Starting phenix.real_space_refine on Sun Jun 29 18:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6u_39001/06_2025/8y6u_39001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6u_39001/06_2025/8y6u_39001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6u_39001/06_2025/8y6u_39001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6u_39001/06_2025/8y6u_39001.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6u_39001/06_2025/8y6u_39001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6u_39001/06_2025/8y6u_39001.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1065 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 137 5.49 5 S 131 5.16 5 C 20810 2.51 5 N 6016 2.21 5 O 6775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33869 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 676 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "1" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1395 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "2" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1427 Classifications: {'DNA': 69} Link IDs: {'rna3p': 68} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10560 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 10369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10369 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" 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: "F" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3977 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 65} Chain breaks: 1 Time building chain proxies: 17.18, per 1000 atoms: 0.51 Number of scatterers: 33869 At special positions: 0 Unit cell: (185.64, 170.17, 170.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 137 15.00 O 6775 8.00 N 6016 7.00 C 20810 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: 7.52 Conformation dependent library (CDL) restraints added in 3.7 seconds 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 46 sheets defined 45.4% alpha, 13.1% beta 44 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 11.05 Creating SS restraints... Processing helix chain 'H' and resid 9 through 21 removed outlier: 3.671A pdb=" N VAL H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA H 18 " --> pdb=" O PHE H 14 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.815A pdb=" N GLU H 28 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 removed outlier: 4.172A pdb=" N SER H 38 " --> pdb=" O GLN H 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER H 43 " --> pdb=" O HIS H 39 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.661A pdb=" N SER H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 71 " --> pdb=" O GLN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 92 removed outlier: 3.526A pdb=" N LEU H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 20 removed outlier: 3.505A pdb=" N PHE J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA J 16 " --> pdb=" O ARG J 12 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA J 17 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA J 18 " --> pdb=" O PHE J 14 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG J 19 " --> pdb=" O ASP J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 27 removed outlier: 3.569A pdb=" N ALA J 27 " --> pdb=" O THR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 48 removed outlier: 3.794A pdb=" N HIS J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER J 43 " --> pdb=" O HIS J 39 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 88 removed outlier: 3.537A pdb=" N GLN J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.023A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 155 through 162 removed outlier: 4.202A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.558A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.936A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.761A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 212 through 229 removed outlier: 3.812A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.714A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.894A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.601A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.584A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.962A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.952A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.770A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.552A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.712A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 removed outlier: 3.575A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.793A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 4.111A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.047A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.631A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.074A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.309A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.907A pdb=" N LEU C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 976 removed outlier: 3.966A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 980 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.831A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1037 removed outlier: 3.812A pdb=" N GLN C1008 " --> pdb=" O ASP C1004 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C1029 " --> pdb=" O PHE C1025 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1100 through 1103 Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.525A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 removed outlier: 3.556A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.671A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 removed outlier: 3.767A pdb=" N LEU C1172 " --> pdb=" O GLU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.564A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.574A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.091A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C1308 " --> pdb=" O MET C1304 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.827A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C1325 " --> pdb=" O GLU C1321 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.700A pdb=" N GLU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.792A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.654A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.839A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.137A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.969A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.545A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.920A pdb=" N LEU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.516A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.220A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 removed outlier: 3.568A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.547A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 removed outlier: 4.196A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.880A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 701 " --> pdb=" O MET D 697 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.581A pdb=" N ARG D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 803 removed outlier: 4.282A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.590A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 removed outlier: 4.725A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.164A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.961A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 4.133A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.529A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 3.551A pdb=" N SER D1324 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.583A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.616A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.269A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.721A pdb=" N VAL E 10 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.257A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.592A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 4.209A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.546A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 134 removed outlier: 3.732A pdb=" N GLY F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.259A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 213 through 237 removed outlier: 4.323A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 Processing helix chain 'F' and resid 262 through 291 removed outlier: 4.077A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 298 through 307 removed outlier: 3.586A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 removed outlier: 3.709A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.870A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.658A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.781A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.748A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 402 through 419 removed outlier: 4.366A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.091A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.826A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 4.546A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 499 removed outlier: 4.314A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 578 Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.699A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 4.459A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 612 removed outlier: 4.424A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 609 through 612' Processing helix chain 'I' and resid 263 through 273 removed outlier: 3.855A pdb=" N LEU I 270 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA I 272 " --> pdb=" O ASN I 268 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU I 273 " --> pdb=" O CYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.860A pdb=" N ARG I 284 " --> pdb=" O ASP I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 290 removed outlier: 3.727A pdb=" N LEU I 290 " --> pdb=" O GLU I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 309 removed outlier: 3.885A pdb=" N SER I 309 " --> pdb=" O ASP I 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 53 through 56 removed outlier: 4.056A pdb=" N ARG H 54 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU H 61 " --> pdb=" O ARG H 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG H 56 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER H 59 " --> pdb=" O ARG H 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 18 removed outlier: 4.782A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.589A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.502A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 105 removed outlier: 8.523A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.677A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.689A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.723A pdb=" N PHE C 186 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.690A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.773A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.069A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.742A pdb=" N TYR C 652 " --> pdb=" O VAL C 615 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.651A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.624A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 798 through 804 removed outlier: 7.852A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.600A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 4.029A pdb=" N VAL C 884 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD2, first strand: chain 'C' and resid 1209 through 1210 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 5.883A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1337 through 1341 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.029A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.895A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE2, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.672A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.398A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.567A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.707A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.667A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1162 through 1164 Processing sheet with id=AE9, first strand: chain 'D' and resid 1173 through 1174 Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 1237 hydrogen bonds defined for protein. 3447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 15.64 Time building geometry restraints manager: 8.98 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: 10951 1.34 - 1.46: 5896 1.46 - 1.58: 17312 1.58 - 1.70: 272 1.70 - 1.82: 230 Bond restraints: 34661 Sorted by residual: bond pdb=" C GLY C 134 " pdb=" N THR C 135 " ideal model delta sigma weight residual 1.328 1.251 0.077 8.50e-03 1.38e+04 8.21e+01 bond pdb=" C PHE J 23 " pdb=" N THR J 24 " ideal model delta sigma weight residual 1.335 1.271 0.064 1.38e-02 5.25e+03 2.16e+01 bond pdb=" C HIS B 23 " pdb=" N ALA B 24 " ideal model delta sigma weight residual 1.331 1.383 -0.052 1.25e-02 6.40e+03 1.71e+01 bond pdb=" N ILE D 124 " pdb=" CA ILE D 124 " ideal model delta sigma weight residual 1.456 1.495 -0.038 9.50e-03 1.11e+04 1.63e+01 bond pdb=" C THR B 22 " pdb=" N HIS B 23 " ideal model delta sigma weight residual 1.330 1.384 -0.054 1.46e-02 4.69e+03 1.39e+01 ... (remaining 34656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 46662 1.98 - 3.95: 652 3.95 - 5.93: 51 5.93 - 7.90: 12 7.90 - 9.88: 9 Bond angle restraints: 47386 Sorted by residual: angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 113.53 105.72 7.81 9.80e-01 1.04e+00 6.35e+01 angle pdb=" O THR B 22 " pdb=" C THR B 22 " pdb=" N HIS B 23 " ideal model delta sigma weight residual 122.10 126.98 -4.88 1.06e+00 8.90e-01 2.12e+01 angle pdb=" CA THR B 22 " pdb=" C THR B 22 " pdb=" N HIS B 23 " ideal model delta sigma weight residual 119.26 114.43 4.83 1.14e+00 7.69e-01 1.79e+01 angle pdb=" N VAL E 22 " pdb=" CA VAL E 22 " pdb=" C VAL E 22 " ideal model delta sigma weight residual 111.90 108.90 3.00 8.10e-01 1.52e+00 1.37e+01 angle pdb=" C SER D 122 " pdb=" N ARG D 123 " pdb=" CA ARG D 123 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 ... (remaining 47381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 20084 35.80 - 71.59: 865 71.59 - 107.39: 43 107.39 - 143.18: 2 143.18 - 178.98: 3 Dihedral angle restraints: 20997 sinusoidal: 9602 harmonic: 11395 Sorted by residual: dihedral pdb=" CA SER F 506 " pdb=" C SER F 506 " pdb=" N MET F 507 " pdb=" CA MET F 507 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DA 2 43 " pdb=" C3' DA 2 43 " pdb=" O3' DA 2 43 " pdb=" P DG 2 44 " ideal model delta sinusoidal sigma weight residual -140.00 38.98 -178.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 20994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4299 0.047 - 0.094: 918 0.094 - 0.142: 189 0.142 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 5410 Sorted by residual: chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE H 76 " pdb=" CA ILE H 76 " pdb=" CG1 ILE H 76 " pdb=" CG2 ILE H 76 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB ILE A 16 " pdb=" CA ILE A 16 " pdb=" CG1 ILE A 16 " pdb=" CG2 ILE A 16 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.26e-01 ... (remaining 5407 not shown) Planarity restraints: 5699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 69 " -0.012 2.00e-02 2.50e+03 2.12e-02 8.97e+00 pdb=" CG TYR H 69 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 69 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR H 69 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 69 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 69 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR H 69 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR H 69 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D1101 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO D1102 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D1102 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D1102 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 292 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO I 293 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 293 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 293 " -0.025 5.00e-02 4.00e+02 ... (remaining 5696 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3221 2.74 - 3.28: 34995 3.28 - 3.82: 58673 3.82 - 4.36: 68962 4.36 - 4.90: 111215 Nonbonded interactions: 277066 Sorted by model distance: nonbonded pdb=" OG1 THR B 111 " pdb=" O PRO B 126 " model vdw 2.200 3.040 nonbonded pdb=" O SER F 389 " pdb=" NZ LYS F 393 " model vdw 2.205 3.120 nonbonded pdb=" O PRO A 179 " pdb=" OG1 THR A 207 " model vdw 2.205 3.040 nonbonded pdb=" OG SER C 318 " pdb=" OD1 ASP C 320 " model vdw 2.210 3.040 nonbonded pdb=" O VAL F 606 " pdb=" OG SER F 609 " model vdw 2.210 3.040 ... (remaining 277061 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 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'H' and resid 6 through 88) selection = (chain 'J' and (resid 6 through 33 or (resid 34 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 88)) } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.320 Process input model: 77.730 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 0.003 0.077 34661 Z= 0.163 Angle : 0.567 9.877 47386 Z= 0.310 Chirality : 0.040 0.236 5410 Planarity : 0.003 0.056 5699 Dihedral : 17.751 178.977 13637 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3919 helix: -0.13 (0.14), residues: 1470 sheet: -0.46 (0.27), residues: 379 loop : -1.11 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 580 HIS 0.004 0.001 HIS I 276 PHE 0.027 0.001 PHE J 31 TYR 0.043 0.001 TYR H 69 ARG 0.010 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.20835 ( 1343) hydrogen bonds : angle 7.54501 ( 3663) covalent geometry : bond 0.00316 (34661) covalent geometry : angle 0.56747 (47386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 73 ILE cc_start: 0.7620 (mm) cc_final: 0.7413 (mm) REVERT: A 205 MET cc_start: 0.8364 (tmm) cc_final: 0.8138 (tmm) REVERT: B 168 ILE cc_start: 0.8333 (mm) cc_final: 0.8111 (mm) REVERT: C 124 MET cc_start: 0.8074 (ppp) cc_final: 0.7728 (ppp) REVERT: C 315 MET cc_start: 0.8353 (mmm) cc_final: 0.8104 (mmp) REVERT: C 403 MET cc_start: 0.9004 (ppp) cc_final: 0.8509 (ppp) REVERT: C 515 MET cc_start: 0.8361 (tmm) cc_final: 0.8070 (tmm) REVERT: C 800 MET cc_start: 0.8504 (pmm) cc_final: 0.8129 (pmm) REVERT: C 1180 MET cc_start: 0.8530 (ppp) cc_final: 0.8281 (ppp) REVERT: D 192 MET cc_start: 0.8363 (ppp) cc_final: 0.7909 (ppp) REVERT: D 724 MET cc_start: 0.8808 (mpp) cc_final: 0.8262 (mpp) REVERT: E 18 ASP cc_start: 0.8870 (m-30) cc_final: 0.8619 (m-30) REVERT: E 60 ASN cc_start: 0.8573 (t0) cc_final: 0.8368 (t0) REVERT: F 273 MET cc_start: 0.7951 (mmp) cc_final: 0.7536 (ttt) REVERT: F 288 MET cc_start: 0.2708 (mpp) cc_final: 0.2447 (mpp) REVERT: F 456 MET cc_start: 0.7623 (mpp) cc_final: 0.7239 (mpp) REVERT: F 489 MET cc_start: 0.7921 (ptt) cc_final: 0.7441 (ptt) REVERT: I 316 MET cc_start: 0.4017 (ppp) cc_final: 0.3764 (ppp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.5224 time to fit residues: 147.1944 Evaluate side-chains 152 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 316 optimal weight: 50.0000 chunk 122 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 366 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN D 274 ASN D 545 HIS D 720 ASN D1023 HIS ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.047328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.033099 restraints weight = 343611.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.033888 restraints weight = 207603.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.034397 restraints weight = 151909.830| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34661 Z= 0.158 Angle : 0.574 9.567 47386 Z= 0.305 Chirality : 0.040 0.168 5410 Planarity : 0.004 0.041 5699 Dihedral : 18.281 178.870 5852 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.15 % Allowed : 6.06 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 3919 helix: -0.06 (0.13), residues: 1535 sheet: -0.52 (0.27), residues: 381 loop : -1.09 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.012 0.001 HIS I 276 PHE 0.039 0.001 PHE J 31 TYR 0.015 0.001 TYR D 631 ARG 0.007 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1343) hydrogen bonds : angle 5.41491 ( 3663) covalent geometry : bond 0.00341 (34661) covalent geometry : angle 0.57448 (47386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 3.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 12 ARG cc_start: 0.7397 (ptt-90) cc_final: 0.7145 (ptt-90) REVERT: J 34 GLN cc_start: 0.8428 (mt0) cc_final: 0.7657 (pp30) REVERT: J 77 PHE cc_start: 0.7587 (t80) cc_final: 0.7192 (m-10) REVERT: A 25 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8716 (mmmt) REVERT: A 205 MET cc_start: 0.8488 (tmm) cc_final: 0.7926 (tmm) REVERT: B 205 MET cc_start: 0.8480 (tmm) cc_final: 0.8255 (tmm) REVERT: C 124 MET cc_start: 0.8196 (ppp) cc_final: 0.7725 (ppp) REVERT: C 315 MET cc_start: 0.8488 (mmm) cc_final: 0.8256 (mmm) REVERT: C 403 MET cc_start: 0.9140 (ppp) cc_final: 0.8676 (ppp) REVERT: C 488 MET cc_start: 0.9087 (mmm) cc_final: 0.8829 (tpp) REVERT: C 515 MET cc_start: 0.8656 (tmm) cc_final: 0.7948 (tmm) REVERT: C 768 MET cc_start: 0.8397 (pmm) cc_final: 0.8077 (pmm) REVERT: C 800 MET cc_start: 0.8480 (pmm) cc_final: 0.8216 (pmm) REVERT: C 805 MET cc_start: 0.8666 (ppp) cc_final: 0.8194 (ppp) REVERT: C 1107 MET cc_start: 0.8917 (mmm) cc_final: 0.8692 (mmm) REVERT: C 1319 MET cc_start: 0.9012 (tpp) cc_final: 0.8810 (tpp) REVERT: D 130 MET cc_start: 0.7491 (mmm) cc_final: 0.7240 (mmm) REVERT: D 192 MET cc_start: 0.8493 (ppp) cc_final: 0.8149 (ppp) REVERT: D 466 MET cc_start: 0.8698 (mmm) cc_final: 0.8370 (tpp) REVERT: D 697 MET cc_start: 0.9148 (tmm) cc_final: 0.8930 (tmm) REVERT: D 724 MET cc_start: 0.8966 (mpp) cc_final: 0.8392 (mpp) REVERT: D 743 MET cc_start: 0.9096 (ptt) cc_final: 0.8870 (ptm) REVERT: D 1189 MET cc_start: 0.8958 (mmp) cc_final: 0.8715 (mmp) REVERT: D 1370 MET cc_start: 0.8914 (mtt) cc_final: 0.8488 (ppp) REVERT: E 18 ASP cc_start: 0.9008 (m-30) cc_final: 0.8805 (m-30) REVERT: F 273 MET cc_start: 0.8124 (mmp) cc_final: 0.7786 (ttt) REVERT: F 288 MET cc_start: 0.3344 (mpp) cc_final: 0.3122 (mpp) REVERT: F 365 MET cc_start: 0.9251 (ppp) cc_final: 0.8777 (ppp) REVERT: F 455 HIS cc_start: 0.8203 (t-90) cc_final: 0.7788 (t-90) REVERT: F 456 MET cc_start: 0.7791 (mpp) cc_final: 0.7439 (mpp) REVERT: F 489 MET cc_start: 0.8225 (ptt) cc_final: 0.8006 (ptt) REVERT: I 316 MET cc_start: 0.4006 (ppp) cc_final: 0.3799 (ppp) outliers start: 5 outliers final: 3 residues processed: 162 average time/residue: 0.4981 time to fit residues: 134.1732 Evaluate side-chains 153 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 76 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 250 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 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 = 0.3454 r_free = 0.3454 target = 0.044595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.030509 restraints weight = 344630.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.031279 restraints weight = 204234.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.031744 restraints weight = 147969.842| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34661 Z= 0.227 Angle : 0.635 11.507 47386 Z= 0.336 Chirality : 0.042 0.158 5410 Planarity : 0.004 0.096 5699 Dihedral : 18.612 179.564 5852 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.56 % Allowed : 10.24 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 3919 helix: -0.02 (0.13), residues: 1570 sheet: -0.48 (0.27), residues: 370 loop : -1.16 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 580 HIS 0.011 0.001 HIS F 242 PHE 0.030 0.002 PHE J 31 TYR 0.021 0.002 TYR D 631 ARG 0.008 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1343) hydrogen bonds : angle 5.06806 ( 3663) covalent geometry : bond 0.00487 (34661) covalent geometry : angle 0.63548 (47386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 12 ARG cc_start: 0.7706 (ptt-90) cc_final: 0.7485 (ptt-90) REVERT: J 34 GLN cc_start: 0.8474 (mt0) cc_final: 0.7736 (pp30) REVERT: J 54 ARG cc_start: 0.8900 (tpm170) cc_final: 0.8414 (mmp-170) REVERT: J 77 PHE cc_start: 0.7494 (t80) cc_final: 0.7155 (m-10) REVERT: A 25 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8574 (mmmm) REVERT: A 51 MET cc_start: 0.8658 (mmm) cc_final: 0.8455 (mmm) REVERT: C 124 MET cc_start: 0.8616 (ppp) cc_final: 0.7934 (ppp) REVERT: C 239 MET cc_start: 0.7241 (tmm) cc_final: 0.6998 (ttm) REVERT: C 403 MET cc_start: 0.9175 (ppp) cc_final: 0.8686 (ppp) REVERT: C 429 MET cc_start: 0.9191 (mmm) cc_final: 0.8972 (mmm) REVERT: C 488 MET cc_start: 0.9196 (mmm) cc_final: 0.8929 (mmm) REVERT: C 653 MET cc_start: 0.8245 (ttt) cc_final: 0.7968 (ttm) REVERT: C 681 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8389 (ptp) REVERT: C 805 MET cc_start: 0.8727 (ppp) cc_final: 0.8210 (ppp) REVERT: C 1066 MET cc_start: 0.8802 (mmm) cc_final: 0.8359 (mmm) REVERT: C 1232 MET cc_start: 0.9031 (mmp) cc_final: 0.8737 (mmp) REVERT: D 525 MET cc_start: 0.7809 (ppp) cc_final: 0.7418 (tmm) REVERT: D 697 MET cc_start: 0.8964 (tmm) cc_final: 0.8749 (tmm) REVERT: D 724 MET cc_start: 0.8887 (mpp) cc_final: 0.8538 (mpp) REVERT: F 273 MET cc_start: 0.8465 (mmp) cc_final: 0.8193 (ttt) REVERT: F 455 HIS cc_start: 0.8227 (t-90) cc_final: 0.7896 (t-90) REVERT: F 456 MET cc_start: 0.8172 (mpp) cc_final: 0.7575 (mpp) REVERT: F 489 MET cc_start: 0.8167 (ptt) cc_final: 0.7734 (ptt) REVERT: I 316 MET cc_start: 0.4527 (ppp) cc_final: 0.4061 (ppp) outliers start: 19 outliers final: 7 residues processed: 170 average time/residue: 0.4811 time to fit residues: 135.7184 Evaluate side-chains 152 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 511 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 237 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 205 optimal weight: 0.4980 chunk 256 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 339 optimal weight: 1.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 777 HIS D1279 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 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 = 0.3468 r_free = 0.3468 target = 0.045312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.031249 restraints weight = 343339.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.031991 restraints weight = 203416.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.032479 restraints weight = 148359.396| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34661 Z= 0.145 Angle : 0.551 11.325 47386 Z= 0.289 Chirality : 0.040 0.145 5410 Planarity : 0.003 0.051 5699 Dihedral : 18.501 177.165 5852 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.89 % Allowed : 12.20 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3919 helix: 0.14 (0.13), residues: 1569 sheet: -0.45 (0.26), residues: 401 loop : -1.07 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.005 0.001 HIS C1023 PHE 0.026 0.001 PHE H 31 TYR 0.025 0.001 TYR J 69 ARG 0.012 0.000 ARG J 85 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 1343) hydrogen bonds : angle 4.79320 ( 3663) covalent geometry : bond 0.00317 (34661) covalent geometry : angle 0.55114 (47386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8654 (mt0) cc_final: 0.8120 (pp30) REVERT: J 54 ARG cc_start: 0.8898 (tpm170) cc_final: 0.8434 (mmp-170) REVERT: J 77 PHE cc_start: 0.7592 (t80) cc_final: 0.7165 (m-10) REVERT: A 25 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8625 (mmmm) REVERT: A 51 MET cc_start: 0.8644 (mmm) cc_final: 0.8406 (mmm) REVERT: A 205 MET cc_start: 0.8620 (tmm) cc_final: 0.8208 (tmm) REVERT: B 51 MET cc_start: 0.8597 (mmm) cc_final: 0.8348 (mmm) REVERT: B 205 MET cc_start: 0.8500 (tmm) cc_final: 0.8298 (tmm) REVERT: C 124 MET cc_start: 0.8570 (ppp) cc_final: 0.7908 (ppp) REVERT: C 239 MET cc_start: 0.7246 (tmm) cc_final: 0.6966 (ttm) REVERT: C 403 MET cc_start: 0.9182 (ppp) cc_final: 0.8668 (ppp) REVERT: C 429 MET cc_start: 0.9228 (mmm) cc_final: 0.8981 (mmm) REVERT: C 653 MET cc_start: 0.8182 (ttt) cc_final: 0.7920 (ttm) REVERT: C 741 MET cc_start: 0.8821 (mmm) cc_final: 0.8608 (mmm) REVERT: C 768 MET cc_start: 0.8319 (pmm) cc_final: 0.8028 (pmm) REVERT: C 805 MET cc_start: 0.8663 (ppp) cc_final: 0.8160 (ppp) REVERT: C 1066 MET cc_start: 0.8811 (mmm) cc_final: 0.8493 (mmm) REVERT: C 1119 MET cc_start: 0.8333 (tpp) cc_final: 0.8103 (tpp) REVERT: D 180 MET cc_start: 0.6485 (tpp) cc_final: 0.6071 (tpp) REVERT: D 525 MET cc_start: 0.7658 (ppp) cc_final: 0.7457 (ppp) REVERT: D 697 MET cc_start: 0.9083 (tmm) cc_final: 0.8726 (tmm) REVERT: D 724 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8603 (mtt) REVERT: D 725 MET cc_start: 0.8930 (ptp) cc_final: 0.8632 (ptp) REVERT: E 75 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8154 (mm-40) REVERT: F 273 MET cc_start: 0.8499 (mmp) cc_final: 0.8288 (ttt) REVERT: F 365 MET cc_start: 0.9389 (ppp) cc_final: 0.8985 (ppp) REVERT: F 455 HIS cc_start: 0.8163 (t-90) cc_final: 0.7938 (t-90) REVERT: F 456 MET cc_start: 0.8276 (mpp) cc_final: 0.7761 (mpp) REVERT: I 316 MET cc_start: 0.4704 (ppp) cc_final: 0.4241 (ppp) outliers start: 30 outliers final: 8 residues processed: 185 average time/residue: 0.4808 time to fit residues: 147.1878 Evaluate side-chains 159 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 511 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 177 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 11 optimal weight: 0.0670 chunk 364 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 15 optimal weight: 9.9990 chunk 399 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 overall best weight: 3.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.045133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.031209 restraints weight = 338708.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.031951 restraints weight = 199535.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.032511 restraints weight = 145658.964| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34661 Z= 0.136 Angle : 0.542 9.578 47386 Z= 0.284 Chirality : 0.039 0.158 5410 Planarity : 0.003 0.047 5699 Dihedral : 18.442 176.994 5852 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.01 % Allowed : 13.09 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3919 helix: 0.24 (0.14), residues: 1570 sheet: -0.36 (0.26), residues: 405 loop : -1.09 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 580 HIS 0.005 0.001 HIS D 450 PHE 0.017 0.001 PHE J 31 TYR 0.033 0.001 TYR J 69 ARG 0.015 0.000 ARG F 373 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 1343) hydrogen bonds : angle 4.68218 ( 3663) covalent geometry : bond 0.00298 (34661) covalent geometry : angle 0.54213 (47386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8480 (mt0) cc_final: 0.8123 (pp30) REVERT: J 53 PHE cc_start: 0.7506 (m-80) cc_final: 0.6490 (m-10) REVERT: J 54 ARG cc_start: 0.8901 (tpm170) cc_final: 0.8423 (mmp-170) REVERT: J 77 PHE cc_start: 0.7602 (t80) cc_final: 0.7206 (m-10) REVERT: A 25 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8614 (mmmm) REVERT: A 205 MET cc_start: 0.8655 (tmm) cc_final: 0.8128 (tmm) REVERT: B 51 MET cc_start: 0.8552 (mmm) cc_final: 0.8347 (mmm) REVERT: B 205 MET cc_start: 0.8516 (tmm) cc_final: 0.8304 (tmm) REVERT: C 124 MET cc_start: 0.8583 (ppp) cc_final: 0.7841 (ppp) REVERT: C 239 MET cc_start: 0.7410 (tmm) cc_final: 0.7124 (ttm) REVERT: C 246 LEU cc_start: 0.9341 (pt) cc_final: 0.8653 (tp) REVERT: C 403 MET cc_start: 0.9173 (ppp) cc_final: 0.8565 (ppp) REVERT: C 429 MET cc_start: 0.9247 (mmm) cc_final: 0.8983 (mmm) REVERT: C 653 MET cc_start: 0.8125 (ttt) cc_final: 0.7845 (ttm) REVERT: C 805 MET cc_start: 0.8692 (ppp) cc_final: 0.8163 (ppp) REVERT: C 1066 MET cc_start: 0.8758 (mmm) cc_final: 0.8483 (mmm) REVERT: C 1119 MET cc_start: 0.8362 (tpp) cc_final: 0.8096 (tpp) REVERT: C 1274 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8803 (mp0) REVERT: D 130 MET cc_start: 0.7799 (mmm) cc_final: 0.7483 (mmm) REVERT: D 180 MET cc_start: 0.6584 (tpp) cc_final: 0.6064 (tpp) REVERT: D 697 MET cc_start: 0.9098 (tmm) cc_final: 0.8809 (tmm) REVERT: D 724 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8632 (mtt) REVERT: D 725 MET cc_start: 0.8980 (ptp) cc_final: 0.8658 (ptp) REVERT: F 273 MET cc_start: 0.8594 (mmp) cc_final: 0.8367 (ttt) REVERT: F 365 MET cc_start: 0.9413 (ppp) cc_final: 0.9090 (ppp) REVERT: F 379 MET cc_start: 0.9273 (tmm) cc_final: 0.8676 (tmm) REVERT: F 455 HIS cc_start: 0.8086 (t-90) cc_final: 0.7866 (t-90) REVERT: F 456 MET cc_start: 0.8350 (mpp) cc_final: 0.7769 (mpp) REVERT: I 316 MET cc_start: 0.4693 (ppp) cc_final: 0.4286 (ppp) outliers start: 34 outliers final: 16 residues processed: 186 average time/residue: 0.4725 time to fit residues: 146.5793 Evaluate side-chains 167 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 511 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 218 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 369 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 302 optimal weight: 0.0060 overall best weight: 6.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 702 GLN D1049 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.043882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030126 restraints weight = 339267.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.030856 restraints weight = 200746.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.031236 restraints weight = 145453.469| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34661 Z= 0.199 Angle : 0.596 13.266 47386 Z= 0.312 Chirality : 0.041 0.179 5410 Planarity : 0.004 0.048 5699 Dihedral : 18.544 177.948 5852 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.42 % Allowed : 14.01 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3919 helix: 0.25 (0.14), residues: 1574 sheet: -0.35 (0.26), residues: 386 loop : -1.16 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.005 0.001 HIS C 273 PHE 0.029 0.001 PHE H 31 TYR 0.033 0.001 TYR J 69 ARG 0.011 0.000 ARG J 85 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1343) hydrogen bonds : angle 4.75709 ( 3663) covalent geometry : bond 0.00429 (34661) covalent geometry : angle 0.59583 (47386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8531 (mt0) cc_final: 0.8071 (pp30) REVERT: J 77 PHE cc_start: 0.7622 (t80) cc_final: 0.7267 (m-10) REVERT: A 25 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8748 (mmmm) REVERT: A 205 MET cc_start: 0.8624 (tmm) cc_final: 0.8365 (tmm) REVERT: B 51 MET cc_start: 0.8621 (mmm) cc_final: 0.8257 (mmm) REVERT: C 41 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: C 124 MET cc_start: 0.8729 (ppp) cc_final: 0.7787 (ppp) REVERT: C 239 MET cc_start: 0.7497 (tmm) cc_final: 0.7254 (ttm) REVERT: C 246 LEU cc_start: 0.9315 (pt) cc_final: 0.8547 (tp) REVERT: C 403 MET cc_start: 0.9158 (ppp) cc_final: 0.8547 (ppp) REVERT: C 429 MET cc_start: 0.9255 (mmm) cc_final: 0.8941 (mmm) REVERT: C 515 MET cc_start: 0.8952 (ppp) cc_final: 0.8670 (tmm) REVERT: C 653 MET cc_start: 0.8306 (ttt) cc_final: 0.8044 (ttm) REVERT: C 741 MET cc_start: 0.8794 (mmm) cc_final: 0.8562 (mmm) REVERT: C 768 MET cc_start: 0.8410 (pmm) cc_final: 0.8114 (pmm) REVERT: C 805 MET cc_start: 0.8785 (ppp) cc_final: 0.8154 (ppp) REVERT: C 1066 MET cc_start: 0.8680 (mmm) cc_final: 0.8470 (mmm) REVERT: C 1107 MET cc_start: 0.9022 (mmm) cc_final: 0.8762 (tpp) REVERT: C 1119 MET cc_start: 0.8432 (tpp) cc_final: 0.8196 (tpp) REVERT: C 1274 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8857 (mp0) REVERT: D 130 MET cc_start: 0.7762 (mmm) cc_final: 0.7473 (mmm) REVERT: D 180 MET cc_start: 0.6666 (tpp) cc_final: 0.6301 (tpp) REVERT: D 697 MET cc_start: 0.9216 (tmm) cc_final: 0.8830 (tmm) REVERT: D 724 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8640 (mtt) REVERT: D 725 MET cc_start: 0.9051 (ptp) cc_final: 0.8732 (ptp) REVERT: D 1189 MET cc_start: 0.8984 (mmm) cc_final: 0.8755 (mmm) REVERT: E 18 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8548 (p0) REVERT: E 26 ARG cc_start: 0.8765 (tpt90) cc_final: 0.8404 (tpt90) REVERT: F 105 MET cc_start: 0.9492 (ppp) cc_final: 0.9157 (ppp) REVERT: F 365 MET cc_start: 0.9435 (ppp) cc_final: 0.9163 (ppp) REVERT: F 379 MET cc_start: 0.9386 (tmm) cc_final: 0.8702 (tmm) REVERT: F 455 HIS cc_start: 0.8108 (t-90) cc_final: 0.7905 (t-90) REVERT: F 456 MET cc_start: 0.8426 (mpp) cc_final: 0.8006 (mpp) REVERT: I 264 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8503 (p) outliers start: 48 outliers final: 20 residues processed: 195 average time/residue: 0.4527 time to fit residues: 147.2832 Evaluate side-chains 169 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain I residue 252 ILE Chi-restraints excluded: chain I residue 264 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 307 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 258 optimal weight: 0.1980 chunk 146 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 386 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN C 760 ASN D1049 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 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 = 0.3444 r_free = 0.3444 target = 0.044377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.030553 restraints weight = 336891.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.031307 restraints weight = 201011.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.031798 restraints weight = 147862.813| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34661 Z= 0.131 Angle : 0.562 12.010 47386 Z= 0.291 Chirality : 0.040 0.145 5410 Planarity : 0.003 0.062 5699 Dihedral : 18.475 175.920 5852 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.25 % Allowed : 15.02 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3919 helix: 0.35 (0.14), residues: 1572 sheet: -0.33 (0.26), residues: 393 loop : -1.12 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.005 0.001 HIS C1023 PHE 0.016 0.001 PHE J 23 TYR 0.033 0.001 TYR J 69 ARG 0.013 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 1343) hydrogen bonds : angle 4.60396 ( 3663) covalent geometry : bond 0.00289 (34661) covalent geometry : angle 0.56175 (47386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 12 ARG cc_start: 0.7447 (ptt-90) cc_final: 0.7221 (ptt-90) REVERT: J 34 GLN cc_start: 0.8461 (mt0) cc_final: 0.8191 (pp30) REVERT: J 77 PHE cc_start: 0.7662 (t80) cc_final: 0.7297 (m-10) REVERT: A 25 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8806 (mmmm) REVERT: A 205 MET cc_start: 0.8597 (tmm) cc_final: 0.8349 (tmm) REVERT: B 51 MET cc_start: 0.8547 (mmm) cc_final: 0.8227 (mmm) REVERT: B 145 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9089 (tptt) REVERT: C 41 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: C 239 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7213 (ttm) REVERT: C 246 LEU cc_start: 0.9282 (pt) cc_final: 0.8497 (tp) REVERT: C 403 MET cc_start: 0.9146 (ppp) cc_final: 0.8540 (ppp) REVERT: C 429 MET cc_start: 0.9234 (mmm) cc_final: 0.9032 (mmm) REVERT: C 515 MET cc_start: 0.8918 (ppp) cc_final: 0.8539 (tmm) REVERT: C 615 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8593 (p) REVERT: C 653 MET cc_start: 0.8136 (ttt) cc_final: 0.7883 (ttm) REVERT: C 741 MET cc_start: 0.8860 (mmm) cc_final: 0.8587 (mmm) REVERT: C 768 MET cc_start: 0.8370 (pmm) cc_final: 0.8062 (pmm) REVERT: C 805 MET cc_start: 0.8718 (ppp) cc_final: 0.8113 (ppp) REVERT: C 1066 MET cc_start: 0.8703 (mmm) cc_final: 0.8495 (mmm) REVERT: C 1107 MET cc_start: 0.8873 (mmm) cc_final: 0.8637 (tpp) REVERT: C 1274 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8837 (mp0) REVERT: D 130 MET cc_start: 0.7777 (mmm) cc_final: 0.7461 (mmm) REVERT: D 180 MET cc_start: 0.6561 (tpp) cc_final: 0.6182 (tpp) REVERT: D 298 MET cc_start: 0.9179 (mmm) cc_final: 0.8744 (mmm) REVERT: D 698 MET cc_start: 0.9432 (mmm) cc_final: 0.9171 (mmm) REVERT: D 725 MET cc_start: 0.9056 (ptp) cc_final: 0.8758 (ptp) REVERT: D 1189 MET cc_start: 0.9067 (mmm) cc_final: 0.8558 (tpp) REVERT: E 18 ASP cc_start: 0.9007 (m-30) cc_final: 0.8696 (p0) REVERT: E 26 ARG cc_start: 0.8806 (tpt90) cc_final: 0.8424 (tpt90) REVERT: F 105 MET cc_start: 0.9501 (ppp) cc_final: 0.9182 (ppp) REVERT: F 273 MET cc_start: 0.9171 (ttt) cc_final: 0.8379 (mmt) REVERT: F 365 MET cc_start: 0.9449 (ppp) cc_final: 0.9154 (ptp) REVERT: F 379 MET cc_start: 0.9345 (tmm) cc_final: 0.8887 (tmm) REVERT: F 456 MET cc_start: 0.8404 (mpp) cc_final: 0.7715 (mpp) REVERT: F 561 MET cc_start: 0.9014 (mmt) cc_final: 0.8126 (mpp) REVERT: I 264 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8482 (p) REVERT: I 316 MET cc_start: 0.4060 (ppp) cc_final: 0.3553 (ppp) REVERT: I 319 GLU cc_start: 0.7972 (pm20) cc_final: 0.7726 (pm20) outliers start: 42 outliers final: 20 residues processed: 194 average time/residue: 0.4859 time to fit residues: 158.2734 Evaluate side-chains 173 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain I residue 264 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 350 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 328 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN J 39 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN D1049 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 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 = 0.3403 r_free = 0.3403 target = 0.043053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.029494 restraints weight = 341677.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030180 restraints weight = 199866.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.030540 restraints weight = 144018.083| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34661 Z= 0.229 Angle : 0.641 11.567 47386 Z= 0.331 Chirality : 0.041 0.156 5410 Planarity : 0.004 0.050 5699 Dihedral : 18.610 177.764 5852 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.37 % Allowed : 15.35 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3919 helix: 0.27 (0.13), residues: 1576 sheet: -0.24 (0.27), residues: 365 loop : -1.19 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.006 0.001 HIS C 273 PHE 0.037 0.002 PHE J 31 TYR 0.039 0.002 TYR J 69 ARG 0.013 0.001 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1343) hydrogen bonds : angle 4.77640 ( 3663) covalent geometry : bond 0.00497 (34661) covalent geometry : angle 0.64070 (47386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8449 (mt0) cc_final: 0.8191 (pp30) REVERT: J 77 PHE cc_start: 0.7803 (t80) cc_final: 0.7415 (m-10) REVERT: A 205 MET cc_start: 0.8649 (tmm) cc_final: 0.8390 (tmm) REVERT: B 51 MET cc_start: 0.8563 (mmm) cc_final: 0.8173 (mmm) REVERT: B 145 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9066 (tptt) REVERT: C 41 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: C 239 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7242 (ttm) REVERT: C 246 LEU cc_start: 0.9216 (pt) cc_final: 0.8471 (tp) REVERT: C 269 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7062 (mp) REVERT: C 403 MET cc_start: 0.9159 (ppp) cc_final: 0.8565 (ppp) REVERT: C 515 MET cc_start: 0.8943 (ppp) cc_final: 0.8519 (ppp) REVERT: C 615 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8665 (p) REVERT: C 741 MET cc_start: 0.8861 (mmm) cc_final: 0.8632 (mmm) REVERT: C 768 MET cc_start: 0.8538 (pmm) cc_final: 0.8251 (pmm) REVERT: C 805 MET cc_start: 0.8797 (ppp) cc_final: 0.8158 (ppp) REVERT: C 1274 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8886 (mp0) REVERT: D 130 MET cc_start: 0.7779 (mmm) cc_final: 0.7553 (mmm) REVERT: D 180 MET cc_start: 0.6371 (tpp) cc_final: 0.6069 (tpp) REVERT: D 298 MET cc_start: 0.9288 (mmm) cc_final: 0.8716 (mmm) REVERT: D 697 MET cc_start: 0.9218 (tmm) cc_final: 0.8934 (tmm) REVERT: D 725 MET cc_start: 0.9099 (ptp) cc_final: 0.8784 (ptp) REVERT: D 1189 MET cc_start: 0.9056 (mmm) cc_final: 0.8599 (tpp) REVERT: E 13 ILE cc_start: 0.8620 (mp) cc_final: 0.7534 (mt) REVERT: E 18 ASP cc_start: 0.8987 (m-30) cc_final: 0.8779 (p0) REVERT: E 26 ARG cc_start: 0.8872 (tpt90) cc_final: 0.8480 (tpt90) REVERT: F 105 MET cc_start: 0.9518 (ppp) cc_final: 0.9213 (ppp) REVERT: F 273 MET cc_start: 0.9224 (ttt) cc_final: 0.8657 (mmp) REVERT: F 276 MET cc_start: 0.9377 (tpt) cc_final: 0.8867 (tpp) REVERT: F 365 MET cc_start: 0.9468 (ppp) cc_final: 0.9208 (ptp) REVERT: F 414 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.8950 (tptp) REVERT: F 561 MET cc_start: 0.9003 (mmt) cc_final: 0.8319 (mpp) REVERT: F 567 MET cc_start: 0.8253 (pmm) cc_final: 0.7782 (pmm) REVERT: I 264 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8745 (p) REVERT: I 316 MET cc_start: 0.4088 (ppp) cc_final: 0.3732 (ppp) outliers start: 46 outliers final: 24 residues processed: 192 average time/residue: 0.4682 time to fit residues: 150.6589 Evaluate side-chains 178 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain I residue 252 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 277 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 99 optimal weight: 40.0000 chunk 242 optimal weight: 0.5980 chunk 262 optimal weight: 30.0000 chunk 241 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 2 optimal weight: 50.0000 chunk 402 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 362 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.042673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.029272 restraints weight = 336847.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029913 restraints weight = 197052.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.030333 restraints weight = 143131.841| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34661 Z= 0.200 Angle : 0.622 17.189 47386 Z= 0.319 Chirality : 0.041 0.156 5410 Planarity : 0.004 0.052 5699 Dihedral : 18.616 175.024 5852 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.13 % Allowed : 16.18 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3919 helix: 0.31 (0.14), residues: 1570 sheet: -0.28 (0.27), residues: 375 loop : -1.24 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 326 HIS 0.008 0.001 HIS F 242 PHE 0.017 0.001 PHE F 221 TYR 0.040 0.001 TYR J 69 ARG 0.012 0.000 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1343) hydrogen bonds : angle 4.73807 ( 3663) covalent geometry : bond 0.00438 (34661) covalent geometry : angle 0.62250 (47386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 77 PHE cc_start: 0.7905 (t80) cc_final: 0.7550 (m-10) REVERT: A 205 MET cc_start: 0.8641 (tmm) cc_final: 0.8414 (tmm) REVERT: B 51 MET cc_start: 0.8560 (mmm) cc_final: 0.8175 (mmm) REVERT: B 145 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9112 (tptp) REVERT: C 41 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: C 246 LEU cc_start: 0.9210 (pt) cc_final: 0.8449 (tp) REVERT: C 269 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7060 (mp) REVERT: C 403 MET cc_start: 0.9117 (ppp) cc_final: 0.8504 (ppp) REVERT: C 515 MET cc_start: 0.8997 (ppp) cc_final: 0.8533 (ppp) REVERT: C 615 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8600 (p) REVERT: C 741 MET cc_start: 0.8853 (mmm) cc_final: 0.8650 (mmm) REVERT: C 768 MET cc_start: 0.8525 (pmm) cc_final: 0.8239 (pmm) REVERT: C 805 MET cc_start: 0.8829 (ppp) cc_final: 0.8177 (ppp) REVERT: C 1274 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8873 (mp0) REVERT: D 180 MET cc_start: 0.6285 (tpp) cc_final: 0.5987 (tpp) REVERT: D 298 MET cc_start: 0.9338 (mmm) cc_final: 0.8782 (mmm) REVERT: D 724 MET cc_start: 0.8873 (mtt) cc_final: 0.8668 (mmm) REVERT: D 743 MET cc_start: 0.8817 (ptt) cc_final: 0.8514 (ppp) REVERT: D 1189 MET cc_start: 0.9027 (mmm) cc_final: 0.8641 (tpp) REVERT: E 13 ILE cc_start: 0.8655 (mp) cc_final: 0.7741 (mt) REVERT: E 18 ASP cc_start: 0.8933 (m-30) cc_final: 0.8714 (p0) REVERT: E 26 ARG cc_start: 0.8912 (tpt90) cc_final: 0.8513 (tpt90) REVERT: F 102 MET cc_start: 0.9215 (mtp) cc_final: 0.8591 (mtp) REVERT: F 105 MET cc_start: 0.9463 (ppp) cc_final: 0.9136 (ppp) REVERT: F 273 MET cc_start: 0.9212 (ttt) cc_final: 0.8869 (mmp) REVERT: F 276 MET cc_start: 0.9441 (tpt) cc_final: 0.9069 (tpp) REVERT: F 288 MET cc_start: 0.4634 (mpp) cc_final: 0.4191 (mmt) REVERT: F 365 MET cc_start: 0.9478 (ppp) cc_final: 0.9202 (ptt) REVERT: F 561 MET cc_start: 0.8948 (mmt) cc_final: 0.8463 (mpp) REVERT: F 567 MET cc_start: 0.8178 (pmm) cc_final: 0.7762 (pmm) REVERT: I 264 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8779 (p) REVERT: I 316 MET cc_start: 0.4330 (ppp) cc_final: 0.3973 (ppp) outliers start: 38 outliers final: 23 residues processed: 184 average time/residue: 0.4566 time to fit residues: 140.0816 Evaluate side-chains 174 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain I residue 252 ILE Chi-restraints excluded: chain I residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 181 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 360 optimal weight: 50.0000 chunk 13 optimal weight: 0.9990 chunk 111 optimal weight: 0.0870 chunk 278 optimal weight: 4.9990 chunk 384 optimal weight: 6.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN A 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1366 HIS ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 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 = 0.3417 r_free = 0.3417 target = 0.043116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029693 restraints weight = 334068.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.030358 restraints weight = 195416.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.030816 restraints weight = 141080.554| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34661 Z= 0.130 Angle : 0.589 13.854 47386 Z= 0.300 Chirality : 0.040 0.182 5410 Planarity : 0.003 0.052 5699 Dihedral : 18.505 175.412 5852 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.89 % Allowed : 16.65 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3919 helix: 0.39 (0.14), residues: 1550 sheet: -0.26 (0.27), residues: 378 loop : -1.11 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 580 HIS 0.006 0.001 HIS F 242 PHE 0.029 0.001 PHE H 31 TYR 0.038 0.001 TYR J 69 ARG 0.010 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 1343) hydrogen bonds : angle 4.57736 ( 3663) covalent geometry : bond 0.00287 (34661) covalent geometry : angle 0.58927 (47386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 77 PHE cc_start: 0.7894 (t80) cc_final: 0.7533 (m-10) REVERT: A 205 MET cc_start: 0.8593 (tmm) cc_final: 0.8326 (tmm) REVERT: B 51 MET cc_start: 0.8484 (mmm) cc_final: 0.8052 (mmm) REVERT: C 41 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: C 246 LEU cc_start: 0.9241 (pt) cc_final: 0.8531 (tp) REVERT: C 269 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7219 (mp) REVERT: C 315 MET cc_start: 0.8848 (mmm) cc_final: 0.8432 (mmm) REVERT: C 403 MET cc_start: 0.9102 (ppp) cc_final: 0.8461 (ppp) REVERT: C 515 MET cc_start: 0.8995 (ppp) cc_final: 0.8504 (ppp) REVERT: C 768 MET cc_start: 0.8458 (pmm) cc_final: 0.8154 (pmm) REVERT: C 805 MET cc_start: 0.8764 (ppp) cc_final: 0.8132 (ppp) REVERT: C 1274 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8838 (mp0) REVERT: D 180 MET cc_start: 0.6268 (tpp) cc_final: 0.6051 (tpp) REVERT: D 298 MET cc_start: 0.9343 (mmm) cc_final: 0.8965 (mmm) REVERT: D 697 MET cc_start: 0.9312 (tmm) cc_final: 0.9032 (tmm) REVERT: D 724 MET cc_start: 0.8842 (mtt) cc_final: 0.8625 (mmm) REVERT: D 743 MET cc_start: 0.8717 (ptt) cc_final: 0.8505 (ppp) REVERT: D 1095 MET cc_start: 0.6463 (ppp) cc_final: 0.6248 (pmm) REVERT: D 1189 MET cc_start: 0.9069 (mmm) cc_final: 0.8666 (tpp) REVERT: E 13 ILE cc_start: 0.8582 (mp) cc_final: 0.7861 (mt) REVERT: E 18 ASP cc_start: 0.8985 (m-30) cc_final: 0.8754 (p0) REVERT: E 26 ARG cc_start: 0.8868 (tpt90) cc_final: 0.8498 (tpt90) REVERT: F 102 MET cc_start: 0.9190 (mtp) cc_final: 0.8566 (mtp) REVERT: F 273 MET cc_start: 0.9242 (ttt) cc_final: 0.8854 (mmp) REVERT: F 276 MET cc_start: 0.9437 (tpt) cc_final: 0.9089 (tpp) REVERT: F 365 MET cc_start: 0.9465 (ppp) cc_final: 0.9195 (ptp) REVERT: F 456 MET cc_start: 0.8744 (mpp) cc_final: 0.8428 (mpp) REVERT: F 561 MET cc_start: 0.8894 (mmt) cc_final: 0.8450 (mpp) REVERT: F 567 MET cc_start: 0.8117 (pmm) cc_final: 0.7753 (pmm) REVERT: I 316 MET cc_start: 0.4324 (ppp) cc_final: 0.3907 (ppp) outliers start: 30 outliers final: 22 residues processed: 179 average time/residue: 0.4789 time to fit residues: 144.0173 Evaluate side-chains 171 residues out of total 3385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain I residue 252 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 224 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 384 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.043151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.029658 restraints weight = 335853.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.030389 restraints weight = 196292.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.030856 restraints weight = 141222.028| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34661 Z= 0.122 Angle : 0.577 14.043 47386 Z= 0.294 Chirality : 0.040 0.186 5410 Planarity : 0.003 0.053 5699 Dihedral : 18.424 176.759 5852 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.89 % Allowed : 16.77 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3919 helix: 0.44 (0.14), residues: 1550 sheet: -0.14 (0.27), residues: 386 loop : -1.07 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 580 HIS 0.008 0.001 HIS F 242 PHE 0.010 0.001 PHE H 31 TYR 0.034 0.001 TYR J 69 ARG 0.009 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 1343) hydrogen bonds : angle 4.49913 ( 3663) covalent geometry : bond 0.00272 (34661) covalent geometry : angle 0.57723 (47386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10935.79 seconds wall clock time: 190 minutes 15.27 seconds (11415.27 seconds total)