Starting phenix.real_space_refine on Mon Sep 30 06:39:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp9_33996/09_2024/7yp9_33996.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp9_33996/09_2024/7yp9_33996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp9_33996/09_2024/7yp9_33996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp9_33996/09_2024/7yp9_33996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp9_33996/09_2024/7yp9_33996.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yp9_33996/09_2024/7yp9_33996.cif" } resolution = 3.58 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 100 5.16 5 C 15232 2.51 5 N 4337 2.21 5 O 4814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24547 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1649 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1583 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 199} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 9548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9548 Classifications: {'peptide': 1230} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1180} Chain breaks: 8 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 121 Chain: "D" Number of atoms: 9937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 9937 Classifications: {'peptide': 1285} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1231} Chain breaks: 8 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 517 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13220 SG CYS D 70 102.849 43.200 55.763 1.00 57.05 S ATOM 13366 SG CYS D 88 105.019 45.869 54.094 1.00 61.37 S ATOM 18828 SG CYS D 814 80.360 62.455 113.857 1.00 50.20 S ATOM 19354 SG CYS D 888 79.640 63.643 109.166 1.00 30.92 S ATOM 19426 SG CYS D 898 77.002 63.070 111.952 1.00 31.94 S Time building chain proxies: 14.38, per 1000 atoms: 0.59 Number of scatterers: 24547 At special positions: 0 Unit cell: (127, 151, 146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 100 16.00 P 61 15.00 Mg 1 11.99 O 4814 8.00 N 4337 7.00 C 15232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.25 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 39 sheets defined 34.4% alpha, 12.6% beta 20 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 7.98 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.567A pdb=" N LEU A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.650A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'B' and resid 34 through 50 removed outlier: 4.220A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.535A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.745A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.668A 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) Processing helix chain 'C' and resid 31 through 40 removed outlier: 3.776A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.628A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.901A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 217 through 225 removed outlier: 4.221A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 removed outlier: 4.116A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 4.302A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.520A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.571A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 359 through 369 removed outlier: 3.538A pdb=" N LEU C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.729A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.883A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) 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 471 Processing helix chain 'C' and resid 471 through 482 removed outlier: 3.658A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 507 removed outlier: 4.493A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.624A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.057A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.723A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.607A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET C 685 " --> pdb=" O MET C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 4.212A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 3.761A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 969 removed outlier: 4.202A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 953 " --> pdb=" O GLU C 949 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 968 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1038 removed outlier: 4.037A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1149 Processing helix chain 'C' and resid 1165 through 1176 removed outlier: 3.677A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.681A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C1196 " --> pdb=" O GLU C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1279 removed outlier: 3.575A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.628A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C1292 " --> pdb=" O GLN C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.797A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.647A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.837A pdb=" N ARG D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 99' Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.572A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 removed outlier: 3.521A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 136' Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.522A pdb=" N LEU D 169 " --> pdb=" O TYR D 165 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.830A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.681A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.684A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 265 through 284 removed outlier: 3.591A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.718A 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: 3.550A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 394 through 404 removed outlier: 3.672A pdb=" N LYS D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 404 " --> pdb=" O MET D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 4.079A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.898A 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 453 through 458 Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.870A pdb=" N GLU D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.671A pdb=" N MET D 513 " --> pdb=" O GLY D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.693A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.807A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 removed outlier: 3.633A pdb=" N MET D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 4.553A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 671 removed outlier: 4.033A pdb=" N HIS D 651 " --> pdb=" O PRO D 647 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.729A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.785A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.511A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.613A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 3.600A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 925 removed outlier: 3.625A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1223 removed outlier: 3.915A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.800A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 4.190A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.720A pdb=" N ILE D1287 " --> pdb=" O SER D1283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D1288 " --> pdb=" O ARG D1284 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.602A pdb=" N SER D1324 " --> pdb=" O ILE D1320 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 3.535A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.754A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.731A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.541A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.611A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.519A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 6.364A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 147 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 7.472A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.552A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 17 removed outlier: 7.115A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.647A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.795A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.143A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.862A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 151 removed outlier: 3.764A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 231 removed outlier: 4.049A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.904A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 529 through 531 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.887A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.546A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.785A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 722 through 727 removed outlier: 3.663A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 798 through 804 removed outlier: 8.168A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C1074 " --> pdb=" O MET C1066 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 839 removed outlier: 3.529A pdb=" N VAL C1052 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C1050 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 934 " --> pdb=" O ILE C1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.591A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.996A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AD3, first strand: chain 'D' and resid 352 through 354 Processing sheet with id=AD4, first strand: chain 'D' and resid 367 through 369 removed outlier: 6.335A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.707A pdb=" N VAL D 548 " --> pdb=" O THR D 572 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 552 through 554 removed outlier: 4.239A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.515A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 982 through 985 Processing sheet with id=AD9, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE1, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 4.193A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.519A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.640A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 10.37 Time building geometry restraints manager: 7.23 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: 7787 1.34 - 1.46: 3336 1.46 - 1.57: 13614 1.57 - 1.69: 119 1.69 - 1.81: 173 Bond restraints: 25029 Sorted by residual: bond pdb=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.61e+00 bond pdb=" N ASN D 962 " pdb=" CA ASN D 962 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.35e+00 bond pdb=" C3' DG G 10 " pdb=" O3' DG G 10 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.69e+00 bond pdb=" N GLY D 231 " pdb=" CA GLY D 231 " ideal model delta sigma weight residual 1.449 1.471 -0.022 1.45e-02 4.76e+03 2.31e+00 bond pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.27e+00 ... (remaining 25024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 33185 1.76 - 3.52: 768 3.52 - 5.28: 88 5.28 - 7.04: 35 7.04 - 8.80: 15 Bond angle restraints: 34091 Sorted by residual: angle pdb=" C VAL B 192 " pdb=" N GLU B 193 " pdb=" CA GLU B 193 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C LEU D 128 " pdb=" N ASP D 129 " pdb=" CA ASP D 129 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C GLY C 64 " pdb=" N ASN C 65 " pdb=" CA ASN C 65 " ideal model delta sigma weight residual 122.08 128.09 -6.01 1.47e+00 4.63e-01 1.67e+01 angle pdb=" C ARG B 158 " pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.49e+01 ... (remaining 34086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 14488 27.87 - 55.75: 689 55.75 - 83.62: 72 83.62 - 111.50: 9 111.50 - 139.37: 1 Dihedral angle restraints: 15259 sinusoidal: 6612 harmonic: 8647 Sorted by residual: dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+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 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DG G 10 " pdb=" C3' DG G 10 " pdb=" O3' DG G 10 " pdb=" P DT G 11 " ideal model delta sinusoidal sigma weight residual 220.00 80.63 139.37 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 15256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2964 0.046 - 0.092: 713 0.092 - 0.137: 236 0.137 - 0.183: 38 0.183 - 0.229: 7 Chirality restraints: 3958 Sorted by residual: chirality pdb=" CA ASP D 129 " pdb=" N ASP D 129 " pdb=" C ASP D 129 " pdb=" CB ASP D 129 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE B 183 " pdb=" CA ILE B 183 " pdb=" CG1 ILE B 183 " pdb=" CG2 ILE B 183 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE D 22 " pdb=" CA ILE D 22 " pdb=" CG1 ILE D 22 " pdb=" CG2 ILE D 22 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3955 not shown) Planarity restraints: 4218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C1103 " -0.047 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO C1104 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C1104 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1104 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO D1139 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO C 552 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " -0.033 5.00e-02 4.00e+02 ... (remaining 4215 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 580 2.69 - 3.24: 21555 3.24 - 3.80: 39302 3.80 - 4.35: 52610 4.35 - 4.90: 84078 Nonbonded interactions: 198125 Sorted by model distance: nonbonded pdb=" NH2 ARG D 425 " pdb=" O3' U H 0 " model vdw 2.140 3.120 nonbonded pdb=" O VAL C 296 " pdb=" OG1 THR C 335 " model vdw 2.258 3.040 nonbonded pdb=" NH1 ARG D 425 " pdb=" O3' U H 0 " model vdw 2.259 3.120 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.286 3.040 nonbonded pdb=" O GLN C1288 " pdb=" OG1 THR C1292 " model vdw 2.320 3.040 ... (remaining 198120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 75 or (resid 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 130 or re \ sid 140 through 144 or (resid 145 and (name N or name CA or name C or name O or \ name CB )) or resid 146 through 157 or resid 168 or resid 172 through 190 or (re \ sid 191 through 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 232)) selection = (chain 'B' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 31 or (resid 32 through 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 149 or (resid 150 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name NE )) or resi \ d 151 through 157 or resid 159 through 191 or (resid 192 and (name N or name CA \ or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or name \ CA or name C or name O or name CB )) or resid 195 through 232)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 64.300 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 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 0.049 25029 Z= 0.186 Angle : 0.657 8.803 34091 Z= 0.357 Chirality : 0.047 0.229 3958 Planarity : 0.005 0.070 4218 Dihedral : 14.963 139.371 9683 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -4.82 (0.11), residues: 2965 helix: -4.78 (0.05), residues: 950 sheet: -1.90 (0.30), residues: 256 loop : -2.52 (0.11), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 580 HIS 0.005 0.001 HIS C 150 PHE 0.013 0.001 PHE D 892 TYR 0.010 0.001 TYR C 47 ARG 0.008 0.000 ARG D 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 672 time to evaluate : 2.752 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: C 476 LYS cc_start: 0.6107 (mttt) cc_final: 0.5485 (tptp) REVERT: C 530 ILE cc_start: 0.9189 (mm) cc_final: 0.8741 (mm) REVERT: C 808 ASN cc_start: 0.6979 (t0) cc_final: 0.6670 (t0) REVERT: C 810 TYR cc_start: 0.8319 (m-80) cc_final: 0.7681 (m-80) REVERT: C 1064 ASP cc_start: 0.6786 (m-30) cc_final: 0.6518 (m-30) REVERT: C 1278 LEU cc_start: 0.8575 (tp) cc_final: 0.8318 (tp) REVERT: D 96 LYS cc_start: 0.7266 (ptmt) cc_final: 0.7058 (ptmt) REVERT: D 133 ARG cc_start: 0.6786 (mpt-90) cc_final: 0.6180 (tpt170) REVERT: D 889 ASP cc_start: 0.4795 (p0) cc_final: 0.4580 (p0) outliers start: 2 outliers final: 1 residues processed: 674 average time/residue: 0.4311 time to fit residues: 427.6189 Evaluate side-chains 439 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 706 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 92 optimal weight: 0.0040 chunk 144 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 7.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 41 ASN A 132 HIS A 208 ASN C 276 GLN C 343 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 762 ASN C 766 ASN C 799 ASN C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1135 GLN C1236 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 164 GLN D 341 ASN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN D 667 GLN D 736 GLN D 865 HIS D 962 ASN D1252 HIS D1366 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25029 Z= 0.303 Angle : 0.638 10.995 34091 Z= 0.330 Chirality : 0.044 0.211 3958 Planarity : 0.006 0.066 4218 Dihedral : 13.641 140.052 4019 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.20 % Allowed : 14.70 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -3.38 (0.13), residues: 2965 helix: -2.96 (0.12), residues: 1002 sheet: -1.66 (0.29), residues: 264 loop : -1.88 (0.13), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 580 HIS 0.007 0.001 HIS D1252 PHE 0.020 0.002 PHE D 437 TYR 0.015 0.002 TYR D 360 ARG 0.010 0.001 ARG D1149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 516 time to evaluate : 2.829 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: A 67 GLU cc_start: 0.7546 (pt0) cc_final: 0.7243 (pt0) REVERT: A 76 GLU cc_start: 0.7033 (tp30) cc_final: 0.6750 (tp30) REVERT: A 181 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 39 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8516 (mm) REVERT: B 51 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.6093 (ttm) REVERT: B 211 ILE cc_start: 0.8178 (pt) cc_final: 0.7914 (pt) REVERT: C 72 SER cc_start: 0.6257 (t) cc_final: 0.5824 (m) REVERT: C 653 MET cc_start: 0.7529 (tmm) cc_final: 0.6885 (ttt) REVERT: C 805 MET cc_start: 0.7180 (ppp) cc_final: 0.6964 (ppp) REVERT: C 807 TRP cc_start: 0.6815 (t60) cc_final: 0.6487 (t60) REVERT: C 810 TYR cc_start: 0.8847 (m-80) cc_final: 0.8578 (m-80) REVERT: C 865 LEU cc_start: 0.6684 (mt) cc_final: 0.6410 (mt) REVERT: C 1232 MET cc_start: 0.6811 (mmt) cc_final: 0.6583 (mmt) REVERT: C 1278 LEU cc_start: 0.8877 (tp) cc_final: 0.8586 (tp) REVERT: C 1336 ASN cc_start: 0.8539 (t0) cc_final: 0.8215 (t0) REVERT: D 133 ARG cc_start: 0.7258 (mpt-90) cc_final: 0.6592 (tpt170) REVERT: D 626 TYR cc_start: 0.7264 (m-10) cc_final: 0.7021 (m-10) REVERT: D 760 THR cc_start: 0.8100 (p) cc_final: 0.7893 (p) outliers start: 80 outliers final: 52 residues processed: 558 average time/residue: 0.3673 time to fit residues: 320.7279 Evaluate side-chains 479 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 425 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 298 optimal weight: 0.0970 chunk 246 optimal weight: 10.0000 chunk 274 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 799 ASN C 811 ASN C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25029 Z= 0.173 Angle : 0.535 10.332 34091 Z= 0.271 Chirality : 0.041 0.185 3958 Planarity : 0.005 0.062 4218 Dihedral : 13.514 137.819 4018 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.72 % Allowed : 17.02 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -2.47 (0.14), residues: 2965 helix: -1.73 (0.15), residues: 1001 sheet: -1.60 (0.30), residues: 262 loop : -1.57 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 236 HIS 0.004 0.001 HIS C1070 PHE 0.014 0.001 PHE C 545 TYR 0.025 0.001 TYR B 177 ARG 0.007 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 471 time to evaluate : 2.560 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: A 67 GLU cc_start: 0.7459 (pt0) cc_final: 0.7184 (pt0) REVERT: B 39 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8656 (mm) REVERT: C 71 VAL cc_start: 0.4393 (OUTLIER) cc_final: 0.3992 (p) REVERT: C 72 SER cc_start: 0.6070 (t) cc_final: 0.5788 (m) REVERT: C 349 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.6014 (tt0) REVERT: C 430 LYS cc_start: 0.7270 (mttp) cc_final: 0.7068 (mttp) REVERT: C 653 MET cc_start: 0.7361 (tmm) cc_final: 0.6844 (ttt) REVERT: C 699 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8012 (mm) REVERT: C 711 ASP cc_start: 0.5513 (m-30) cc_final: 0.5172 (m-30) REVERT: C 808 ASN cc_start: 0.7556 (t0) cc_final: 0.7331 (t0) REVERT: C 1089 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5588 (mm-30) REVERT: C 1107 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6337 (mmp) REVERT: C 1216 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7348 (mtm-85) REVERT: C 1232 MET cc_start: 0.6727 (mmt) cc_final: 0.6400 (mmt) REVERT: C 1278 LEU cc_start: 0.8920 (tp) cc_final: 0.8541 (tp) REVERT: C 1290 MET cc_start: 0.8037 (tpp) cc_final: 0.7751 (mmt) REVERT: C 1336 ASN cc_start: 0.8470 (t0) cc_final: 0.8063 (t0) REVERT: D 78 LEU cc_start: 0.3145 (OUTLIER) cc_final: 0.2691 (mp) REVERT: D 133 ARG cc_start: 0.7289 (mpt-90) cc_final: 0.6535 (tpt170) REVERT: D 432 LEU cc_start: 0.9132 (mm) cc_final: 0.8892 (mt) REVERT: D 475 GLU cc_start: 0.7415 (pt0) cc_final: 0.7119 (mt-10) REVERT: D 571 ASP cc_start: 0.7103 (t70) cc_final: 0.6870 (p0) outliers start: 93 outliers final: 47 residues processed: 524 average time/residue: 0.3422 time to fit residues: 287.6176 Evaluate side-chains 468 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 415 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain E residue 4 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.0270 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 277 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 ASN D1098 GLN D1326 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25029 Z= 0.286 Angle : 0.594 12.907 34091 Z= 0.299 Chirality : 0.042 0.201 3958 Planarity : 0.004 0.064 4218 Dihedral : 13.563 137.106 4018 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.68 % Allowed : 19.30 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.95 (0.14), residues: 2965 helix: -1.16 (0.16), residues: 998 sheet: -1.48 (0.29), residues: 293 loop : -1.30 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.011 0.001 HIS C 273 PHE 0.017 0.002 PHE C 405 TYR 0.014 0.002 TYR D 360 ARG 0.014 0.001 ARG C 647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 486 time to evaluate : 2.993 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: B 39 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 84 ASN cc_start: 0.8395 (m110) cc_final: 0.7792 (m110) REVERT: C 133 ASN cc_start: 0.7199 (t0) cc_final: 0.6886 (t0) REVERT: C 138 ILE cc_start: 0.7311 (mm) cc_final: 0.7109 (mm) REVERT: C 653 MET cc_start: 0.7584 (tmm) cc_final: 0.7274 (ttt) REVERT: C 1232 MET cc_start: 0.7043 (mmt) cc_final: 0.6729 (mmt) REVERT: C 1274 GLU cc_start: 0.7100 (mp0) cc_final: 0.6717 (mp0) REVERT: C 1278 LEU cc_start: 0.9086 (tp) cc_final: 0.8676 (tp) REVERT: C 1291 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7904 (pp) REVERT: D 78 LEU cc_start: 0.3809 (OUTLIER) cc_final: 0.3207 (mp) REVERT: D 133 ARG cc_start: 0.7458 (mpt-90) cc_final: 0.6769 (tpt170) REVERT: D 347 VAL cc_start: 0.9329 (t) cc_final: 0.9048 (m) REVERT: D 432 LEU cc_start: 0.9300 (mm) cc_final: 0.9060 (mt) REVERT: D 725 MET cc_start: 0.7706 (mtm) cc_final: 0.7249 (mtm) REVERT: D 754 ILE cc_start: 0.8768 (mm) cc_final: 0.8541 (mt) REVERT: D 957 SER cc_start: 0.8038 (m) cc_final: 0.7793 (t) outliers start: 92 outliers final: 65 residues processed: 543 average time/residue: 0.3557 time to fit residues: 306.4894 Evaluate side-chains 486 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 418 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1247 SER Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 263 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN A 147 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25029 Z= 0.221 Angle : 0.570 11.484 34091 Z= 0.284 Chirality : 0.041 0.176 3958 Planarity : 0.004 0.051 4218 Dihedral : 13.532 134.444 4018 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.16 % Allowed : 20.93 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.58 (0.15), residues: 2965 helix: -0.76 (0.16), residues: 1001 sheet: -1.26 (0.30), residues: 290 loop : -1.15 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 236 HIS 0.004 0.001 HIS C 343 PHE 0.016 0.001 PHE C 545 TYR 0.013 0.001 TYR D 360 ARG 0.007 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 448 time to evaluate : 3.959 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: B 39 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 129 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8248 (mt) REVERT: C 133 ASN cc_start: 0.7201 (t0) cc_final: 0.6867 (t0) REVERT: C 653 MET cc_start: 0.7634 (tmm) cc_final: 0.7331 (ttt) REVERT: C 1107 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6797 (mmp) REVERT: C 1180 MET cc_start: 0.8098 (tpp) cc_final: 0.7717 (ttm) REVERT: C 1265 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6394 (t80) REVERT: C 1274 GLU cc_start: 0.7037 (mp0) cc_final: 0.6593 (mp0) REVERT: C 1278 LEU cc_start: 0.9000 (tp) cc_final: 0.8617 (tp) REVERT: C 1291 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7818 (pp) REVERT: D 133 ARG cc_start: 0.7527 (mpt-90) cc_final: 0.6796 (tpt170) REVERT: D 172 PHE cc_start: 0.6127 (t80) cc_final: 0.5918 (t80) REVERT: D 347 VAL cc_start: 0.9264 (t) cc_final: 0.8938 (m) REVERT: D 432 LEU cc_start: 0.9264 (mm) cc_final: 0.9032 (mt) REVERT: D 457 TYR cc_start: 0.8390 (m-80) cc_final: 0.8120 (m-80) REVERT: D 581 MET cc_start: 0.6787 (mtm) cc_final: 0.6550 (mtm) REVERT: D 725 MET cc_start: 0.7761 (mtm) cc_final: 0.7337 (mtm) REVERT: D 822 MET cc_start: 0.7264 (mmp) cc_final: 0.7013 (mmm) REVERT: D 957 SER cc_start: 0.7997 (m) cc_final: 0.7773 (t) REVERT: D 1251 LYS cc_start: 0.8616 (pttm) cc_final: 0.8223 (pttp) outliers start: 104 outliers final: 77 residues processed: 515 average time/residue: 0.3391 time to fit residues: 281.4241 Evaluate side-chains 491 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 409 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 294 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 458 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25029 Z= 0.281 Angle : 0.603 12.923 34091 Z= 0.301 Chirality : 0.043 0.224 3958 Planarity : 0.004 0.046 4218 Dihedral : 13.552 133.067 4018 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.95 % Allowed : 20.50 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.48 (0.15), residues: 2965 helix: -0.60 (0.16), residues: 1004 sheet: -1.19 (0.31), residues: 286 loop : -1.14 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.005 0.001 HIS D 80 PHE 0.014 0.002 PHE C 464 TYR 0.012 0.002 TYR D 537 ARG 0.006 0.001 ARG C1223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 449 time to evaluate : 2.560 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: B 39 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8794 (mm) REVERT: C 133 ASN cc_start: 0.7200 (t0) cc_final: 0.6878 (t0) REVERT: C 336 LEU cc_start: 0.7886 (pp) cc_final: 0.7641 (pp) REVERT: C 542 ARG cc_start: 0.6177 (mpt180) cc_final: 0.5593 (mmt-90) REVERT: C 653 MET cc_start: 0.7767 (tmm) cc_final: 0.7566 (ttt) REVERT: C 657 THR cc_start: 0.8263 (t) cc_final: 0.8032 (p) REVERT: C 711 ASP cc_start: 0.6631 (m-30) cc_final: 0.6357 (m-30) REVERT: C 1079 ILE cc_start: 0.8737 (mm) cc_final: 0.8471 (mm) REVERT: C 1107 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6878 (mmp) REVERT: C 1146 GLN cc_start: 0.8528 (tp40) cc_final: 0.8164 (tp40) REVERT: C 1180 MET cc_start: 0.8131 (tpp) cc_final: 0.7792 (ttm) REVERT: C 1274 GLU cc_start: 0.7170 (mp0) cc_final: 0.6798 (mp0) REVERT: D 133 ARG cc_start: 0.7673 (mpt-90) cc_final: 0.6963 (tpt170) REVERT: D 304 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.6107 (t0) REVERT: D 347 VAL cc_start: 0.9307 (t) cc_final: 0.9050 (m) REVERT: D 362 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.7305 (mtp85) REVERT: D 432 LEU cc_start: 0.9308 (mm) cc_final: 0.9001 (mt) REVERT: D 475 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7385 (mp0) REVERT: D 725 MET cc_start: 0.7900 (mtm) cc_final: 0.7566 (mtm) REVERT: D 957 SER cc_start: 0.8045 (m) cc_final: 0.7815 (t) REVERT: D 1251 LYS cc_start: 0.8772 (pttm) cc_final: 0.8465 (pttp) outliers start: 124 outliers final: 92 residues processed: 527 average time/residue: 0.3556 time to fit residues: 296.9720 Evaluate side-chains 510 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 415 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25029 Z= 0.289 Angle : 0.613 12.661 34091 Z= 0.307 Chirality : 0.043 0.207 3958 Planarity : 0.004 0.052 4218 Dihedral : 13.595 131.182 4018 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.63 % Allowed : 21.57 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.41 (0.15), residues: 2965 helix: -0.58 (0.16), residues: 1007 sheet: -1.19 (0.32), residues: 281 loop : -1.07 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.005 0.001 HIS D1252 PHE 0.017 0.002 PHE C 545 TYR 0.012 0.002 TYR D 360 ARG 0.015 0.001 ARG D 838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 451 time to evaluate : 3.065 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: C 68 LEU cc_start: 0.8160 (tp) cc_final: 0.7925 (tp) REVERT: C 129 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8517 (mt) REVERT: C 133 ASN cc_start: 0.7256 (t0) cc_final: 0.6924 (t0) REVERT: C 179 TYR cc_start: 0.7298 (t80) cc_final: 0.6683 (t80) REVERT: C 542 ARG cc_start: 0.6170 (mpt180) cc_final: 0.5763 (mmt-90) REVERT: C 611 GLU cc_start: 0.7686 (tt0) cc_final: 0.7462 (tt0) REVERT: C 657 THR cc_start: 0.8235 (t) cc_final: 0.7978 (p) REVERT: C 711 ASP cc_start: 0.6856 (m-30) cc_final: 0.6523 (m-30) REVERT: C 1079 ILE cc_start: 0.8845 (mm) cc_final: 0.8595 (mm) REVERT: C 1107 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6933 (mmp) REVERT: C 1180 MET cc_start: 0.8140 (tpp) cc_final: 0.7856 (ttm) REVERT: C 1274 GLU cc_start: 0.7208 (mp0) cc_final: 0.6847 (mp0) REVERT: C 1307 ASN cc_start: 0.6868 (t0) cc_final: 0.6476 (t0) REVERT: D 133 ARG cc_start: 0.7743 (mpt-90) cc_final: 0.7009 (tpt170) REVERT: D 298 MET cc_start: 0.6728 (tpp) cc_final: 0.6421 (mmt) REVERT: D 304 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6391 (t0) REVERT: D 347 VAL cc_start: 0.9270 (t) cc_final: 0.8973 (m) REVERT: D 362 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7291 (mtp85) REVERT: D 432 LEU cc_start: 0.9273 (mm) cc_final: 0.9004 (mt) REVERT: D 437 PHE cc_start: 0.9304 (m-80) cc_final: 0.9104 (m-80) REVERT: D 725 MET cc_start: 0.7984 (mtm) cc_final: 0.7671 (mtm) outliers start: 116 outliers final: 96 residues processed: 530 average time/residue: 0.3434 time to fit residues: 290.3307 Evaluate side-chains 511 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 412 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1220 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25029 Z= 0.234 Angle : 0.598 11.314 34091 Z= 0.300 Chirality : 0.043 0.201 3958 Planarity : 0.004 0.051 4218 Dihedral : 13.557 131.218 4018 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.35 % Allowed : 22.13 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.28 (0.15), residues: 2965 helix: -0.44 (0.16), residues: 1009 sheet: -1.18 (0.31), residues: 287 loop : -1.00 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 236 HIS 0.007 0.001 HIS D1227 PHE 0.018 0.001 PHE C 545 TYR 0.015 0.001 TYR C 73 ARG 0.010 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 437 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ASN cc_start: 0.8446 (m-40) cc_final: 0.8056 (m-40) REVERT: C 68 LEU cc_start: 0.8155 (tp) cc_final: 0.7949 (tp) REVERT: C 129 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8520 (mt) REVERT: C 179 TYR cc_start: 0.7084 (t80) cc_final: 0.6719 (t80) REVERT: C 407 ARG cc_start: 0.7195 (mmm-85) cc_final: 0.6937 (mtp85) REVERT: C 542 ARG cc_start: 0.6073 (mpt180) cc_final: 0.5610 (mmt180) REVERT: C 611 GLU cc_start: 0.7560 (tt0) cc_final: 0.7312 (tt0) REVERT: C 657 THR cc_start: 0.8154 (t) cc_final: 0.7924 (p) REVERT: C 711 ASP cc_start: 0.6805 (m-30) cc_final: 0.6459 (m-30) REVERT: C 1079 ILE cc_start: 0.8807 (mm) cc_final: 0.8535 (mm) REVERT: C 1107 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6973 (mmp) REVERT: C 1180 MET cc_start: 0.8079 (tpp) cc_final: 0.7813 (ttm) REVERT: C 1274 GLU cc_start: 0.7088 (mp0) cc_final: 0.6805 (mp0) REVERT: D 133 ARG cc_start: 0.7767 (mpt-90) cc_final: 0.7005 (tpt170) REVERT: D 298 MET cc_start: 0.6630 (tpp) cc_final: 0.6337 (mmt) REVERT: D 304 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6316 (t0) REVERT: D 347 VAL cc_start: 0.9266 (t) cc_final: 0.9046 (m) REVERT: D 362 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7166 (mtp85) REVERT: D 432 LEU cc_start: 0.9209 (mm) cc_final: 0.8975 (mt) REVERT: D 725 MET cc_start: 0.7954 (mtm) cc_final: 0.7650 (mtm) REVERT: E 69 ARG cc_start: 0.7373 (ptp-110) cc_final: 0.7007 (mtt-85) outliers start: 109 outliers final: 91 residues processed: 510 average time/residue: 0.3418 time to fit residues: 280.0966 Evaluate side-chains 513 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 419 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 7.9990 chunk 280 optimal weight: 0.5980 chunk 256 optimal weight: 8.9990 chunk 273 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1220 GLN D1235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25029 Z= 0.297 Angle : 0.639 13.082 34091 Z= 0.320 Chirality : 0.044 0.337 3958 Planarity : 0.004 0.050 4218 Dihedral : 13.607 132.019 4018 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.43 % Allowed : 22.09 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.28 (0.15), residues: 2965 helix: -0.45 (0.16), residues: 1012 sheet: -1.14 (0.32), residues: 279 loop : -1.00 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 236 HIS 0.005 0.001 HIS D1252 PHE 0.018 0.002 PHE C 545 TYR 0.013 0.002 TYR C 73 ARG 0.009 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 447 time to evaluate : 2.607 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: A 25 LYS cc_start: 0.8400 (tttt) cc_final: 0.8077 (tttt) REVERT: A 114 ASP cc_start: 0.7433 (t70) cc_final: 0.7038 (t0) REVERT: A 227 GLN cc_start: 0.7357 (tp40) cc_final: 0.7089 (tp-100) REVERT: B 84 ASN cc_start: 0.8494 (m-40) cc_final: 0.8131 (m-40) REVERT: C 129 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8442 (mp) REVERT: C 179 TYR cc_start: 0.7166 (t80) cc_final: 0.6764 (t80) REVERT: C 407 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6996 (mtp85) REVERT: C 542 ARG cc_start: 0.6107 (mpt180) cc_final: 0.5686 (mmt180) REVERT: C 601 ASP cc_start: 0.7155 (m-30) cc_final: 0.6923 (m-30) REVERT: C 611 GLU cc_start: 0.7508 (tt0) cc_final: 0.7241 (tt0) REVERT: C 657 THR cc_start: 0.8169 (t) cc_final: 0.7940 (p) REVERT: C 711 ASP cc_start: 0.6908 (m-30) cc_final: 0.6531 (m-30) REVERT: C 1079 ILE cc_start: 0.8860 (mm) cc_final: 0.8648 (mm) REVERT: C 1107 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7013 (mmp) REVERT: C 1180 MET cc_start: 0.8197 (tpp) cc_final: 0.7886 (ttm) REVERT: C 1212 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8634 (pt) REVERT: D 133 ARG cc_start: 0.7801 (mpt-90) cc_final: 0.7028 (tpt170) REVERT: D 298 MET cc_start: 0.6532 (tpp) cc_final: 0.6219 (mmt) REVERT: D 304 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6266 (t0) REVERT: D 347 VAL cc_start: 0.9284 (t) cc_final: 0.9048 (m) REVERT: D 362 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7248 (mtp85) REVERT: D 387 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7348 (tp) REVERT: D 432 LEU cc_start: 0.9245 (mm) cc_final: 0.9024 (mt) REVERT: D 578 ILE cc_start: 0.8829 (mm) cc_final: 0.8520 (mm) REVERT: D 725 MET cc_start: 0.8018 (mtm) cc_final: 0.7774 (mtm) REVERT: D 822 MET cc_start: 0.7341 (mmp) cc_final: 0.6325 (mmm) REVERT: E 69 ARG cc_start: 0.7345 (ptp-110) cc_final: 0.6973 (mtt-85) outliers start: 111 outliers final: 92 residues processed: 525 average time/residue: 0.3588 time to fit residues: 301.2130 Evaluate side-chains 525 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 428 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 20.0000 chunk 288 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 200 optimal weight: 0.0980 chunk 302 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 186 optimal weight: 0.1980 chunk 147 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN E 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25029 Z= 0.207 Angle : 0.614 11.732 34091 Z= 0.306 Chirality : 0.043 0.308 3958 Planarity : 0.004 0.049 4218 Dihedral : 13.549 132.525 4018 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.56 % Allowed : 23.17 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.13 (0.15), residues: 2965 helix: -0.30 (0.17), residues: 1009 sheet: -1.13 (0.32), residues: 285 loop : -0.91 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 236 HIS 0.005 0.001 HIS C1070 PHE 0.022 0.001 PHE A 35 TYR 0.015 0.001 TYR C 73 ARG 0.011 0.001 ARG C 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 446 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.7307 (tp40) cc_final: 0.7062 (tp40) REVERT: B 84 ASN cc_start: 0.8368 (m-40) cc_final: 0.8093 (m-40) REVERT: C 129 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 407 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6976 (mtp85) REVERT: C 542 ARG cc_start: 0.5988 (mpt180) cc_final: 0.5673 (mmt-90) REVERT: C 601 ASP cc_start: 0.7131 (m-30) cc_final: 0.6915 (m-30) REVERT: C 657 THR cc_start: 0.8033 (t) cc_final: 0.7813 (p) REVERT: C 711 ASP cc_start: 0.6728 (m-30) cc_final: 0.6401 (m-30) REVERT: C 1079 ILE cc_start: 0.8826 (mm) cc_final: 0.8602 (mm) REVERT: C 1084 ASP cc_start: 0.8441 (m-30) cc_final: 0.8161 (m-30) REVERT: C 1107 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6999 (mmp) REVERT: C 1180 MET cc_start: 0.8056 (tpp) cc_final: 0.7835 (ttm) REVERT: C 1274 GLU cc_start: 0.7108 (mp0) cc_final: 0.6678 (mp0) REVERT: D 133 ARG cc_start: 0.7762 (mpt-90) cc_final: 0.6970 (tpt170) REVERT: D 298 MET cc_start: 0.6503 (tpp) cc_final: 0.6181 (mmt) REVERT: D 304 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6224 (t0) REVERT: D 330 MET cc_start: 0.6483 (ptm) cc_final: 0.6111 (ptm) REVERT: D 347 VAL cc_start: 0.9234 (t) cc_final: 0.8983 (m) REVERT: D 362 ARG cc_start: 0.7566 (ttp-110) cc_final: 0.7107 (mtp85) REVERT: D 432 LEU cc_start: 0.9172 (mm) cc_final: 0.8855 (mm) REVERT: D 484 MET cc_start: 0.8737 (mmm) cc_final: 0.8524 (mmm) REVERT: D 725 MET cc_start: 0.7920 (mtm) cc_final: 0.7678 (mtm) REVERT: D 822 MET cc_start: 0.6920 (mmp) cc_final: 0.6593 (mmm) REVERT: E 69 ARG cc_start: 0.7341 (ptp-110) cc_final: 0.7014 (mtt-85) outliers start: 89 outliers final: 77 residues processed: 505 average time/residue: 0.3823 time to fit residues: 308.0301 Evaluate side-chains 512 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 432 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157104 restraints weight = 33134.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158169 restraints weight = 23942.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159256 restraints weight = 19787.450| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25029 Z= 0.246 Angle : 0.624 11.580 34091 Z= 0.311 Chirality : 0.043 0.326 3958 Planarity : 0.004 0.049 4218 Dihedral : 13.563 133.675 4018 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.60 % Allowed : 23.37 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.14 (0.15), residues: 2965 helix: -0.26 (0.17), residues: 1015 sheet: -1.07 (0.32), residues: 281 loop : -0.97 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 236 HIS 0.004 0.001 HIS C1070 PHE 0.019 0.002 PHE D 461 TYR 0.013 0.001 TYR C 73 ARG 0.007 0.001 ARG C 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5889.33 seconds wall clock time: 105 minutes 17.16 seconds (6317.16 seconds total)