Starting phenix.real_space_refine on Fri Jul 26 21:45:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6u_39001/07_2024/8y6u_39001.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6u_39001/07_2024/8y6u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6u_39001/07_2024/8y6u_39001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6u_39001/07_2024/8y6u_39001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6u_39001/07_2024/8y6u_39001.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6u_39001/07_2024/8y6u_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 Residue "H GLU 65": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "J PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 17.35, 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 - 3.50 Amino acid : False - 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: 14.81 Conformation dependent library (CDL) restraints added in 5.4 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: 11.00 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: 15.98 Time building geometry restraints manager: 15.74 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: 97.13 - 104.51: 942 104.51 - 111.89: 17133 111.89 - 119.27: 12080 119.27 - 126.65: 16516 126.65 - 134.03: 715 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 2.440 nonbonded pdb=" O SER F 389 " pdb=" NZ LYS F 393 " model vdw 2.205 2.520 nonbonded pdb=" O PRO A 179 " pdb=" OG1 THR A 207 " model vdw 2.205 2.440 nonbonded pdb=" OG SER C 318 " pdb=" OD1 ASP C 320 " model vdw 2.210 2.440 nonbonded pdb=" O VAL F 606 " pdb=" OG SER F 609 " model vdw 2.210 2.440 ... (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 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.270 Set scattering table: 0.300 Process input model: 96.490 Find NCS groups from input model: 0.740 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.800 ------------------------------------------------------------------------------- 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= 0.205 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 3.757 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: 0.4737 time to fit residues: 132.4122 Evaluate side-chains 152 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 3.771 ------------------------------------------------------------------------------- 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: 20.0000 chunk 306 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 366 optimal weight: 50.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 387 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D 720 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34661 Z= 0.222 Angle : 0.564 9.668 47386 Z= 0.298 Chirality : 0.040 0.172 5410 Planarity : 0.003 0.040 5699 Dihedral : 18.253 178.559 5852 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.15 % Allowed : 6.47 % Favored : 93.38 % 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: -0.92 (0.13), residues: 3919 helix: -0.01 (0.14), residues: 1540 sheet: -0.47 (0.26), residues: 385 loop : -1.08 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.013 0.001 HIS I 276 PHE 0.043 0.001 PHE J 31 TYR 0.015 0.001 TYR D 631 ARG 0.006 0.000 ARG J 12 *********************** 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 165 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 3.988 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 12 ARG cc_start: 0.7419 (ptt-90) cc_final: 0.7153 (ptt-90) REVERT: J 77 PHE cc_start: 0.7614 (t80) cc_final: 0.7213 (m-10) REVERT: A 25 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8720 (mmmt) REVERT: A 205 MET cc_start: 0.8436 (tmm) cc_final: 0.7958 (tmm) REVERT: B 205 MET cc_start: 0.8532 (tmm) cc_final: 0.8270 (tmm) REVERT: C 124 MET cc_start: 0.8193 (ppp) cc_final: 0.7722 (ppp) REVERT: C 403 MET cc_start: 0.9036 (ppp) cc_final: 0.8617 (ppp) REVERT: C 515 MET cc_start: 0.8700 (tmm) cc_final: 0.8015 (tmm) REVERT: C 800 MET cc_start: 0.8372 (pmm) cc_final: 0.7959 (pmm) REVERT: C 805 MET cc_start: 0.8584 (ppp) cc_final: 0.8132 (ppp) REVERT: C 1107 MET cc_start: 0.8861 (mmm) cc_final: 0.8648 (mmm) REVERT: D 130 MET cc_start: 0.7388 (mmm) cc_final: 0.7180 (mmm) REVERT: D 192 MET cc_start: 0.8419 (ppp) cc_final: 0.8061 (ppp) REVERT: D 466 MET cc_start: 0.8687 (mmm) cc_final: 0.8391 (tpp) REVERT: D 724 MET cc_start: 0.8951 (mpp) cc_final: 0.8397 (mpp) REVERT: D 1189 MET cc_start: 0.8948 (mmp) cc_final: 0.8695 (mmp) REVERT: E 60 ASN cc_start: 0.8618 (t0) cc_final: 0.8409 (t0) REVERT: E 75 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7523 (mm-40) REVERT: F 273 MET cc_start: 0.8038 (mmp) cc_final: 0.7700 (ttt) REVERT: F 288 MET cc_start: 0.2930 (mpp) cc_final: 0.2588 (mpp) REVERT: F 365 MET cc_start: 0.9241 (ppp) cc_final: 0.8815 (ppp) REVERT: F 455 HIS cc_start: 0.8153 (t-90) cc_final: 0.7573 (t-90) REVERT: F 456 MET cc_start: 0.7429 (mpp) cc_final: 0.7133 (mpp) REVERT: F 489 MET cc_start: 0.8224 (ptt) cc_final: 0.7952 (ptt) REVERT: I 316 MET cc_start: 0.4020 (ppp) cc_final: 0.3807 (ppp) outliers start: 5 outliers final: 3 residues processed: 160 average time/residue: 0.4909 time to fit residues: 129.8000 Evaluate side-chains 152 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain E residue 8 ASP 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 203 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 305 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 397 optimal weight: 0.9990 chunk 327 optimal weight: 1.9990 chunk 364 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 618 GLN C 952 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 GLN ** F 362 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34661 Z= 0.160 Angle : 0.515 11.288 47386 Z= 0.270 Chirality : 0.039 0.178 5410 Planarity : 0.003 0.043 5699 Dihedral : 18.231 177.415 5852 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.36 % Allowed : 9.38 % Favored : 90.26 % 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: -0.72 (0.14), residues: 3919 helix: 0.25 (0.14), residues: 1543 sheet: -0.46 (0.26), residues: 391 loop : -1.03 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.008 0.001 HIS F 242 PHE 0.016 0.001 PHE H 70 TYR 0.012 0.001 TYR J 69 ARG 0.008 0.000 ARG E 69 *********************** 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 171 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 3.874 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 12 ARG cc_start: 0.7510 (ptt-90) cc_final: 0.7301 (ptt-90) REVERT: J 34 GLN cc_start: 0.8526 (mt0) cc_final: 0.7773 (pp30) REVERT: J 77 PHE cc_start: 0.7597 (t80) cc_final: 0.7222 (m-10) REVERT: A 25 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8755 (mmmm) REVERT: B 205 MET cc_start: 0.8580 (tmm) cc_final: 0.8338 (tmm) REVERT: C 124 MET cc_start: 0.8309 (ppp) cc_final: 0.7893 (ppp) REVERT: C 239 MET cc_start: 0.6981 (tmm) cc_final: 0.6613 (ttm) REVERT: C 403 MET cc_start: 0.9039 (ppp) cc_final: 0.8595 (ppp) REVERT: C 488 MET cc_start: 0.8552 (tpp) cc_final: 0.8268 (tpp) REVERT: C 800 MET cc_start: 0.8325 (pmm) cc_final: 0.7953 (pmm) REVERT: C 1066 MET cc_start: 0.8890 (mmm) cc_final: 0.8638 (mmm) REVERT: C 1232 MET cc_start: 0.9030 (mmp) cc_final: 0.8829 (mmp) REVERT: D 130 MET cc_start: 0.7707 (mmm) cc_final: 0.7484 (mmm) REVERT: D 151 MET cc_start: 0.7630 (ptp) cc_final: 0.6970 (ptt) REVERT: D 698 MET cc_start: 0.9386 (mmm) cc_final: 0.9113 (mmm) REVERT: D 724 MET cc_start: 0.8804 (mpp) cc_final: 0.8377 (mpp) REVERT: D 1189 MET cc_start: 0.8993 (mmp) cc_final: 0.8735 (mmp) REVERT: F 273 MET cc_start: 0.8145 (mmp) cc_final: 0.7872 (ttt) REVERT: F 288 MET cc_start: 0.2833 (mpp) cc_final: 0.2525 (mpp) REVERT: F 365 MET cc_start: 0.9288 (ppp) cc_final: 0.8963 (ppp) REVERT: F 455 HIS cc_start: 0.8032 (t-90) cc_final: 0.7570 (t-90) REVERT: F 456 MET cc_start: 0.7605 (mpp) cc_final: 0.7164 (mpp) REVERT: I 316 MET cc_start: 0.4307 (ppp) cc_final: 0.4020 (ppp) outliers start: 12 outliers final: 5 residues processed: 166 average time/residue: 0.4775 time to fit residues: 130.6295 Evaluate side-chains 153 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 8 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 390 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 349 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 519 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN ** F 362 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2440 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= 0.295 Angle : 0.593 10.048 47386 Z= 0.311 Chirality : 0.040 0.139 5410 Planarity : 0.004 0.045 5699 Dihedral : 18.461 179.506 5852 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.80 % Allowed : 11.43 % Favored : 87.77 % 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: -0.75 (0.14), residues: 3919 helix: 0.21 (0.14), residues: 1563 sheet: -0.38 (0.25), residues: 409 loop : -1.07 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.006 0.001 HIS D 80 PHE 0.029 0.002 PHE H 31 TYR 0.021 0.002 TYR J 69 ARG 0.010 0.001 ARG E 69 *********************** 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 185 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 3.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8356 (mt0) cc_final: 0.7612 (pp30) REVERT: J 77 PHE cc_start: 0.7476 (t80) cc_final: 0.7087 (m-10) REVERT: A 25 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8622 (mmmm) REVERT: A 205 MET cc_start: 0.8603 (tmm) cc_final: 0.8178 (tmm) REVERT: B 51 MET cc_start: 0.8777 (mmm) cc_final: 0.8540 (mmm) REVERT: B 205 MET cc_start: 0.8429 (tmm) cc_final: 0.8171 (tmm) REVERT: C 124 MET cc_start: 0.8635 (ppp) cc_final: 0.7922 (ppp) REVERT: C 239 MET cc_start: 0.7110 (tmm) cc_final: 0.6843 (ttm) REVERT: C 246 LEU cc_start: 0.9308 (pt) cc_final: 0.8639 (tp) REVERT: C 369 MET cc_start: 0.9216 (tmm) cc_final: 0.8960 (tmm) REVERT: C 403 MET cc_start: 0.9044 (ppp) cc_final: 0.8607 (ppp) REVERT: C 800 MET cc_start: 0.8494 (pmm) cc_final: 0.8219 (pmm) REVERT: C 805 MET cc_start: 0.8672 (ppp) cc_final: 0.8133 (ppp) REVERT: C 1107 MET cc_start: 0.8872 (mmm) cc_final: 0.8534 (tpp) REVERT: D 180 MET cc_start: 0.6107 (tpp) cc_final: 0.5855 (tpp) REVERT: D 525 MET cc_start: 0.7522 (ppp) cc_final: 0.7117 (tmm) REVERT: D 697 MET cc_start: 0.9063 (tmm) cc_final: 0.8798 (tmm) REVERT: F 105 MET cc_start: 0.9408 (ppp) cc_final: 0.9089 (ppp) REVERT: F 273 MET cc_start: 0.8439 (mmp) cc_final: 0.8229 (ttt) REVERT: F 379 MET cc_start: 0.9328 (tmm) cc_final: 0.8818 (tmm) REVERT: F 455 HIS cc_start: 0.8132 (t-90) cc_final: 0.7785 (t-90) REVERT: F 456 MET cc_start: 0.7842 (mpp) cc_final: 0.7151 (mpp) REVERT: F 561 MET cc_start: 0.8974 (mmt) cc_final: 0.8201 (mpp) REVERT: F 567 MET cc_start: 0.8338 (pmm) cc_final: 0.8033 (pmm) REVERT: I 316 MET cc_start: 0.4445 (ppp) cc_final: 0.4155 (ppp) outliers start: 27 outliers final: 11 residues processed: 179 average time/residue: 0.4597 time to fit residues: 136.5622 Evaluate side-chains 154 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain I residue 277 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 5.9990 chunk 221 optimal weight: 0.0060 chunk 5 optimal weight: 40.0000 chunk 290 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 333 optimal weight: 30.0000 chunk 269 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 199 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- 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** B 75 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 387 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2785 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= 0.217 Angle : 0.549 13.343 47386 Z= 0.287 Chirality : 0.039 0.152 5410 Planarity : 0.003 0.047 5699 Dihedral : 18.444 176.441 5852 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.98 % Allowed : 12.88 % Favored : 86.14 % 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: -0.63 (0.14), residues: 3919 helix: 0.37 (0.14), residues: 1555 sheet: -0.43 (0.25), residues: 411 loop : -1.01 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.005 0.001 HIS F 242 PHE 0.013 0.001 PHE H 70 TYR 0.031 0.001 TYR J 69 ARG 0.010 0.000 ARG J 56 *********************** 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 193 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 3.957 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: 0.8366 (mt0) cc_final: 0.7859 (pp30) REVERT: J 77 PHE cc_start: 0.7634 (t80) cc_final: 0.7264 (m-10) REVERT: A 25 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8663 (mmmm) REVERT: B 51 MET cc_start: 0.8645 (mmm) cc_final: 0.8258 (mmm) REVERT: B 205 MET cc_start: 0.8518 (tmm) cc_final: 0.8251 (tmm) REVERT: C 124 MET cc_start: 0.8609 (ppp) cc_final: 0.7860 (ppp) REVERT: C 239 MET cc_start: 0.7179 (tmm) cc_final: 0.6895 (ttm) REVERT: C 246 LEU cc_start: 0.9242 (pt) cc_final: 0.8481 (tp) REVERT: C 369 MET cc_start: 0.9242 (tmm) cc_final: 0.8991 (tmm) REVERT: C 403 MET cc_start: 0.9032 (ppp) cc_final: 0.8550 (ppp) REVERT: C 488 MET cc_start: 0.8484 (tpp) cc_final: 0.8000 (tpp) REVERT: C 800 MET cc_start: 0.8392 (pmm) cc_final: 0.8147 (pmm) REVERT: C 805 MET cc_start: 0.8659 (ppp) cc_final: 0.8126 (ppp) REVERT: C 1149 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: D 180 MET cc_start: 0.6117 (tpp) cc_final: 0.5498 (tpp) REVERT: D 237 MET cc_start: 0.8572 (mmm) cc_final: 0.8333 (tpp) REVERT: D 298 MET cc_start: 0.9229 (mmm) cc_final: 0.8901 (mmm) REVERT: D 525 MET cc_start: 0.7484 (ppp) cc_final: 0.7205 (tmm) REVERT: D 697 MET cc_start: 0.9071 (tmm) cc_final: 0.8790 (tmm) REVERT: D 1189 MET cc_start: 0.9094 (mmm) cc_final: 0.8753 (mmm) REVERT: F 105 MET cc_start: 0.9393 (ppp) cc_final: 0.9060 (ppp) REVERT: F 365 MET cc_start: 0.9379 (ppp) cc_final: 0.9046 (ppp) REVERT: F 379 MET cc_start: 0.9262 (tmm) cc_final: 0.8687 (tmm) REVERT: F 455 HIS cc_start: 0.8121 (t-90) cc_final: 0.7906 (t-90) REVERT: F 456 MET cc_start: 0.7810 (mpp) cc_final: 0.7266 (mpp) REVERT: F 489 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8007 (ptt) REVERT: F 567 MET cc_start: 0.8187 (pmm) cc_final: 0.7965 (pmm) REVERT: I 316 MET cc_start: 0.4723 (ppp) cc_final: 0.4432 (ppp) outliers start: 33 outliers final: 15 residues processed: 185 average time/residue: 0.4708 time to fit residues: 144.2036 Evaluate side-chains 163 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 3.856 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 489 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 chunk 390 optimal weight: 6.9990 chunk 324 optimal weight: 0.0870 chunk 180 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- 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** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34661 Z= 0.224 Angle : 0.553 10.077 47386 Z= 0.289 Chirality : 0.039 0.183 5410 Planarity : 0.003 0.082 5699 Dihedral : 18.450 176.536 5852 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.25 % Allowed : 13.71 % Favored : 85.04 % 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: 0.41 (0.14), residues: 1550 sheet: -0.39 (0.25), residues: 416 loop : -0.99 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 315 HIS 0.005 0.001 HIS F 242 PHE 0.031 0.001 PHE H 31 TYR 0.035 0.001 TYR J 69 ARG 0.012 0.000 ARG J 56 *********************** 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 192 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8325 (mt0) cc_final: 0.7903 (pp30) REVERT: J 77 PHE cc_start: 0.7642 (t80) cc_final: 0.7249 (m-10) REVERT: A 25 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8848 (mmmm) REVERT: A 205 MET cc_start: 0.8600 (tmm) cc_final: 0.8205 (tmm) REVERT: B 51 MET cc_start: 0.8593 (mmm) cc_final: 0.8264 (mmm) REVERT: B 205 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8163 (tmm) REVERT: C 124 MET cc_start: 0.8642 (ppp) cc_final: 0.7810 (ppp) REVERT: C 369 MET cc_start: 0.9240 (tmm) cc_final: 0.8730 (tmm) REVERT: C 403 MET cc_start: 0.9043 (ppp) cc_final: 0.8541 (ppp) REVERT: C 800 MET cc_start: 0.8410 (pmm) cc_final: 0.8187 (pmm) REVERT: C 805 MET cc_start: 0.8659 (ppp) cc_final: 0.8112 (ppp) REVERT: C 1066 MET cc_start: 0.8827 (mmm) cc_final: 0.8355 (mmm) REVERT: C 1107 MET cc_start: 0.8827 (mmt) cc_final: 0.8550 (mmt) REVERT: C 1149 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8039 (m-10) REVERT: D 180 MET cc_start: 0.6155 (tpp) cc_final: 0.5814 (tpp) REVERT: D 298 MET cc_start: 0.9253 (mmm) cc_final: 0.8902 (mmm) REVERT: D 697 MET cc_start: 0.9099 (tmm) cc_final: 0.8819 (tmm) REVERT: F 105 MET cc_start: 0.9380 (ppp) cc_final: 0.9041 (ppp) REVERT: F 273 MET cc_start: 0.9010 (ttt) cc_final: 0.8413 (mmp) REVERT: F 365 MET cc_start: 0.9357 (ppp) cc_final: 0.9043 (ptt) REVERT: F 379 MET cc_start: 0.9213 (tmm) cc_final: 0.8639 (tmm) REVERT: F 456 MET cc_start: 0.8020 (mpp) cc_final: 0.7550 (mpp) REVERT: F 567 MET cc_start: 0.8232 (pmm) cc_final: 0.7897 (pmm) REVERT: I 316 MET cc_start: 0.4846 (ppp) cc_final: 0.4562 (ppp) outliers start: 42 outliers final: 22 residues processed: 185 average time/residue: 0.4562 time to fit residues: 140.6282 Evaluate side-chains 166 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 3.821 ------------------------------------------------------------------------------- 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 B residue 205 MET 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 933 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1233 LEU 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 849 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain I residue 277 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 221 optimal weight: 0.0670 chunk 329 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 389 optimal weight: 30.0000 chunk 243 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- 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** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3475 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= 0.210 Angle : 0.561 13.721 47386 Z= 0.290 Chirality : 0.040 0.251 5410 Planarity : 0.003 0.057 5699 Dihedral : 18.468 176.043 5852 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.22 % Allowed : 14.37 % Favored : 84.42 % 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: -0.55 (0.14), residues: 3919 helix: 0.46 (0.14), residues: 1548 sheet: -0.36 (0.25), residues: 419 loop : -1.00 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.004 0.001 HIS D 450 PHE 0.017 0.001 PHE J 23 TYR 0.035 0.001 TYR J 69 ARG 0.012 0.000 ARG J 56 *********************** 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 195 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 3.854 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: 0.8419 (mt0) cc_final: 0.7878 (pp30) REVERT: J 77 PHE cc_start: 0.7658 (t80) cc_final: 0.7325 (m-10) REVERT: A 25 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8905 (mmmm) REVERT: A 205 MET cc_start: 0.8592 (tmm) cc_final: 0.8154 (tmm) REVERT: B 51 MET cc_start: 0.8559 (mmm) cc_final: 0.8201 (mmm) REVERT: C 124 MET cc_start: 0.8718 (ppp) cc_final: 0.7844 (ppp) REVERT: C 369 MET cc_start: 0.9204 (tmm) cc_final: 0.8689 (tmm) REVERT: C 403 MET cc_start: 0.9032 (ppp) cc_final: 0.8507 (ppp) REVERT: C 805 MET cc_start: 0.8613 (ppp) cc_final: 0.8029 (ppp) REVERT: C 1066 MET cc_start: 0.8786 (mmm) cc_final: 0.8457 (mmm) REVERT: C 1107 MET cc_start: 0.8793 (mmt) cc_final: 0.8453 (mmt) REVERT: C 1149 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: D 180 MET cc_start: 0.6287 (tpp) cc_final: 0.5451 (tpp) REVERT: D 237 MET cc_start: 0.8623 (mmm) cc_final: 0.8337 (mmm) REVERT: D 298 MET cc_start: 0.9229 (mmm) cc_final: 0.8892 (mmm) REVERT: D 697 MET cc_start: 0.9099 (tmm) cc_final: 0.8784 (tmm) REVERT: E 13 ILE cc_start: 0.8618 (mp) cc_final: 0.7549 (mt) REVERT: E 18 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8694 (p0) REVERT: E 26 ARG cc_start: 0.8777 (tpt90) cc_final: 0.8380 (tpt90) REVERT: F 105 MET cc_start: 0.9414 (ppp) cc_final: 0.9092 (ppp) REVERT: F 273 MET cc_start: 0.9125 (ttt) cc_final: 0.8481 (mmt) REVERT: F 365 MET cc_start: 0.9363 (ppp) cc_final: 0.9155 (ptt) REVERT: F 379 MET cc_start: 0.9228 (tmm) cc_final: 0.8892 (tmm) REVERT: F 561 MET cc_start: 0.9196 (mmm) cc_final: 0.8304 (mpp) REVERT: F 567 MET cc_start: 0.8229 (pmm) cc_final: 0.7920 (pmm) REVERT: I 316 MET cc_start: 0.4890 (ppp) cc_final: 0.4632 (ppp) outliers start: 41 outliers final: 24 residues processed: 190 average time/residue: 0.4666 time to fit residues: 147.8467 Evaluate side-chains 172 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 4.254 ------------------------------------------------------------------------------- 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 107 ILE Chi-restraints excluded: chain B residue 153 VAL 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 663 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1233 LEU 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 545 HIS Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 244 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 232 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 306 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34661 Z= 0.146 Angle : 0.540 13.603 47386 Z= 0.277 Chirality : 0.039 0.150 5410 Planarity : 0.003 0.061 5699 Dihedral : 18.373 175.221 5852 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.22 % Allowed : 14.66 % Favored : 84.12 % 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: -0.44 (0.14), residues: 3919 helix: 0.53 (0.14), residues: 1551 sheet: -0.24 (0.26), residues: 394 loop : -0.94 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 315 HIS 0.009 0.001 HIS J 39 PHE 0.034 0.001 PHE J 31 TYR 0.035 0.001 TYR J 69 ARG 0.011 0.000 ARG J 56 *********************** 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 194 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 3.803 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: 0.8494 (mt0) cc_final: 0.8195 (pp30) REVERT: J 77 PHE cc_start: 0.7661 (t80) cc_final: 0.7279 (m-10) REVERT: A 205 MET cc_start: 0.8563 (tmm) cc_final: 0.8064 (tmm) REVERT: B 51 MET cc_start: 0.8612 (mmm) cc_final: 0.8258 (mmm) REVERT: C 124 MET cc_start: 0.8533 (ppp) cc_final: 0.7685 (ppp) REVERT: C 403 MET cc_start: 0.8995 (ppp) cc_final: 0.8366 (ppp) REVERT: C 805 MET cc_start: 0.8546 (ppp) cc_final: 0.7981 (ppp) REVERT: C 1066 MET cc_start: 0.8799 (mmm) cc_final: 0.8505 (mmm) REVERT: C 1107 MET cc_start: 0.8708 (mmt) cc_final: 0.8347 (mmt) REVERT: C 1149 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: D 180 MET cc_start: 0.6258 (tpp) cc_final: 0.5074 (tpp) REVERT: D 298 MET cc_start: 0.9151 (mmm) cc_final: 0.8889 (mmt) REVERT: D 697 MET cc_start: 0.9091 (tmm) cc_final: 0.8772 (tmm) REVERT: D 743 MET cc_start: 0.8670 (ptt) cc_final: 0.8313 (ppp) REVERT: E 13 ILE cc_start: 0.8589 (mp) cc_final: 0.7680 (mt) REVERT: E 18 ASP cc_start: 0.8961 (m-30) cc_final: 0.8585 (p0) REVERT: E 26 ARG cc_start: 0.8880 (tpt90) cc_final: 0.8474 (tpt90) REVERT: F 105 MET cc_start: 0.9388 (ppp) cc_final: 0.9041 (ppp) REVERT: F 273 MET cc_start: 0.9065 (ttt) cc_final: 0.8356 (mmt) REVERT: F 365 MET cc_start: 0.9366 (ppp) cc_final: 0.9145 (ptt) REVERT: F 567 MET cc_start: 0.8264 (pmm) cc_final: 0.7963 (pmm) REVERT: I 264 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8487 (p) REVERT: I 316 MET cc_start: 0.5141 (ppp) cc_final: 0.4838 (ppp) outliers start: 41 outliers final: 24 residues processed: 190 average time/residue: 0.4571 time to fit residues: 144.5349 Evaluate side-chains 173 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL 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 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 408 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 E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain I residue 252 ILE Chi-restraints excluded: chain I residue 264 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 362 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 343 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34661 Z= 0.194 Angle : 0.557 13.397 47386 Z= 0.284 Chirality : 0.039 0.144 5410 Planarity : 0.003 0.059 5699 Dihedral : 18.375 176.845 5852 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.89 % Allowed : 15.41 % Favored : 83.70 % 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: -0.44 (0.14), residues: 3919 helix: 0.54 (0.14), residues: 1560 sheet: -0.25 (0.26), residues: 419 loop : -0.96 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 580 HIS 0.005 0.001 HIS D 450 PHE 0.011 0.001 PHE J 23 TYR 0.033 0.001 TYR J 69 ARG 0.014 0.000 ARG J 56 *********************** 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 176 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 34 GLN cc_start: 0.8433 (mt0) cc_final: 0.8192 (pp30) REVERT: J 77 PHE cc_start: 0.7773 (t80) cc_final: 0.7394 (m-10) REVERT: A 205 MET cc_start: 0.8637 (tmm) cc_final: 0.8207 (tmm) REVERT: B 51 MET cc_start: 0.8611 (mmm) cc_final: 0.8203 (mmm) REVERT: C 403 MET cc_start: 0.9001 (ppp) cc_final: 0.8384 (ppp) REVERT: C 459 MET cc_start: 0.8854 (mtt) cc_final: 0.8636 (mpp) REVERT: C 805 MET cc_start: 0.8578 (ppp) cc_final: 0.8003 (ppp) REVERT: C 1066 MET cc_start: 0.8759 (mmm) cc_final: 0.8490 (mmm) REVERT: C 1107 MET cc_start: 0.8710 (mmt) cc_final: 0.8369 (mmt) REVERT: C 1149 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: D 180 MET cc_start: 0.6355 (tpp) cc_final: 0.5902 (tpp) REVERT: D 298 MET cc_start: 0.9188 (mmm) cc_final: 0.8912 (mmt) REVERT: D 697 MET cc_start: 0.9110 (tmm) cc_final: 0.8757 (tmm) REVERT: D 1189 MET cc_start: 0.8937 (mmm) cc_final: 0.8649 (tpt) REVERT: E 13 ILE cc_start: 0.8633 (mp) cc_final: 0.7893 (mt) REVERT: E 18 ASP cc_start: 0.8942 (m-30) cc_final: 0.8706 (p0) REVERT: E 26 ARG cc_start: 0.8806 (tpt90) cc_final: 0.8399 (tpt90) REVERT: F 105 MET cc_start: 0.9428 (ppp) cc_final: 0.9103 (ppp) REVERT: F 273 MET cc_start: 0.9112 (ttt) cc_final: 0.8450 (mmt) REVERT: F 276 MET cc_start: 0.9376 (tpt) cc_final: 0.8839 (tpp) REVERT: F 365 MET cc_start: 0.9384 (ppp) cc_final: 0.9142 (ptt) REVERT: F 561 MET cc_start: 0.9191 (mmm) cc_final: 0.8302 (mpp) REVERT: F 567 MET cc_start: 0.8267 (pmm) cc_final: 0.7994 (pmm) REVERT: I 264 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (p) REVERT: I 316 MET cc_start: 0.5335 (ppp) cc_final: 0.5048 (ppp) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 0.4733 time to fit residues: 136.0444 Evaluate side-chains 169 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 3.727 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 92 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 1169 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 583 THR 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 361 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 383 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 402 optimal weight: 8.9990 chunk 370 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 387 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34661 Z= 0.249 Angle : 0.614 15.131 47386 Z= 0.312 Chirality : 0.040 0.198 5410 Planarity : 0.004 0.059 5699 Dihedral : 18.496 176.880 5852 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.95 % Allowed : 15.52 % Favored : 83.53 % 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: -0.47 (0.14), residues: 3919 helix: 0.53 (0.14), residues: 1549 sheet: -0.19 (0.26), residues: 388 loop : -0.99 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 580 HIS 0.010 0.001 HIS F 242 PHE 0.029 0.001 PHE H 31 TYR 0.038 0.001 TYR J 69 ARG 0.015 0.000 ARG J 56 ********************** 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 186 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 3.818 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 77 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: A 205 MET cc_start: 0.8518 (tmm) cc_final: 0.8158 (tmm) REVERT: B 51 MET cc_start: 0.8628 (mmm) cc_final: 0.8242 (mmm) REVERT: C 315 MET cc_start: 0.8881 (mmm) cc_final: 0.8352 (mmm) REVERT: C 403 MET cc_start: 0.8972 (ppp) cc_final: 0.8372 (ppp) REVERT: C 488 MET cc_start: 0.8971 (mmm) cc_final: 0.8529 (mmm) REVERT: C 805 MET cc_start: 0.8651 (ppp) cc_final: 0.8051 (ppp) REVERT: C 1066 MET cc_start: 0.8740 (mmm) cc_final: 0.8468 (mmm) REVERT: C 1107 MET cc_start: 0.8812 (mmt) cc_final: 0.8456 (mmt) REVERT: C 1149 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8159 (m-10) REVERT: D 180 MET cc_start: 0.6550 (tpp) cc_final: 0.5958 (tpp) REVERT: D 298 MET cc_start: 0.9216 (mmm) cc_final: 0.8902 (mmt) REVERT: D 697 MET cc_start: 0.9085 (tmm) cc_final: 0.8733 (tmm) REVERT: D 743 MET cc_start: 0.8755 (ptt) cc_final: 0.8296 (ppp) REVERT: D 1189 MET cc_start: 0.9150 (mmm) cc_final: 0.8901 (tpp) REVERT: E 13 ILE cc_start: 0.8713 (mp) cc_final: 0.7993 (mt) REVERT: E 26 ARG cc_start: 0.8871 (tpt90) cc_final: 0.8499 (tpt90) REVERT: F 102 MET cc_start: 0.9245 (mtp) cc_final: 0.8449 (mtp) REVERT: F 105 MET cc_start: 0.9466 (ppp) cc_final: 0.9136 (ppp) REVERT: F 273 MET cc_start: 0.9210 (ttt) cc_final: 0.8523 (mmt) REVERT: F 276 MET cc_start: 0.9468 (tpt) cc_final: 0.9042 (tpp) REVERT: F 365 MET cc_start: 0.9406 (ppp) cc_final: 0.9127 (ptt) REVERT: F 567 MET cc_start: 0.8182 (pmm) cc_final: 0.7924 (pmm) REVERT: I 264 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8673 (p) REVERT: I 316 MET cc_start: 0.5510 (ppp) cc_final: 0.5235 (ppp) outliers start: 32 outliers final: 22 residues processed: 180 average time/residue: 0.4795 time to fit residues: 144.4077 Evaluate side-chains 169 residues out of total 3385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 77 PHE 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 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 976 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain E residue 8 ASP 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 583 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 341 optimal weight: 0.0050 chunk 98 optimal weight: 0.2980 chunk 295 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 329 optimal weight: 0.9980 chunk 40 optimal weight: 30.0000 overall best weight: 2.0598 ------------------------------------------------------------------------------- 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** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.043918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.030545 restraints weight = 331208.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.031293 restraints weight = 194025.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.031650 restraints weight = 139811.005| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34661 Z= 0.156 Angle : 0.563 13.114 47386 Z= 0.285 Chirality : 0.039 0.176 5410 Planarity : 0.003 0.062 5699 Dihedral : 18.421 175.288 5852 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.83 % Allowed : 15.79 % Favored : 83.38 % 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: -0.42 (0.14), residues: 3919 helix: 0.57 (0.14), residues: 1547 sheet: -0.23 (0.27), residues: 392 loop : -0.94 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 326 HIS 0.008 0.001 HIS F 242 PHE 0.011 0.001 PHE H 77 TYR 0.035 0.001 TYR J 69 ARG 0.013 0.000 ARG J 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4934.34 seconds wall clock time: 90 minutes 51.71 seconds (5451.71 seconds total)