 412 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 316 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 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 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 229 ILE 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 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 654 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 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL 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 J residue 22 ILE Chi-restraints excluded: chain J residue 72 CYS 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 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 472 LEU 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 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 728 SER Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 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 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU 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 259 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 96 optimal weight: 0.0370 chunk 101 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 314 ASN I1023 HIS J1098 GLN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097701 restraints weight = 42205.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098494 restraints weight = 24262.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099078 restraints weight = 19346.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099510 restraints weight = 16662.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099563 restraints weight = 15572.580| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26781 Z= 0.114 Angle : 0.588 11.994 36454 Z= 0.296 Chirality : 0.042 0.284 4176 Planarity : 0.004 0.100 4545 Dihedral : 14.491 177.552 4339 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.18 % Allowed : 19.41 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 3174 helix: 1.16 (0.16), residues: 1137 sheet: -0.87 (0.29), residues: 364 loop : -1.39 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 133 TYR 0.024 0.001 TYR G 152 PHE 0.014 0.001 PHE I 812 TRP 0.011 0.001 TRP J1193 HIS 0.009 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00259 (26773) covalent geometry : angle 0.58634 (36442) hydrogen bonds : bond 0.03257 ( 1034) hydrogen bonds : angle 4.08266 ( 2879) metal coordination : bond 0.00684 ( 8) metal coordination : angle 2.52309 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 347 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 111 THR cc_start: 0.8983 (p) cc_final: 0.8706 (p) REVERT: H 79 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8248 (mm) REVERT: H 142 MET cc_start: 0.7263 (pmm) cc_final: 0.6910 (ptp) REVERT: I 357 ASN cc_start: 0.7953 (t0) cc_final: 0.7647 (t0) REVERT: I 387 ASN cc_start: 0.8242 (m110) cc_final: 0.7952 (p0) REVERT: I 434 ASP cc_start: 0.8197 (m-30) cc_final: 0.7891 (m-30) REVERT: I 463 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: I 488 MET cc_start: 0.8159 (mmp) cc_final: 0.7840 (mmp) REVERT: I 976 ARG cc_start: 0.6743 (ttm-80) cc_final: 0.6404 (ttm-80) REVERT: I 997 TRP cc_start: 0.7577 (m-10) cc_final: 0.6321 (m100) REVERT: I 1085 MET cc_start: 0.9145 (mmm) cc_final: 0.8826 (mmm) REVERT: I 1188 ASP cc_start: 0.8162 (t70) cc_final: 0.7680 (t70) REVERT: I 1240 ASP cc_start: 0.8263 (p0) cc_final: 0.7967 (p0) REVERT: I 1290 MET cc_start: 0.8911 (mmt) cc_final: 0.8703 (mmt) REVERT: J 180 MET cc_start: 0.7626 (ttm) cc_final: 0.7023 (ttm) REVERT: J 227 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: J 474 LEU cc_start: 0.9292 (tp) cc_final: 0.9051 (tp) REVERT: J 560 ASN cc_start: 0.6801 (p0) cc_final: 0.6206 (p0) REVERT: J 698 MET cc_start: 0.8192 (tpt) cc_final: 0.7361 (tpt) REVERT: J 702 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6270 (pp30) REVERT: J 822 MET cc_start: 0.8999 (mmt) cc_final: 0.8646 (mmt) REVERT: J 936 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6258 (m90) REVERT: J 1095 MET cc_start: 0.7007 (tpp) cc_final: 0.6750 (ppp) REVERT: J 1158 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6199 (tm-30) REVERT: J 1283 SER cc_start: 0.8949 (m) cc_final: 0.8675 (p) REVERT: K 60 ASN cc_start: 0.7981 (p0) cc_final: 0.7698 (p0) outliers start: 86 outliers final: 72 residues processed: 412 average time/residue: 0.1573 time to fit residues: 105.1212 Evaluate side-chains 416 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 339 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 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 28 LEU 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 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 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 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 999 GLU 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 J residue 22 ILE Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 90 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 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 472 LEU 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 710 ASP Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 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 8 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 53 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 311 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 227 optimal weight: 0.0270 chunk 170 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 658 GLN I1023 HIS ** J1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.097512 restraints weight = 42387.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099654 restraints weight = 32401.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099672 restraints weight = 22029.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100101 restraints weight = 18533.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100135 restraints weight = 16606.145| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26781 Z= 0.151 Angle : 0.601 11.846 36454 Z= 0.303 Chirality : 0.043 0.272 4176 Planarity : 0.004 0.099 4545 Dihedral : 14.495 178.479 4337 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.18 % Allowed : 19.70 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 3174 helix: 1.17 (0.16), residues: 1130 sheet: -0.87 (0.28), residues: 384 loop : -1.39 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 133 TYR 0.025 0.001 TYR G 152 PHE 0.020 0.001 PHE I 812 TRP 0.013 0.001 TRP J1193 HIS 0.009 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00354 (26773) covalent geometry : angle 0.59962 (36442) hydrogen bonds : bond 0.03350 ( 1034) hydrogen bonds : angle 4.09894 ( 2879) metal coordination : bond 0.00950 ( 8) metal coordination : angle 2.51021 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3872.82 seconds wall clock time: 67 minutes 54.24 seconds (4074.24 seconds total)