Starting phenix.real_space_refine on Mon Sep 14 00:00:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q0k_13746/09_2026/7q0k_13746.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 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 69 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16276 2.51 5 N 4658 2.21 5 O 5205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26317 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 498 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "T" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1694 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10548 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1280} Chain breaks: 1 Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15793 SG CYS D 70 23.011 52.004 96.115 1.00152.66 S ATOM 15807 SG CYS D 72 22.890 49.845 98.770 1.00157.24 S ATOM 21627 SG CYS D 814 42.733 118.516 89.653 1.00109.56 S ATOM 22192 SG CYS D 888 43.855 114.708 91.007 1.00 99.88 S ATOM 22243 SG CYS D 895 43.075 115.802 87.423 1.00103.42 S ATOM 22264 SG CYS D 898 45.940 116.942 88.854 1.00 98.02 S Time building chain proxies: 5.48, per 1000 atoms: 0.21 Number of scatterers: 26317 At special positions: 0 Unit cell: (133.1, 162.8, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 69 15.00 Mg 1 11.99 O 5205 8.00 N 4658 7.00 C 16276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5876 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 44 sheets defined 37.5% alpha, 15.0% beta 33 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.222A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.077A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.950A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.754A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.835A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.571A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.028A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.105A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.606A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 4.014A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.684A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.694A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.782A pdb=" N ALA C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.545A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.570A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 4.020A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 862 Processing helix chain 'C' and resid 898 through 906 removed outlier: 3.612A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 903 " --> pdb=" O GLU C 899 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.673A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.694A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.224A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.672A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.957A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.598A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.575A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.620A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.729A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.747A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.867A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 394 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.277A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.541A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.683A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.843A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.567A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 588 through 592' Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.608A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.550A pdb=" N ASP D 643 " --> pdb=" O GLY D 640 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 640 through 644' Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.965A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.558A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.744A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.738A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1073 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.086A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.497A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.855A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.856A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.744A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 3.796A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 33 removed outlier: 4.145A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.588A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.082A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.681A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 171 " --> pdb=" O VAL A 59 " (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 108 through 111 removed outlier: 3.851A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.885A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.048A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 3.829A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.870A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.084A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.798A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.457A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.524A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.519A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 231 removed outlier: 3.663A pdb=" N VAL C 228 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.485A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.862A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.618A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.618A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 617 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.852A pdb=" N ALA C 716 " --> pdb=" O ALA C 784 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 750 removed outlier: 7.236A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.976A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.562A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.757A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.736A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.519A pdb=" N ILE D 447 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.690A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.100A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.587A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.742A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.721A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.392A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 3.596A pdb=" N VAL D1027 " --> pdb=" O ALA D1122 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 3.627A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE7, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.889A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 948 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 3.06 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: 8639 1.34 - 1.46: 3807 1.46 - 1.58: 14084 1.58 - 1.70: 134 1.70 - 1.82: 184 Bond restraints: 26848 Sorted by residual: bond pdb=" C3' DC N 13 " pdb=" C2' DC N 13 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC N 35 " pdb=" C2' DC N 35 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG T 28 " pdb=" C2' DG T 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C1' DC T 20 " pdb=" N1 DC T 20 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.54e+00 bond pdb=" C3' DA T 17 " pdb=" C2' DA T 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.98e+00 ... (remaining 26843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 35934 2.25 - 4.49: 565 4.49 - 6.74: 46 6.74 - 8.99: 8 8.99 - 11.23: 3 Bond angle restraints: 36556 Sorted by residual: angle pdb=" C3' U R 4 " pdb=" O3' U R 4 " pdb=" P C R 5 " ideal model delta sigma weight residual 119.70 125.04 -5.34 1.20e+00 6.94e-01 1.98e+01 angle pdb=" N3 DT T 4 " pdb=" C4 DT T 4 " pdb=" O4 DT T 4 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 36551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 15853 34.97 - 69.94: 442 69.94 - 104.90: 29 104.90 - 139.87: 2 139.87 - 174.84: 2 Dihedral angle restraints: 16328 sinusoidal: 7193 harmonic: 9135 Sorted by residual: dihedral pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.86 72.20 1 3.10e+00 1.04e-01 6.94e+02 dihedral pdb=" C4' U R 4 " pdb=" C3' U R 4 " pdb=" C2' U R 4 " pdb=" C1' U R 4 " ideal model delta sinusoidal sigma weight residual 36.34 -29.56 65.91 1 3.10e+00 1.04e-01 5.91e+02 dihedral pdb=" O4' C R 5 " pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " ideal model delta sinusoidal sigma weight residual -35.15 26.20 -61.34 1 4.00e+00 6.25e-02 3.12e+02 ... (remaining 16325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3613 0.066 - 0.132: 546 0.132 - 0.198: 11 0.198 - 0.264: 11 0.264 - 0.330: 3 Chirality restraints: 4184 Sorted by residual: chirality pdb=" P C R 5 " pdb=" OP1 C R 5 " pdb=" OP2 C R 5 " pdb=" O5' C R 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C2' U R 4 " pdb=" C3' U R 4 " pdb=" O2' U R 4 " pdb=" C1' U R 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' C R 5 " pdb=" C3' C R 5 " pdb=" O2' C R 5 " pdb=" C1' C R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4181 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO D 851 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C1103 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO C1104 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C1104 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1104 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 109 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.06e+00 pdb=" N PRO C 110 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.031 5.00e-02 4.00e+02 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 204 2.54 - 3.13: 20773 3.13 - 3.72: 41307 3.72 - 4.31: 52243 4.31 - 4.90: 84262 Nonbonded interactions: 198789 Sorted by model distance: nonbonded pdb=" OG1 THR C 135 " pdb=" OE2 GLU C 142 " model vdw 1.955 3.040 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.079 2.310 nonbonded pdb=" OG1 THR B 22 " pdb=" O THR B 207 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASP C 826 " pdb=" OG1 THR C 829 " model vdw 2.144 3.040 nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 2.152 2.496 ... (remaining 198784 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 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.004 0.107 26854 Z= 0.223 Angle : 0.682 21.397 36562 Z= 0.392 Chirality : 0.046 0.330 4184 Planarity : 0.004 0.060 4544 Dihedral : 15.540 174.839 10452 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3164 helix: 0.89 (0.16), residues: 1027 sheet: -0.37 (0.30), residues: 297 loop : -1.70 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 137 TYR 0.018 0.001 TYR C 105 PHE 0.019 0.001 PHE C 337 TRP 0.018 0.001 TRP D 115 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.22 (26848) covalent geometry : angle 0.66608 / 0.39 (36556) hydrogen bonds : bond 0.19476 / 21.76 ( 1030) hydrogen bonds : angle 6.63235 / 6.31 ( 2816) metal coordination : bond 0.06015 / 3.48 ( 6) metal coordination : angle 11.57134 / 23.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 858 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 35 PHE cc_start: 0.7478 (m-10) cc_final: 0.6674 (m-10) REVERT: A 77 ASP cc_start: 0.7221 (m-30) cc_final: 0.6762 (m-30) REVERT: A 91 ARG cc_start: 0.7422 (ttt180) cc_final: 0.7180 (ttp80) REVERT: A 118 ASP cc_start: 0.7683 (p0) cc_final: 0.6949 (p0) REVERT: A 120 ASP cc_start: 0.8179 (p0) cc_final: 0.7406 (p0) REVERT: A 153 VAL cc_start: 0.8722 (t) cc_final: 0.8428 (p) REVERT: A 222 THR cc_start: 0.7704 (m) cc_final: 0.7436 (p) REVERT: A 229 GLU cc_start: 0.6957 (tt0) cc_final: 0.6703 (tt0) REVERT: A 233 ASP cc_start: 0.7204 (t0) cc_final: 0.6968 (t0) REVERT: B 23 HIS cc_start: 0.7435 (t70) cc_final: 0.7048 (t-90) REVERT: B 41 ASN cc_start: 0.8266 (m-40) cc_final: 0.7920 (m-40) REVERT: B 95 LYS cc_start: 0.8231 (mtpp) cc_final: 0.8013 (mtpp) REVERT: B 142 MET cc_start: 0.6776 (mmm) cc_final: 0.6069 (mmm) REVERT: B 174 ASP cc_start: 0.6899 (m-30) cc_final: 0.6412 (m-30) REVERT: B 177 TYR cc_start: 0.7589 (m-80) cc_final: 0.6696 (m-80) REVERT: B 214 GLU cc_start: 0.8377 (mp0) cc_final: 0.8034 (mm-30) REVERT: B 226 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 8 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7277 (mttt) REVERT: C 14 ASP cc_start: 0.6746 (t0) cc_final: 0.6496 (t0) REVERT: C 70 TYR cc_start: 0.6060 (t80) cc_final: 0.5762 (t80) REVERT: C 93 SER cc_start: 0.8140 (p) cc_final: 0.7543 (p) REVERT: C 130 MET cc_start: 0.7685 (tpp) cc_final: 0.7318 (tpp) REVERT: C 150 HIS cc_start: 0.7980 (p90) cc_final: 0.7672 (p90) REVERT: C 180 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7283 (ttp80) REVERT: C 191 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8390 (mtmm) REVERT: C 218 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 245 ARG cc_start: 0.8175 (mtm180) cc_final: 0.7917 (mpp80) REVERT: C 278 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 279 LYS cc_start: 0.8603 (mptt) cc_final: 0.8297 (ptmm) REVERT: C 300 ASP cc_start: 0.7107 (m-30) cc_final: 0.6814 (m-30) REVERT: C 330 HIS cc_start: 0.6533 (m90) cc_final: 0.5932 (m-70) REVERT: C 392 GLU cc_start: 0.7754 (tp30) cc_final: 0.7274 (tp30) REVERT: C 394 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7547 (ttm110) REVERT: C 422 LYS cc_start: 0.7951 (pttm) cc_final: 0.7745 (pttp) REVERT: C 425 ILE cc_start: 0.8228 (tp) cc_final: 0.7997 (tt) REVERT: C 430 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8076 (ttpp) REVERT: C 447 HIS cc_start: 0.7544 (t-170) cc_final: 0.7209 (t-170) REVERT: C 461 GLU cc_start: 0.7990 (tt0) cc_final: 0.7179 (tm-30) REVERT: C 488 MET cc_start: 0.7330 (mmp) cc_final: 0.7086 (mmp) REVERT: C 491 ASP cc_start: 0.7251 (p0) cc_final: 0.6672 (p0) REVERT: C 510 GLN cc_start: 0.7905 (tt0) cc_final: 0.7303 (tp40) REVERT: C 516 ASP cc_start: 0.6445 (t0) cc_final: 0.6167 (t0) REVERT: C 519 ASN cc_start: 0.8033 (m110) cc_final: 0.7660 (m110) REVERT: C 531 SER cc_start: 0.8317 (t) cc_final: 0.7891 (p) REVERT: C 540 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7774 (mtm110) REVERT: C 541 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 603 ILE cc_start: 0.7936 (mp) cc_final: 0.7671 (mm) REVERT: C 653 MET cc_start: 0.7406 (tpp) cc_final: 0.7170 (tpt) REVERT: C 668 ILE cc_start: 0.8299 (mm) cc_final: 0.7977 (mt) REVERT: C 674 ASP cc_start: 0.8020 (t0) cc_final: 0.7751 (t0) REVERT: C 681 MET cc_start: 0.7287 (tpp) cc_final: 0.6797 (ttm) REVERT: C 711 ASP cc_start: 0.7459 (t0) cc_final: 0.7259 (t0) REVERT: C 719 LYS cc_start: 0.7425 (tptp) cc_final: 0.7097 (mmmt) REVERT: C 737 ASN cc_start: 0.8315 (m-40) cc_final: 0.7540 (m110) REVERT: C 755 LYS cc_start: 0.7362 (mmmt) cc_final: 0.7056 (mmtt) REVERT: C 761 GLN cc_start: 0.7666 (mm110) cc_final: 0.7275 (mp10) REVERT: C 775 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 781 ASP cc_start: 0.6391 (t0) cc_final: 0.6108 (t0) REVERT: C 793 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6553 (mt-10) REVERT: C 820 GLU cc_start: 0.7660 (pt0) cc_final: 0.7452 (pt0) REVERT: C 825 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 853 ASP cc_start: 0.8270 (m-30) cc_final: 0.7501 (p0) REVERT: C 864 LYS cc_start: 0.7243 (mmtp) cc_final: 0.6957 (mmtp) REVERT: C 870 ILE cc_start: 0.7793 (mm) cc_final: 0.7587 (mm) REVERT: C 930 ASP cc_start: 0.7027 (t0) cc_final: 0.6791 (t0) REVERT: C 941 LYS cc_start: 0.8548 (mttt) cc_final: 0.8321 (mttt) REVERT: C 951 MET cc_start: 0.8612 (mtp) cc_final: 0.8238 (mtp) REVERT: C 954 LYS cc_start: 0.8510 (mtmm) cc_final: 0.7436 (ptpt) REVERT: C 955 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7626 (tp-100) REVERT: C 957 LYS cc_start: 0.8964 (pptt) cc_final: 0.8592 (pptt) REVERT: C 1026 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 1030 GLU cc_start: 0.8378 (tp30) cc_final: 0.8082 (tp30) REVERT: C 1059 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7494 (mtp85) REVERT: C 1073 LYS cc_start: 0.7897 (ptpt) cc_final: 0.6875 (ptpt) REVERT: C 1085 MET cc_start: 0.7931 (mmt) cc_final: 0.7617 (mmm) REVERT: C 1088 ASP cc_start: 0.7156 (p0) cc_final: 0.6947 (p0) REVERT: C 1119 MET cc_start: 0.7583 (tpp) cc_final: 0.7348 (tmm) REVERT: C 1122 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7452 (mmmm) REVERT: C 1142 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7798 (mtt-85) REVERT: C 1145 ILE cc_start: 0.7572 (mm) cc_final: 0.7348 (mt) REVERT: C 1177 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7749 (ptm160) REVERT: C 1178 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8097 (mmtt) REVERT: C 1180 MET cc_start: 0.7428 (tpt) cc_final: 0.7076 (tpp) REVERT: C 1220 GLN cc_start: 0.7838 (tt0) cc_final: 0.7050 (tm-30) REVERT: C 1238 LEU cc_start: 0.8358 (mm) cc_final: 0.8023 (mt) REVERT: C 1244 HIS cc_start: 0.7529 (t-170) cc_final: 0.7097 (t-170) REVERT: C 1270 PHE cc_start: 0.7196 (t80) cc_final: 0.6015 (t80) REVERT: C 1273 MET cc_start: 0.7606 (mtm) cc_final: 0.7363 (mtp) REVERT: C 1274 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6958 (tp30) REVERT: C 1287 LEU cc_start: 0.8096 (tt) cc_final: 0.7831 (tp) REVERT: C 1290 MET cc_start: 0.7095 (tmm) cc_final: 0.6558 (tmm) REVERT: C 1304 MET cc_start: 0.7028 (tpp) cc_final: 0.6364 (tpp) REVERT: C 1329 GLU cc_start: 0.7586 (tt0) cc_final: 0.6600 (mt-10) REVERT: C 1332 SER cc_start: 0.7861 (t) cc_final: 0.7592 (p) REVERT: C 1337 ILE cc_start: 0.8184 (tp) cc_final: 0.7833 (tt) REVERT: D 21 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7605 (mmtm) REVERT: D 32 SER cc_start: 0.8703 (m) cc_final: 0.8439 (p) REVERT: D 60 ARG cc_start: 0.7514 (ptm-80) cc_final: 0.7059 (tmm-80) REVERT: D 66 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7893 (mmmm) REVERT: D 69 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6926 (tm-30) REVERT: D 84 ILE cc_start: 0.7605 (pt) cc_final: 0.7325 (mp) REVERT: D 130 MET cc_start: 0.7537 (mmt) cc_final: 0.7315 (mmm) REVERT: D 133 ARG cc_start: 0.7132 (tmt170) cc_final: 0.6883 (ttp80) REVERT: D 163 GLU cc_start: 0.8404 (pm20) cc_final: 0.7958 (pm20) REVERT: D 179 LYS cc_start: 0.8149 (mttt) cc_final: 0.7730 (mttt) REVERT: D 183 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 190 LYS cc_start: 0.7869 (ptpp) cc_final: 0.7198 (ptpp) REVERT: D 200 GLN cc_start: 0.8158 (pp30) cc_final: 0.7691 (pp30) REVERT: D 211 GLU cc_start: 0.8138 (pp20) cc_final: 0.7857 (pp20) REVERT: D 215 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8286 (mmtt) REVERT: D 219 LYS cc_start: 0.8373 (mttt) cc_final: 0.8077 (mttt) REVERT: D 221 ILE cc_start: 0.8610 (tp) cc_final: 0.8393 (tp) REVERT: D 222 LYS cc_start: 0.8155 (mptt) cc_final: 0.7788 (mptt) REVERT: D 225 GLU cc_start: 0.7958 (tp30) cc_final: 0.7752 (tp30) REVERT: D 233 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7764 (mmtm) REVERT: D 237 MET cc_start: 0.7834 (tpp) cc_final: 0.7047 (tpp) REVERT: D 244 VAL cc_start: 0.7991 (m) cc_final: 0.7702 (p) REVERT: D 278 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7837 (ttm-80) REVERT: D 280 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8350 (mmmm) REVERT: D 294 ASN cc_start: 0.8054 (t0) cc_final: 0.7711 (t0) REVERT: D 295 GLU cc_start: 0.7949 (tt0) cc_final: 0.7624 (tt0) REVERT: D 297 ARG cc_start: 0.8396 (tmm-80) cc_final: 0.8043 (tmm-80) REVERT: D 301 GLU cc_start: 0.7895 (tp30) cc_final: 0.7330 (tm-30) REVERT: D 304 ASP cc_start: 0.7031 (m-30) cc_final: 0.6562 (m-30) REVERT: D 330 MET cc_start: 0.7459 (ttt) cc_final: 0.7101 (ttt) REVERT: D 339 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7704 (ptm160) REVERT: D 340 GLN cc_start: 0.6903 (tm-30) cc_final: 0.6507 (tp-100) REVERT: D 341 ASN cc_start: 0.7673 (m-40) cc_final: 0.7346 (t0) REVERT: D 378 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7150 (mtpp) REVERT: D 381 ILE cc_start: 0.8106 (mm) cc_final: 0.7749 (mp) REVERT: D 399 LYS cc_start: 0.8190 (mppt) cc_final: 0.7703 (mmtt) REVERT: D 400 MET cc_start: 0.8072 (mtm) cc_final: 0.7139 (mtt) REVERT: D 402 GLU cc_start: 0.7597 (pp20) cc_final: 0.7285 (pp20) REVERT: D 403 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7687 (ttm110) REVERT: D 405 GLU cc_start: 0.7240 (mp0) cc_final: 0.6775 (mp0) REVERT: D 432 LEU cc_start: 0.8415 (mm) cc_final: 0.8049 (mt) REVERT: D 442 ILE cc_start: 0.8450 (tt) cc_final: 0.8111 (tt) REVERT: D 443 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6714 (mm-30) REVERT: D 454 CYS cc_start: 0.7633 (m) cc_final: 0.7430 (m) REVERT: D 479 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7708 (tm-30) REVERT: D 484 MET cc_start: 0.7455 (mmm) cc_final: 0.7243 (mmm) REVERT: D 485 MET cc_start: 0.7580 (mmt) cc_final: 0.7293 (mmp) REVERT: D 506 VAL cc_start: 0.8165 (m) cc_final: 0.7804 (p) REVERT: D 511 TYR cc_start: 0.7651 (t80) cc_final: 0.7107 (t80) REVERT: D 531 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7929 (ttmm) REVERT: D 536 LEU cc_start: 0.8240 (mt) cc_final: 0.8010 (mt) REVERT: D 547 ARG cc_start: 0.7099 (mpt-90) cc_final: 0.6810 (mmt90) REVERT: D 625 MET cc_start: 0.7959 (tmm) cc_final: 0.7643 (tmm) REVERT: D 644 MET cc_start: 0.8174 (mpp) cc_final: 0.7719 (mtm) REVERT: D 658 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8431 (mm-30) REVERT: D 678 ARG cc_start: 0.8483 (ppt170) cc_final: 0.8230 (ttp80) REVERT: D 715 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7897 (ttpp) REVERT: D 722 ILE cc_start: 0.8473 (tp) cc_final: 0.8190 (tt) REVERT: D 724 MET cc_start: 0.8061 (ttp) cc_final: 0.7553 (ttp) REVERT: D 728 SER cc_start: 0.8479 (p) cc_final: 0.7967 (t) REVERT: D 733 SER cc_start: 0.7908 (t) cc_final: 0.6940 (p) REVERT: D 739 GLN cc_start: 0.7945 (tt0) cc_final: 0.7547 (tt0) REVERT: D 747 MET cc_start: 0.6640 (mmp) cc_final: 0.6167 (mmp) REVERT: D 756 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7245 (mm-30) REVERT: D 757 THR cc_start: 0.8674 (t) cc_final: 0.8473 (m) REVERT: D 780 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7749 (ttm170) REVERT: D 781 LYS cc_start: 0.8658 (tptp) cc_final: 0.8241 (tppt) REVERT: D 808 VAL cc_start: 0.8399 (t) cc_final: 0.7986 (p) REVERT: D 822 MET cc_start: 0.7983 (tpp) cc_final: 0.7671 (tpp) REVERT: D 839 VAL cc_start: 0.8090 (t) cc_final: 0.7824 (p) REVERT: D 860 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7227 (ptm160) REVERT: D 873 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 905 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6773 (mmm-85) REVERT: D 911 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8213 (ttmt) REVERT: D 964 LYS cc_start: 0.8028 (tppt) cc_final: 0.7713 (tppt) REVERT: D 992 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7823 (mmtt) REVERT: D 995 TYR cc_start: 0.7543 (m-80) cc_final: 0.7271 (m-10) REVERT: D 1007 ASP cc_start: 0.8355 (t70) cc_final: 0.8064 (t0) REVERT: D 1020 TRP cc_start: 0.7585 (p-90) cc_final: 0.7061 (p-90) REVERT: D 1119 ASP cc_start: 0.7606 (t0) cc_final: 0.7207 (m-30) REVERT: D 1144 LEU cc_start: 0.8034 (mm) cc_final: 0.6805 (mt) REVERT: D 1146 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 1152 GLU cc_start: 0.7268 (mp0) cc_final: 0.6998 (mp0) REVERT: D 1173 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6526 (ttp-110) REVERT: D 1188 GLU cc_start: 0.7808 (pm20) cc_final: 0.7295 (pm20) REVERT: D 1189 MET cc_start: 0.7263 (mmp) cc_final: 0.7040 (mmp) REVERT: D 1193 TRP cc_start: 0.7380 (p-90) cc_final: 0.7145 (p-90) REVERT: D 1222 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8084 (ptm-80) REVERT: D 1223 LEU cc_start: 0.8399 (mm) cc_final: 0.7662 (mm) REVERT: D 1235 ASN cc_start: 0.7580 (m110) cc_final: 0.6913 (m-40) REVERT: D 1236 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6581 (tm-30) REVERT: D 1239 ASP cc_start: 0.7492 (m-30) cc_final: 0.7074 (m-30) REVERT: D 1254 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6491 (tm-30) REVERT: D 1292 LEU cc_start: 0.8482 (tp) cc_final: 0.8207 (tp) REVERT: D 1325 PHE cc_start: 0.6490 (t80) cc_final: 0.6235 (t80) REVERT: D 1334 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7550 (mm-30) REVERT: E 3 ARG cc_start: 0.6738 (mmp-170) cc_final: 0.6505 (mmp-170) REVERT: E 68 GLU cc_start: 0.8190 (tp30) cc_final: 0.7974 (tp30) outliers start: 0 outliers final: 0 residues processed: 858 average time/residue: 0.2206 time to fit residues: 282.1631 Evaluate side-chains 756 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 756 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 554 HIS C 760 ASN C 824 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1175 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS D 665 GLN D 669 GLN D 777 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108019 restraints weight = 49724.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111606 restraints weight = 25691.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114011 restraints weight = 15973.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115621 restraints weight = 11341.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116439 restraints weight = 8957.463| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26854 Z= 0.211 Angle : 0.762 21.792 36562 Z= 0.386 Chirality : 0.055 1.373 4184 Planarity : 0.005 0.080 4544 Dihedral : 14.285 176.069 4233 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.62 % Allowed : 11.74 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3164 helix: 0.65 (0.16), residues: 1053 sheet: -0.40 (0.27), residues: 344 loop : -1.75 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 919 TYR 0.019 0.002 TYR C1229 PHE 0.017 0.002 PHE D1319 TRP 0.026 0.002 TRP D1193 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (26848) covalent geometry : angle 0.75978 / 0.39 (36556) hydrogen bonds : bond 0.05732 / 6.33 ( 1030) hydrogen bonds : angle 5.23806 / 5.30 ( 2816) metal coordination : bond 0.02133 / 1.45 ( 6) metal coordination : angle 4.65607 / 8.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 808 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6590 (tm-30) REVERT: A 64 VAL cc_start: 0.8709 (p) cc_final: 0.8504 (t) REVERT: A 68 TYR cc_start: 0.8488 (m-10) cc_final: 0.8125 (m-10) REVERT: A 77 ASP cc_start: 0.6908 (m-30) cc_final: 0.6446 (m-30) REVERT: A 80 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6806 (tm-30) REVERT: A 118 ASP cc_start: 0.7438 (p0) cc_final: 0.6937 (p0) REVERT: A 120 ASP cc_start: 0.7522 (p0) cc_final: 0.7055 (p0) REVERT: A 153 VAL cc_start: 0.8655 (t) cc_final: 0.8366 (p) REVERT: A 205 MET cc_start: 0.7333 (ttp) cc_final: 0.6998 (ttm) REVERT: A 206 GLU cc_start: 0.7461 (pp20) cc_final: 0.6891 (tm-30) REVERT: B 23 HIS cc_start: 0.7615 (t70) cc_final: 0.7331 (t70) REVERT: B 84 ASN cc_start: 0.7877 (t0) cc_final: 0.7607 (t0) REVERT: B 142 MET cc_start: 0.6287 (mmm) cc_final: 0.6024 (mmm) REVERT: B 174 ASP cc_start: 0.7236 (m-30) cc_final: 0.6700 (m-30) REVERT: B 177 TYR cc_start: 0.7607 (m-80) cc_final: 0.6645 (m-80) REVERT: B 214 GLU cc_start: 0.8272 (mp0) cc_final: 0.7954 (mm-30) REVERT: C 8 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7241 (mttt) REVERT: C 54 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7280 (mtm-85) REVERT: C 124 MET cc_start: 0.7296 (ttp) cc_final: 0.7070 (tmm) REVERT: C 130 MET cc_start: 0.7793 (tpp) cc_final: 0.7273 (tpp) REVERT: C 133 ASN cc_start: 0.7737 (m110) cc_final: 0.7519 (m110) REVERT: C 151 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7431 (mmm-85) REVERT: C 169 LYS cc_start: 0.7820 (tmtt) cc_final: 0.7501 (tmtt) REVERT: C 191 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8132 (mtmm) REVERT: C 197 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6806 (mtp85) REVERT: C 201 ARG cc_start: 0.5731 (mtm180) cc_final: 0.5345 (mtm180) REVERT: C 283 LYS cc_start: 0.8236 (tppt) cc_final: 0.7749 (tppt) REVERT: C 330 HIS cc_start: 0.7112 (m90) cc_final: 0.6829 (m-70) REVERT: C 334 GLU cc_start: 0.5654 (pp20) cc_final: 0.4195 (tm-30) REVERT: C 366 ILE cc_start: 0.8071 (mm) cc_final: 0.7615 (mm) REVERT: C 392 GLU cc_start: 0.7602 (tp30) cc_final: 0.7151 (tp30) REVERT: C 394 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7495 (ttm110) REVERT: C 425 ILE cc_start: 0.8388 (tp) cc_final: 0.7663 (tt) REVERT: C 429 MET cc_start: 0.8208 (mtt) cc_final: 0.7730 (mtm) REVERT: C 447 HIS cc_start: 0.7517 (t-170) cc_final: 0.7267 (t-170) REVERT: C 461 GLU cc_start: 0.7878 (tt0) cc_final: 0.7060 (tp30) REVERT: C 510 GLN cc_start: 0.7930 (tt0) cc_final: 0.7390 (tp40) REVERT: C 519 ASN cc_start: 0.7897 (m110) cc_final: 0.7582 (m110) REVERT: C 524 ILE cc_start: 0.7530 (mm) cc_final: 0.7270 (tp) REVERT: C 540 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7892 (mtm110) REVERT: C 620 ASN cc_start: 0.7910 (p0) cc_final: 0.7661 (p0) REVERT: C 668 ILE cc_start: 0.8124 (mm) cc_final: 0.7916 (mt) REVERT: C 674 ASP cc_start: 0.8016 (t0) cc_final: 0.7657 (t0) REVERT: C 681 MET cc_start: 0.7239 (tpp) cc_final: 0.6748 (ttm) REVERT: C 685 MET cc_start: 0.6820 (mpp) cc_final: 0.6424 (mpp) REVERT: C 737 ASN cc_start: 0.8496 (m-40) cc_final: 0.7676 (m110) REVERT: C 755 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6999 (mmtt) REVERT: C 758 ARG cc_start: 0.8419 (ttt-90) cc_final: 0.8083 (ttt90) REVERT: C 761 GLN cc_start: 0.7795 (mm110) cc_final: 0.7280 (mp10) REVERT: C 775 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 793 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6487 (mt-10) REVERT: C 825 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 853 ASP cc_start: 0.7932 (m-30) cc_final: 0.7390 (p0) REVERT: C 930 ASP cc_start: 0.7052 (t0) cc_final: 0.6760 (t0) REVERT: C 951 MET cc_start: 0.8161 (mtp) cc_final: 0.7877 (mtp) REVERT: C 952 GLN cc_start: 0.8271 (mp10) cc_final: 0.8046 (mm-40) REVERT: C 954 LYS cc_start: 0.8618 (mtmm) cc_final: 0.7388 (ptpt) REVERT: C 955 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7186 (tp-100) REVERT: C 957 LYS cc_start: 0.8868 (pptt) cc_final: 0.8500 (pptt) REVERT: C 1023 HIS cc_start: 0.7324 (m90) cc_final: 0.7107 (m90) REVERT: C 1030 GLU cc_start: 0.8078 (tp30) cc_final: 0.7835 (tp30) REVERT: C 1079 ILE cc_start: 0.8123 (mm) cc_final: 0.7068 (mm) REVERT: C 1095 ASP cc_start: 0.7603 (m-30) cc_final: 0.7397 (m-30) REVERT: C 1119 MET cc_start: 0.7696 (tpp) cc_final: 0.7438 (tmm) REVERT: C 1142 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7941 (mtt-85) REVERT: C 1145 ILE cc_start: 0.7919 (mm) cc_final: 0.7686 (mt) REVERT: C 1178 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8248 (mmtt) REVERT: C 1180 MET cc_start: 0.7481 (tpt) cc_final: 0.7177 (tpp) REVERT: C 1200 LYS cc_start: 0.8187 (tptp) cc_final: 0.7937 (tptp) REVERT: C 1268 GLN cc_start: 0.7729 (mp10) cc_final: 0.6927 (mp10) REVERT: C 1270 PHE cc_start: 0.7480 (t80) cc_final: 0.6377 (t80) REVERT: C 1274 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6796 (mm-30) REVERT: C 1287 LEU cc_start: 0.8202 (tt) cc_final: 0.8000 (tp) REVERT: C 1290 MET cc_start: 0.7268 (tmm) cc_final: 0.6854 (tmm) REVERT: C 1329 GLU cc_start: 0.7522 (tt0) cc_final: 0.6603 (mt-10) REVERT: C 1332 SER cc_start: 0.7934 (t) cc_final: 0.7668 (p) REVERT: D 32 SER cc_start: 0.8783 (m) cc_final: 0.8515 (p) REVERT: D 35 PHE cc_start: 0.6943 (m-80) cc_final: 0.6577 (m-80) REVERT: D 50 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8761 (tmtt) REVERT: D 60 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.7156 (tmm-80) REVERT: D 66 LYS cc_start: 0.8325 (mmmm) cc_final: 0.8107 (mmmm) REVERT: D 69 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6979 (tm-30) REVERT: D 84 ILE cc_start: 0.7807 (pt) cc_final: 0.7550 (mp) REVERT: D 130 MET cc_start: 0.7634 (mmt) cc_final: 0.7377 (mmm) REVERT: D 141 PHE cc_start: 0.7648 (m-10) cc_final: 0.7374 (m-10) REVERT: D 163 GLU cc_start: 0.8051 (pm20) cc_final: 0.7767 (pm20) REVERT: D 179 LYS cc_start: 0.8473 (mttt) cc_final: 0.7957 (mttt) REVERT: D 180 MET cc_start: 0.7180 (ppp) cc_final: 0.6811 (ppp) REVERT: D 183 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 190 LYS cc_start: 0.8012 (ptpp) cc_final: 0.7426 (ptpp) REVERT: D 200 GLN cc_start: 0.8229 (pp30) cc_final: 0.7642 (pp30) REVERT: D 211 GLU cc_start: 0.7996 (pp20) cc_final: 0.7456 (pp20) REVERT: D 215 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8200 (mmtt) REVERT: D 221 ILE cc_start: 0.8502 (tp) cc_final: 0.8180 (tp) REVERT: D 222 LYS cc_start: 0.8211 (mptt) cc_final: 0.7389 (mptt) REVERT: D 233 LYS cc_start: 0.8228 (mmmm) cc_final: 0.7818 (mmtm) REVERT: D 237 MET cc_start: 0.7879 (tpp) cc_final: 0.7354 (tpp) REVERT: D 239 LEU cc_start: 0.7894 (tp) cc_final: 0.7638 (tp) REVERT: D 294 ASN cc_start: 0.8178 (t0) cc_final: 0.6117 (t0) REVERT: D 295 GLU cc_start: 0.7867 (tt0) cc_final: 0.7500 (tt0) REVERT: D 297 ARG cc_start: 0.8258 (tmm-80) cc_final: 0.7685 (tmm-80) REVERT: D 298 MET cc_start: 0.7596 (mmp) cc_final: 0.6221 (mmt) REVERT: D 301 GLU cc_start: 0.7701 (tp30) cc_final: 0.7296 (tm-30) REVERT: D 311 ARG cc_start: 0.7363 (tpp80) cc_final: 0.7133 (tpp80) REVERT: D 330 MET cc_start: 0.7417 (ttt) cc_final: 0.7138 (ttt) REVERT: D 341 ASN cc_start: 0.7754 (m-40) cc_final: 0.7385 (t0) REVERT: D 378 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7515 (mtpp) REVERT: D 382 TYR cc_start: 0.8072 (m-10) cc_final: 0.7320 (m-10) REVERT: D 399 LYS cc_start: 0.8342 (mppt) cc_final: 0.7755 (mppt) REVERT: D 400 MET cc_start: 0.7918 (mtm) cc_final: 0.7447 (mtt) REVERT: D 402 GLU cc_start: 0.7435 (pp20) cc_final: 0.7061 (pp20) REVERT: D 403 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7460 (ttm110) REVERT: D 418 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7051 (mm-30) REVERT: D 431 ARG cc_start: 0.8083 (ttp-110) cc_final: 0.7799 (ttp-110) REVERT: D 432 LEU cc_start: 0.8434 (mm) cc_final: 0.8003 (mm) REVERT: D 438 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6520 (tm-30) REVERT: D 472 LEU cc_start: 0.8147 (tp) cc_final: 0.7848 (tt) REVERT: D 479 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 506 VAL cc_start: 0.8359 (m) cc_final: 0.8026 (p) REVERT: D 511 TYR cc_start: 0.7893 (t80) cc_final: 0.7331 (t80) REVERT: D 516 ASP cc_start: 0.7370 (p0) cc_final: 0.7004 (t70) REVERT: D 531 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7993 (ttmm) REVERT: D 534 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7139 (tm-30) REVERT: D 556 GLU cc_start: 0.6805 (tp30) cc_final: 0.6427 (tm-30) REVERT: D 579 LEU cc_start: 0.8343 (mt) cc_final: 0.7706 (tp) REVERT: D 604 MET cc_start: 0.7583 (tmm) cc_final: 0.7168 (tmm) REVERT: D 644 MET cc_start: 0.8150 (mpp) cc_final: 0.7542 (mtm) REVERT: D 658 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8225 (mm-30) REVERT: D 660 GLU cc_start: 0.7657 (tt0) cc_final: 0.7399 (pp20) REVERT: D 685 ILE cc_start: 0.7136 (tp) cc_final: 0.6840 (tt) REVERT: D 698 MET cc_start: 0.7509 (tpt) cc_final: 0.7152 (tpp) REVERT: D 715 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7929 (ttmm) REVERT: D 722 ILE cc_start: 0.8506 (tp) cc_final: 0.8269 (tt) REVERT: D 724 MET cc_start: 0.7845 (ttp) cc_final: 0.7512 (mtp) REVERT: D 728 SER cc_start: 0.8558 (p) cc_final: 0.8002 (t) REVERT: D 738 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7257 (ttm110) REVERT: D 765 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6751 (tm-30) REVERT: D 780 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7924 (ttm170) REVERT: D 781 LYS cc_start: 0.8685 (tptp) cc_final: 0.8231 (tppt) REVERT: D 789 LYS cc_start: 0.7789 (ptmm) cc_final: 0.7440 (tttm) REVERT: D 808 VAL cc_start: 0.8480 (t) cc_final: 0.8171 (p) REVERT: D 848 VAL cc_start: 0.8292 (p) cc_final: 0.8041 (m) REVERT: D 860 ARG cc_start: 0.7901 (ptm160) cc_final: 0.7565 (ptm160) REVERT: D 873 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 877 VAL cc_start: 0.8078 (t) cc_final: 0.7797 (m) REVERT: D 898 CYS cc_start: 0.6552 (m) cc_final: 0.6344 (m) REVERT: D 911 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8292 (ttmm) REVERT: D 992 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7929 (mmtt) REVERT: D 1040 MET cc_start: 0.4291 (OUTLIER) cc_final: 0.3242 (tpp) REVERT: D 1095 MET cc_start: 0.6561 (pmm) cc_final: 0.6247 (pmm) REVERT: D 1140 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7744 (tpt90) REVERT: D 1144 LEU cc_start: 0.8632 (mm) cc_final: 0.7932 (mm) REVERT: D 1148 ARG cc_start: 0.7423 (ptp-170) cc_final: 0.7011 (ptm160) REVERT: D 1220 ILE cc_start: 0.8436 (mt) cc_final: 0.8211 (tp) REVERT: D 1236 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6983 (tm-30) REVERT: D 1244 GLN cc_start: 0.8040 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 1334 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7398 (mm-30) REVERT: D 1342 ASP cc_start: 0.7304 (t0) cc_final: 0.6445 (p0) REVERT: E 68 GLU cc_start: 0.7886 (tp30) cc_final: 0.7678 (tp30) outliers start: 44 outliers final: 27 residues processed: 816 average time/residue: 0.2229 time to fit residues: 270.4811 Evaluate side-chains 785 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 756 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1140 ARG Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain D residue 1370 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 180 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 0 optimal weight: 80.0000 chunk 222 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 197 optimal weight: 0.0010 chunk 138 optimal weight: 40.0000 chunk 307 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 147 GLN B 41 ASN B 132 HIS C 150 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 628 HIS C 760 ASN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN C1244 HIS ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 545 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107534 restraints weight = 48704.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111269 restraints weight = 25177.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113716 restraints weight = 15670.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115470 restraints weight = 11233.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116306 restraints weight = 8862.469| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26854 Z= 0.184 Angle : 0.722 13.677 36562 Z= 0.367 Chirality : 0.051 1.322 4184 Planarity : 0.005 0.061 4544 Dihedral : 14.298 172.969 4233 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.84 % Allowed : 15.92 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3164 helix: 0.57 (0.16), residues: 1059 sheet: -0.45 (0.27), residues: 351 loop : -1.78 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 16 TYR 0.032 0.002 TYR C 584 PHE 0.021 0.001 PHE C 224 TRP 0.016 0.002 TRP D 33 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (26848) covalent geometry : angle 0.71980 / 0.37 (36556) hydrogen bonds : bond 0.05197 / 5.66 ( 1030) hydrogen bonds : angle 4.92055 / 5.10 ( 2816) metal coordination : bond 0.00997 / 1.09 ( 6) metal coordination : angle 4.70517 / 8.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 779 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8349 (mtpp) cc_final: 0.8076 (mtpp) REVERT: A 77 ASP cc_start: 0.6923 (m-30) cc_final: 0.6423 (m-30) REVERT: A 80 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 118 ASP cc_start: 0.7524 (p0) cc_final: 0.7052 (p0) REVERT: A 120 ASP cc_start: 0.7633 (p0) cc_final: 0.7018 (p0) REVERT: A 153 VAL cc_start: 0.8697 (t) cc_final: 0.8383 (p) REVERT: A 206 GLU cc_start: 0.7427 (pp20) cc_final: 0.6913 (tm-30) REVERT: B 84 ASN cc_start: 0.7890 (t0) cc_final: 0.7645 (t0) REVERT: B 142 MET cc_start: 0.6433 (mmm) cc_final: 0.6204 (mmm) REVERT: B 174 ASP cc_start: 0.7188 (m-30) cc_final: 0.6589 (m-30) REVERT: B 177 TYR cc_start: 0.7478 (m-80) cc_final: 0.6571 (m-80) REVERT: B 185 TYR cc_start: 0.7391 (p90) cc_final: 0.7117 (p90) REVERT: B 188 GLU cc_start: 0.7001 (pm20) cc_final: 0.6323 (mp0) REVERT: B 226 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7321 (tm-30) REVERT: C 7 GLU cc_start: 0.6786 (mp0) cc_final: 0.6582 (mp0) REVERT: C 8 LYS cc_start: 0.7808 (mtpp) cc_final: 0.7403 (mptt) REVERT: C 54 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7274 (mtm-85) REVERT: C 124 MET cc_start: 0.7308 (ttp) cc_final: 0.7076 (tmm) REVERT: C 126 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6793 (tp30) REVERT: C 169 LYS cc_start: 0.7843 (tmtt) cc_final: 0.7438 (tmtt) REVERT: C 177 ILE cc_start: 0.7948 (mm) cc_final: 0.7520 (tp) REVERT: C 191 LYS cc_start: 0.8341 (mtmm) cc_final: 0.8112 (mtmm) REVERT: C 197 ARG cc_start: 0.7356 (mtp-110) cc_final: 0.7014 (mtp85) REVERT: C 201 ARG cc_start: 0.5724 (mtm180) cc_final: 0.5499 (mtm180) REVERT: C 275 ARG cc_start: 0.8386 (mmm160) cc_final: 0.8116 (tpp80) REVERT: C 334 GLU cc_start: 0.5669 (pp20) cc_final: 0.4225 (tm-30) REVERT: C 366 ILE cc_start: 0.8112 (mm) cc_final: 0.7719 (mm) REVERT: C 392 GLU cc_start: 0.7660 (tp30) cc_final: 0.7181 (tp30) REVERT: C 394 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7361 (ttm110) REVERT: C 425 ILE cc_start: 0.8415 (tp) cc_final: 0.7679 (tt) REVERT: C 426 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8315 (pp) REVERT: C 429 MET cc_start: 0.8166 (mtt) cc_final: 0.7723 (mtm) REVERT: C 447 HIS cc_start: 0.7540 (t-170) cc_final: 0.7318 (t-170) REVERT: C 461 GLU cc_start: 0.7889 (tt0) cc_final: 0.7024 (tp30) REVERT: C 519 ASN cc_start: 0.7923 (m110) cc_final: 0.7663 (m110) REVERT: C 524 ILE cc_start: 0.7776 (mm) cc_final: 0.7506 (tp) REVERT: C 620 ASN cc_start: 0.7914 (p0) cc_final: 0.7681 (p0) REVERT: C 653 MET cc_start: 0.7201 (tpt) cc_final: 0.6984 (tpp) REVERT: C 668 ILE cc_start: 0.8161 (mm) cc_final: 0.7939 (mt) REVERT: C 674 ASP cc_start: 0.7978 (t0) cc_final: 0.7622 (t0) REVERT: C 681 MET cc_start: 0.7182 (tpp) cc_final: 0.6776 (mtt) REVERT: C 737 ASN cc_start: 0.8604 (m-40) cc_final: 0.7588 (m110) REVERT: C 761 GLN cc_start: 0.7728 (mm110) cc_final: 0.7228 (mp10) REVERT: C 775 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 793 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6508 (mt-10) REVERT: C 814 ASP cc_start: 0.7455 (t0) cc_final: 0.7182 (t0) REVERT: C 825 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7465 (mm-30) REVERT: C 853 ASP cc_start: 0.7904 (m-30) cc_final: 0.7398 (p0) REVERT: C 864 LYS cc_start: 0.7321 (mmtp) cc_final: 0.6998 (mmtp) REVERT: C 928 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8631 (m) REVERT: C 930 ASP cc_start: 0.7105 (t0) cc_final: 0.6822 (t0) REVERT: C 941 LYS cc_start: 0.8583 (mttt) cc_final: 0.8331 (mttt) REVERT: C 951 MET cc_start: 0.8251 (mtp) cc_final: 0.7922 (mtp) REVERT: C 952 GLN cc_start: 0.8356 (mp10) cc_final: 0.8141 (mm-40) REVERT: C 954 LYS cc_start: 0.8590 (mtmm) cc_final: 0.7372 (ptpt) REVERT: C 955 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7253 (tp-100) REVERT: C 957 LYS cc_start: 0.8890 (pptt) cc_final: 0.8524 (pptt) REVERT: C 1030 GLU cc_start: 0.8166 (tp30) cc_final: 0.7950 (tp30) REVERT: C 1073 LYS cc_start: 0.7471 (ptpp) cc_final: 0.6763 (ptpp) REVERT: C 1178 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8248 (mmtt) REVERT: C 1192 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7414 (mp0) REVERT: C 1200 LYS cc_start: 0.8216 (tptp) cc_final: 0.7980 (tptp) REVERT: C 1270 PHE cc_start: 0.7436 (t80) cc_final: 0.6292 (t80) REVERT: C 1274 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6760 (mm-30) REVERT: C 1279 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7051 (mm-30) REVERT: C 1287 LEU cc_start: 0.8078 (tt) cc_final: 0.7851 (tp) REVERT: C 1290 MET cc_start: 0.7402 (tmm) cc_final: 0.6979 (tmm) REVERT: C 1303 LYS cc_start: 0.8027 (tppp) cc_final: 0.7697 (ttmm) REVERT: C 1329 GLU cc_start: 0.7444 (tt0) cc_final: 0.6467 (mt-10) REVERT: D 32 SER cc_start: 0.8740 (m) cc_final: 0.8537 (p) REVERT: D 35 PHE cc_start: 0.6888 (m-80) cc_final: 0.6641 (m-80) REVERT: D 50 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8661 (tmtt) REVERT: D 66 LYS cc_start: 0.8310 (mmmm) cc_final: 0.8089 (mmmm) REVERT: D 69 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7169 (tm-30) REVERT: D 84 ILE cc_start: 0.7838 (pt) cc_final: 0.7584 (mp) REVERT: D 94 GLN cc_start: 0.7066 (tp40) cc_final: 0.6839 (tp40) REVERT: D 102 MET cc_start: 0.7668 (mtp) cc_final: 0.7040 (mtt) REVERT: D 115 TRP cc_start: 0.8625 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: D 141 PHE cc_start: 0.7782 (m-10) cc_final: 0.7390 (m-10) REVERT: D 163 GLU cc_start: 0.8191 (pm20) cc_final: 0.7983 (pm20) REVERT: D 179 LYS cc_start: 0.8364 (mttt) cc_final: 0.7675 (mttt) REVERT: D 180 MET cc_start: 0.7012 (ppp) cc_final: 0.6697 (ppp) REVERT: D 183 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 190 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7396 (ptpp) REVERT: D 200 GLN cc_start: 0.8163 (pp30) cc_final: 0.7661 (pp30) REVERT: D 211 GLU cc_start: 0.8057 (pp20) cc_final: 0.7669 (pp20) REVERT: D 215 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8160 (mmtt) REVERT: D 219 LYS cc_start: 0.8422 (mttt) cc_final: 0.8071 (mttt) REVERT: D 221 ILE cc_start: 0.8535 (tp) cc_final: 0.8292 (tp) REVERT: D 222 LYS cc_start: 0.8180 (mptt) cc_final: 0.7874 (mptt) REVERT: D 233 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7848 (mmtm) REVERT: D 236 TRP cc_start: 0.8796 (m-10) cc_final: 0.8506 (m-10) REVERT: D 237 MET cc_start: 0.7879 (tpp) cc_final: 0.7289 (tpp) REVERT: D 239 LEU cc_start: 0.7979 (tp) cc_final: 0.7737 (tp) REVERT: D 241 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7743 (p) REVERT: D 248 ASP cc_start: 0.7639 (m-30) cc_final: 0.7298 (p0) REVERT: D 278 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7907 (ttm110) REVERT: D 294 ASN cc_start: 0.8183 (t0) cc_final: 0.6392 (t0) REVERT: D 295 GLU cc_start: 0.7975 (tt0) cc_final: 0.7503 (tt0) REVERT: D 297 ARG cc_start: 0.8260 (tmm-80) cc_final: 0.7771 (tmm-80) REVERT: D 298 MET cc_start: 0.7615 (mmp) cc_final: 0.6256 (mmt) REVERT: D 301 GLU cc_start: 0.7777 (tp30) cc_final: 0.7316 (tm-30) REVERT: D 330 MET cc_start: 0.7407 (ttt) cc_final: 0.6949 (ttt) REVERT: D 341 ASN cc_start: 0.8368 (m-40) cc_final: 0.7370 (t0) REVERT: D 378 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7689 (mtpp) REVERT: D 398 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7915 (mmmt) REVERT: D 399 LYS cc_start: 0.8345 (mppt) cc_final: 0.7803 (mppt) REVERT: D 400 MET cc_start: 0.8094 (mtm) cc_final: 0.7585 (mtm) REVERT: D 402 GLU cc_start: 0.7367 (pp20) cc_final: 0.7026 (pp20) REVERT: D 403 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7405 (ttm110) REVERT: D 417 ARG cc_start: 0.7538 (tpp80) cc_final: 0.7030 (ttp80) REVERT: D 431 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7822 (ttp-110) REVERT: D 432 LEU cc_start: 0.8394 (mm) cc_final: 0.7922 (mm) REVERT: D 454 CYS cc_start: 0.7435 (p) cc_final: 0.7064 (m) REVERT: D 462 ASP cc_start: 0.7372 (m-30) cc_final: 0.7149 (m-30) REVERT: D 479 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 504 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: D 506 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7953 (p) REVERT: D 511 TYR cc_start: 0.7906 (t80) cc_final: 0.7225 (t80) REVERT: D 531 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7959 (ttmm) REVERT: D 556 GLU cc_start: 0.6780 (tp30) cc_final: 0.6349 (tm-30) REVERT: D 566 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7607 (mtpp) REVERT: D 587 LEU cc_start: 0.8241 (mm) cc_final: 0.7962 (mt) REVERT: D 604 MET cc_start: 0.7559 (tmm) cc_final: 0.7218 (tmm) REVERT: D 625 MET cc_start: 0.7750 (tmm) cc_final: 0.7504 (tmm) REVERT: D 644 MET cc_start: 0.8091 (mpp) cc_final: 0.7665 (mtm) REVERT: D 658 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8240 (mm-30) REVERT: D 692 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7947 (ttm110) REVERT: D 698 MET cc_start: 0.7604 (tpt) cc_final: 0.7392 (tpt) REVERT: D 703 THR cc_start: 0.7985 (m) cc_final: 0.7614 (m) REVERT: D 715 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7830 (tppt) REVERT: D 722 ILE cc_start: 0.8501 (tp) cc_final: 0.8280 (tt) REVERT: D 724 MET cc_start: 0.7852 (ttp) cc_final: 0.7616 (mtp) REVERT: D 728 SER cc_start: 0.8548 (p) cc_final: 0.7973 (t) REVERT: D 739 GLN cc_start: 0.7823 (tt0) cc_final: 0.7623 (tp40) REVERT: D 757 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8348 (m) REVERT: D 765 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6889 (tm-30) REVERT: D 780 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7896 (ttm170) REVERT: D 781 LYS cc_start: 0.8697 (tptp) cc_final: 0.8254 (tppt) REVERT: D 789 LYS cc_start: 0.7825 (ptmm) cc_final: 0.7348 (tttt) REVERT: D 808 VAL cc_start: 0.8471 (t) cc_final: 0.8169 (p) REVERT: D 821 MET cc_start: 0.7178 (tpt) cc_final: 0.6933 (pmm) REVERT: D 873 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 903 LEU cc_start: 0.8295 (tp) cc_final: 0.7873 (tp) REVERT: D 983 LYS cc_start: 0.7414 (mppt) cc_final: 0.6940 (ptpp) REVERT: D 992 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7902 (mmtt) REVERT: D 1095 MET cc_start: 0.6465 (pmm) cc_final: 0.6131 (pmm) REVERT: D 1148 ARG cc_start: 0.7390 (ptp-170) cc_final: 0.7017 (ptm160) REVERT: D 1231 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.6432 (ttm-80) REVERT: D 1236 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6721 (tm-30) REVERT: D 1239 ASP cc_start: 0.7361 (m-30) cc_final: 0.6819 (m-30) REVERT: D 1247 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7727 (ttmt) REVERT: D 1254 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6473 (tm-30) REVERT: D 1334 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7405 (mm-30) REVERT: D 1342 ASP cc_start: 0.7102 (t0) cc_final: 0.6154 (p0) REVERT: D 1352 ILE cc_start: 0.8385 (tp) cc_final: 0.7990 (tt) REVERT: E 53 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6965 (mm-30) REVERT: E 55 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: E 68 GLU cc_start: 0.7882 (tp30) cc_final: 0.7662 (tp30) outliers start: 77 outliers final: 38 residues processed: 801 average time/residue: 0.2205 time to fit residues: 263.7721 Evaluate side-chains 795 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 748 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 55 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 254 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 236 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 168 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 204 optimal weight: 0.3980 chunk 271 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS C 133 ASN C 150 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 760 ASN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108828 restraints weight = 49124.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112638 restraints weight = 25235.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115164 restraints weight = 15626.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116904 restraints weight = 11073.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117969 restraints weight = 8717.022| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26854 Z= 0.130 Angle : 0.683 13.416 36562 Z= 0.346 Chirality : 0.048 1.220 4184 Planarity : 0.005 0.064 4544 Dihedral : 14.255 172.441 4233 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.84 % Allowed : 17.80 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3164 helix: 0.65 (0.16), residues: 1059 sheet: -0.29 (0.28), residues: 326 loop : -1.67 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1369 TYR 0.025 0.001 TYR C 70 PHE 0.028 0.001 PHE C1025 TRP 0.022 0.002 TRP D 33 HIS 0.009 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (26848) covalent geometry : angle 0.68165 / 0.35 (36556) hydrogen bonds : bond 0.04534 / 4.89 ( 1030) hydrogen bonds : angle 4.72035 / 4.97 ( 2816) metal coordination : bond 0.00464 / 0.53 ( 6) metal coordination : angle 3.93980 / 7.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 765 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8023 (mtpp) REVERT: A 68 TYR cc_start: 0.8486 (m-10) cc_final: 0.8096 (m-10) REVERT: A 77 ASP cc_start: 0.6769 (m-30) cc_final: 0.6489 (m-30) REVERT: A 80 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6745 (tm-30) REVERT: A 118 ASP cc_start: 0.7572 (p0) cc_final: 0.7126 (p0) REVERT: A 120 ASP cc_start: 0.7543 (p0) cc_final: 0.6948 (p0) REVERT: A 153 VAL cc_start: 0.8577 (t) cc_final: 0.8282 (p) REVERT: A 206 GLU cc_start: 0.7360 (pp20) cc_final: 0.6813 (tm-30) REVERT: B 41 ASN cc_start: 0.8361 (m-40) cc_final: 0.8086 (m110) REVERT: B 84 ASN cc_start: 0.7829 (t0) cc_final: 0.7599 (t0) REVERT: B 140 ILE cc_start: 0.8141 (tp) cc_final: 0.7411 (tp) REVERT: B 142 MET cc_start: 0.6419 (mmm) cc_final: 0.5799 (mmm) REVERT: B 174 ASP cc_start: 0.7184 (m-30) cc_final: 0.6583 (m-30) REVERT: B 177 TYR cc_start: 0.7557 (m-80) cc_final: 0.6636 (m-80) REVERT: B 185 TYR cc_start: 0.7334 (p90) cc_final: 0.6997 (p90) REVERT: B 188 GLU cc_start: 0.6901 (pm20) cc_final: 0.6268 (mp0) REVERT: C 8 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7314 (mttt) REVERT: C 54 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7377 (mtm-85) REVERT: C 83 GLN cc_start: 0.8282 (mp10) cc_final: 0.7994 (mm110) REVERT: C 124 MET cc_start: 0.7292 (ttp) cc_final: 0.6404 (tmm) REVERT: C 126 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6810 (tp30) REVERT: C 151 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6863 (tmm-80) REVERT: C 169 LYS cc_start: 0.7850 (tmtt) cc_final: 0.7435 (tmtt) REVERT: C 191 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8105 (mtmm) REVERT: C 197 ARG cc_start: 0.7321 (mtp-110) cc_final: 0.6795 (mtp85) REVERT: C 199 ASP cc_start: 0.7595 (t0) cc_final: 0.7358 (t0) REVERT: C 201 ARG cc_start: 0.5697 (mtm180) cc_final: 0.5319 (mtm180) REVERT: C 283 LYS cc_start: 0.8147 (tppt) cc_final: 0.7685 (tppt) REVERT: C 366 ILE cc_start: 0.8104 (mm) cc_final: 0.7810 (mm) REVERT: C 392 GLU cc_start: 0.7604 (tp30) cc_final: 0.7062 (tp30) REVERT: C 394 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7471 (ttm110) REVERT: C 427 ASP cc_start: 0.7891 (m-30) cc_final: 0.7569 (m-30) REVERT: C 447 HIS cc_start: 0.7542 (t-170) cc_final: 0.7307 (t-170) REVERT: C 461 GLU cc_start: 0.7945 (tt0) cc_final: 0.6994 (tp30) REVERT: C 510 GLN cc_start: 0.7958 (tt0) cc_final: 0.7622 (tp40) REVERT: C 519 ASN cc_start: 0.7909 (m110) cc_final: 0.7538 (m-40) REVERT: C 524 ILE cc_start: 0.7731 (mm) cc_final: 0.7484 (tp) REVERT: C 553 THR cc_start: 0.8166 (p) cc_final: 0.7894 (p) REVERT: C 580 GLN cc_start: 0.7540 (mt0) cc_final: 0.7290 (mt0) REVERT: C 620 ASN cc_start: 0.7892 (p0) cc_final: 0.7659 (p0) REVERT: C 668 ILE cc_start: 0.8142 (mm) cc_final: 0.7899 (mt) REVERT: C 674 ASP cc_start: 0.7971 (t0) cc_final: 0.7591 (t0) REVERT: C 681 MET cc_start: 0.7204 (tpp) cc_final: 0.6765 (mtt) REVERT: C 737 ASN cc_start: 0.8605 (m-40) cc_final: 0.7675 (m110) REVERT: C 755 LYS cc_start: 0.7323 (mmtt) cc_final: 0.7091 (mmtt) REVERT: C 761 GLN cc_start: 0.7652 (mm110) cc_final: 0.7117 (mp10) REVERT: C 775 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 814 ASP cc_start: 0.7348 (t0) cc_final: 0.7075 (t0) REVERT: C 825 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 853 ASP cc_start: 0.7892 (m-30) cc_final: 0.7583 (p0) REVERT: C 864 LYS cc_start: 0.7338 (mmtp) cc_final: 0.6979 (mmtp) REVERT: C 930 ASP cc_start: 0.7087 (t0) cc_final: 0.6747 (t0) REVERT: C 951 MET cc_start: 0.8238 (mtp) cc_final: 0.7846 (mtp) REVERT: C 954 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7643 (mtmt) REVERT: C 955 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7278 (tp-100) REVERT: C 957 LYS cc_start: 0.8890 (pptt) cc_final: 0.8518 (pptt) REVERT: C 1030 GLU cc_start: 0.8159 (tp30) cc_final: 0.7934 (tp30) REVERT: C 1073 LYS cc_start: 0.7382 (ptpp) cc_final: 0.6701 (ptpp) REVERT: C 1119 MET cc_start: 0.7911 (tmm) cc_final: 0.7677 (tmm) REVERT: C 1122 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7688 (mmmm) REVERT: C 1131 MET cc_start: 0.7452 (tpp) cc_final: 0.7135 (tpp) REVERT: C 1142 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7912 (mtt-85) REVERT: C 1178 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8303 (mmtt) REVERT: C 1200 LYS cc_start: 0.8183 (tptp) cc_final: 0.7945 (tptp) REVERT: C 1216 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7193 (ttm-80) REVERT: C 1270 PHE cc_start: 0.7303 (t80) cc_final: 0.6155 (t80) REVERT: C 1274 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6766 (mm-30) REVERT: C 1279 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 1287 LEU cc_start: 0.8098 (tt) cc_final: 0.7840 (tp) REVERT: C 1290 MET cc_start: 0.7411 (tmm) cc_final: 0.7089 (tmm) REVERT: C 1304 MET cc_start: 0.7210 (tpt) cc_final: 0.6940 (tpp) REVERT: C 1329 GLU cc_start: 0.7345 (tt0) cc_final: 0.5953 (mt-10) REVERT: C 1338 GLU cc_start: 0.6994 (pp20) cc_final: 0.6769 (pp20) REVERT: D 32 SER cc_start: 0.8742 (m) cc_final: 0.8506 (p) REVERT: D 35 PHE cc_start: 0.6858 (m-80) cc_final: 0.6599 (m-80) REVERT: D 69 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7067 (tm-30) REVERT: D 84 ILE cc_start: 0.7850 (pt) cc_final: 0.7629 (mp) REVERT: D 94 GLN cc_start: 0.6707 (tp40) cc_final: 0.6490 (tp40) REVERT: D 115 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: D 130 MET cc_start: 0.7698 (mmt) cc_final: 0.7467 (mmm) REVERT: D 141 PHE cc_start: 0.7695 (m-10) cc_final: 0.7208 (m-10) REVERT: D 179 LYS cc_start: 0.8342 (mttt) cc_final: 0.7635 (mttt) REVERT: D 183 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7364 (tm-30) REVERT: D 190 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7308 (ptpp) REVERT: D 200 GLN cc_start: 0.8111 (pp30) cc_final: 0.7724 (pp30) REVERT: D 211 GLU cc_start: 0.8031 (pp20) cc_final: 0.7493 (pp20) REVERT: D 215 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8138 (mmtt) REVERT: D 219 LYS cc_start: 0.8386 (mttt) cc_final: 0.8020 (mttt) REVERT: D 221 ILE cc_start: 0.8545 (tp) cc_final: 0.8300 (tp) REVERT: D 222 LYS cc_start: 0.8252 (mptt) cc_final: 0.7916 (mptt) REVERT: D 233 LYS cc_start: 0.8329 (mmmm) cc_final: 0.7860 (mmtm) REVERT: D 236 TRP cc_start: 0.8771 (m-10) cc_final: 0.8514 (m-10) REVERT: D 237 MET cc_start: 0.7806 (tpp) cc_final: 0.7135 (tpp) REVERT: D 241 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7758 (p) REVERT: D 248 ASP cc_start: 0.7671 (m-30) cc_final: 0.7290 (p0) REVERT: D 278 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7830 (ttm110) REVERT: D 294 ASN cc_start: 0.8156 (t0) cc_final: 0.6402 (t0) REVERT: D 295 GLU cc_start: 0.7988 (tt0) cc_final: 0.7476 (tt0) REVERT: D 297 ARG cc_start: 0.8306 (tmm-80) cc_final: 0.7759 (tmm-80) REVERT: D 298 MET cc_start: 0.7582 (mmp) cc_final: 0.6339 (mmt) REVERT: D 301 GLU cc_start: 0.7816 (tp30) cc_final: 0.7311 (tm-30) REVERT: D 311 ARG cc_start: 0.7357 (tpp80) cc_final: 0.7125 (tpp80) REVERT: D 330 MET cc_start: 0.7413 (ttt) cc_final: 0.7095 (ttt) REVERT: D 334 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7583 (mmmt) REVERT: D 341 ASN cc_start: 0.8417 (m-40) cc_final: 0.7393 (t0) REVERT: D 378 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7921 (mmmm) REVERT: D 398 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8104 (mmtt) REVERT: D 399 LYS cc_start: 0.8313 (mppt) cc_final: 0.7739 (mppt) REVERT: D 400 MET cc_start: 0.8147 (mtm) cc_final: 0.7905 (mtm) REVERT: D 402 GLU cc_start: 0.7380 (pp20) cc_final: 0.7069 (pp20) REVERT: D 403 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7469 (ttm110) REVERT: D 432 LEU cc_start: 0.8355 (mm) cc_final: 0.7920 (mm) REVERT: D 454 CYS cc_start: 0.7359 (p) cc_final: 0.6977 (m) REVERT: D 462 ASP cc_start: 0.7352 (m-30) cc_final: 0.7120 (m-30) REVERT: D 479 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7423 (tm-30) REVERT: D 504 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: D 506 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8019 (p) REVERT: D 511 TYR cc_start: 0.7766 (t80) cc_final: 0.7139 (t80) REVERT: D 531 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7959 (ttmm) REVERT: D 556 GLU cc_start: 0.6747 (tp30) cc_final: 0.6270 (tm-30) REVERT: D 566 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7620 (mtpp) REVERT: D 587 LEU cc_start: 0.8254 (mm) cc_final: 0.8021 (mt) REVERT: D 604 MET cc_start: 0.7494 (tmm) cc_final: 0.7132 (tmm) REVERT: D 622 ASP cc_start: 0.6764 (p0) cc_final: 0.6519 (p0) REVERT: D 625 MET cc_start: 0.7733 (tmm) cc_final: 0.7474 (tmm) REVERT: D 644 MET cc_start: 0.8044 (mpp) cc_final: 0.7647 (mtm) REVERT: D 658 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 660 GLU cc_start: 0.7563 (tt0) cc_final: 0.7333 (tt0) REVERT: D 698 MET cc_start: 0.7569 (tpt) cc_final: 0.7138 (tpp) REVERT: D 703 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7527 (m) REVERT: D 715 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7804 (tppt) REVERT: D 722 ILE cc_start: 0.8455 (tp) cc_final: 0.8227 (tt) REVERT: D 724 MET cc_start: 0.7838 (ttp) cc_final: 0.7588 (mtp) REVERT: D 728 SER cc_start: 0.8419 (p) cc_final: 0.7943 (t) REVERT: D 739 GLN cc_start: 0.7836 (tt0) cc_final: 0.7390 (tp40) REVERT: D 757 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 780 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7921 (ttm170) REVERT: D 781 LYS cc_start: 0.8681 (tptp) cc_final: 0.8226 (tppt) REVERT: D 789 LYS cc_start: 0.7721 (ptmm) cc_final: 0.7238 (tttt) REVERT: D 808 VAL cc_start: 0.8448 (t) cc_final: 0.8120 (p) REVERT: D 839 VAL cc_start: 0.8518 (t) cc_final: 0.8279 (p) REVERT: D 873 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 877 VAL cc_start: 0.8101 (t) cc_final: 0.7839 (p) REVERT: D 898 CYS cc_start: 0.6481 (m) cc_final: 0.6273 (m) REVERT: D 911 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8470 (ttmt) REVERT: D 921 GLN cc_start: 0.7850 (tt0) cc_final: 0.7250 (tt0) REVERT: D 964 LYS cc_start: 0.7585 (tppt) cc_final: 0.7383 (tppt) REVERT: D 982 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7221 (pp) REVERT: D 992 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7900 (mmtt) REVERT: D 1095 MET cc_start: 0.6486 (pmm) cc_final: 0.6052 (pmm) REVERT: D 1144 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8148 (mt) REVERT: D 1148 ARG cc_start: 0.7395 (ptp-170) cc_final: 0.6976 (ptm160) REVERT: D 1231 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.6582 (ttm-80) REVERT: D 1247 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7807 (ttmt) REVERT: D 1263 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7572 (mmtm) REVERT: D 1330 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7373 (mtm110) REVERT: D 1334 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7418 (mm-30) REVERT: D 1342 ASP cc_start: 0.6943 (t0) cc_final: 0.6092 (p0) REVERT: D 1352 ILE cc_start: 0.8323 (tp) cc_final: 0.8006 (tt) REVERT: E 53 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6584 (mm-30) REVERT: E 59 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7630 (mp) REVERT: E 68 GLU cc_start: 0.7895 (tp30) cc_final: 0.7654 (tp30) outliers start: 77 outliers final: 42 residues processed: 793 average time/residue: 0.2159 time to fit residues: 256.7910 Evaluate side-chains 788 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 735 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 146 optimal weight: 20.0000 chunk 178 optimal weight: 0.6980 chunk 255 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 148 optimal weight: 0.0570 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 132 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 628 HIS C 760 ASN C 952 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 545 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109617 restraints weight = 48915.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113437 restraints weight = 25231.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116022 restraints weight = 15683.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117661 restraints weight = 11106.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118789 restraints weight = 8810.551| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26854 Z= 0.124 Angle : 0.665 12.385 36562 Z= 0.338 Chirality : 0.045 0.507 4184 Planarity : 0.004 0.064 4544 Dihedral : 14.251 171.648 4233 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.40 % Allowed : 18.13 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3164 helix: 0.72 (0.16), residues: 1051 sheet: -0.13 (0.28), residues: 322 loop : -1.59 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1171 TYR 0.028 0.001 TYR C 70 PHE 0.023 0.001 PHE C 224 TRP 0.028 0.002 TRP D 33 HIS 0.011 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (26848) covalent geometry : angle 0.66373 / 0.34 (36556) hydrogen bonds : bond 0.04268 / 4.60 ( 1030) hydrogen bonds : angle 4.61475 / 4.86 ( 2816) metal coordination : bond 0.00399 / 0.50 ( 6) metal coordination : angle 3.83690 / 6.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 754 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8276 (mtpp) cc_final: 0.8014 (mtpp) REVERT: A 67 GLU cc_start: 0.7698 (tp30) cc_final: 0.7471 (tm-30) REVERT: A 77 ASP cc_start: 0.6847 (m-30) cc_final: 0.6625 (m-30) REVERT: A 80 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6699 (tm-30) REVERT: A 93 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6967 (pp30) REVERT: A 153 VAL cc_start: 0.8595 (t) cc_final: 0.8303 (p) REVERT: A 206 GLU cc_start: 0.7422 (pp20) cc_final: 0.6810 (tm-30) REVERT: B 140 ILE cc_start: 0.8136 (tp) cc_final: 0.7457 (tp) REVERT: B 142 MET cc_start: 0.6260 (mmm) cc_final: 0.5715 (mmm) REVERT: B 174 ASP cc_start: 0.7196 (m-30) cc_final: 0.6487 (m-30) REVERT: B 177 TYR cc_start: 0.7563 (m-80) cc_final: 0.6600 (m-80) REVERT: B 186 ASN cc_start: 0.8207 (t0) cc_final: 0.7705 (t0) REVERT: B 188 GLU cc_start: 0.6834 (pm20) cc_final: 0.6026 (mp0) REVERT: C 8 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7345 (mttt) REVERT: C 83 GLN cc_start: 0.8243 (mp10) cc_final: 0.7870 (mm110) REVERT: C 124 MET cc_start: 0.7260 (ttp) cc_final: 0.6325 (tmm) REVERT: C 126 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6763 (tp30) REVERT: C 169 LYS cc_start: 0.7900 (tmtt) cc_final: 0.7434 (tmtt) REVERT: C 191 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8102 (mtmm) REVERT: C 199 ASP cc_start: 0.7637 (t0) cc_final: 0.7387 (t0) REVERT: C 283 LYS cc_start: 0.8233 (tppt) cc_final: 0.7788 (tppt) REVERT: C 392 GLU cc_start: 0.7563 (tp30) cc_final: 0.7064 (tp30) REVERT: C 394 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7399 (ttm110) REVERT: C 427 ASP cc_start: 0.7786 (m-30) cc_final: 0.7493 (m-30) REVERT: C 447 HIS cc_start: 0.7538 (t-170) cc_final: 0.7304 (t-170) REVERT: C 461 GLU cc_start: 0.7939 (tt0) cc_final: 0.6992 (tp30) REVERT: C 519 ASN cc_start: 0.7872 (m110) cc_final: 0.7540 (m-40) REVERT: C 580 GLN cc_start: 0.7480 (mt0) cc_final: 0.7228 (mt0) REVERT: C 668 ILE cc_start: 0.8164 (mm) cc_final: 0.7947 (mt) REVERT: C 674 ASP cc_start: 0.7970 (t0) cc_final: 0.7590 (t0) REVERT: C 681 MET cc_start: 0.7210 (tpp) cc_final: 0.6750 (mtt) REVERT: C 737 ASN cc_start: 0.8612 (m-40) cc_final: 0.7623 (m110) REVERT: C 761 GLN cc_start: 0.7643 (mm110) cc_final: 0.7007 (mp10) REVERT: C 775 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 793 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6570 (mt-10) REVERT: C 800 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7380 (ptm) REVERT: C 814 ASP cc_start: 0.7248 (t0) cc_final: 0.6954 (t0) REVERT: C 825 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 853 ASP cc_start: 0.7917 (m-30) cc_final: 0.7614 (p0) REVERT: C 864 LYS cc_start: 0.7331 (mmtp) cc_final: 0.6973 (mmtp) REVERT: C 928 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 930 ASP cc_start: 0.7113 (t0) cc_final: 0.6810 (t0) REVERT: C 951 MET cc_start: 0.8211 (mtp) cc_final: 0.7596 (mtp) REVERT: C 954 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7453 (mtmt) REVERT: C 955 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7235 (tp-100) REVERT: C 957 LYS cc_start: 0.8861 (pptt) cc_final: 0.8508 (pptt) REVERT: C 1030 GLU cc_start: 0.8130 (tp30) cc_final: 0.7857 (tp30) REVERT: C 1073 LYS cc_start: 0.7388 (ptpp) cc_final: 0.6698 (ptpp) REVERT: C 1095 ASP cc_start: 0.7455 (m-30) cc_final: 0.7135 (t0) REVERT: C 1131 MET cc_start: 0.7424 (tpp) cc_final: 0.7162 (tpp) REVERT: C 1142 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7850 (mtt-85) REVERT: C 1171 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7778 (ttp-170) REVERT: C 1178 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8245 (mmtt) REVERT: C 1200 LYS cc_start: 0.8272 (tptp) cc_final: 0.7992 (tptp) REVERT: C 1270 PHE cc_start: 0.7276 (t80) cc_final: 0.6048 (t80) REVERT: C 1274 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6770 (mm-30) REVERT: C 1279 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6925 (mm-30) REVERT: C 1287 LEU cc_start: 0.8163 (tt) cc_final: 0.7940 (tp) REVERT: C 1289 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 1290 MET cc_start: 0.7390 (tmm) cc_final: 0.7020 (tmm) REVERT: C 1304 MET cc_start: 0.7140 (tpt) cc_final: 0.6916 (tpp) REVERT: C 1321 GLU cc_start: 0.6842 (pm20) cc_final: 0.6457 (pp20) REVERT: C 1329 GLU cc_start: 0.7367 (tt0) cc_final: 0.6807 (mt-10) REVERT: D 21 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7371 (mmtp) REVERT: D 32 SER cc_start: 0.8730 (m) cc_final: 0.8462 (p) REVERT: D 35 PHE cc_start: 0.6783 (m-80) cc_final: 0.6545 (m-80) REVERT: D 50 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8653 (tmtt) REVERT: D 69 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7064 (tm-30) REVERT: D 84 ILE cc_start: 0.7868 (pt) cc_final: 0.7642 (mp) REVERT: D 94 GLN cc_start: 0.6693 (tp40) cc_final: 0.6438 (tp40) REVERT: D 115 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: D 117 LEU cc_start: 0.7909 (mm) cc_final: 0.7556 (mm) REVERT: D 130 MET cc_start: 0.7652 (mmt) cc_final: 0.7443 (mmm) REVERT: D 141 PHE cc_start: 0.7532 (m-10) cc_final: 0.7294 (m-10) REVERT: D 179 LYS cc_start: 0.8299 (mttt) cc_final: 0.7580 (tttt) REVERT: D 180 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6624 (ppp) REVERT: D 183 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 190 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7300 (ptpp) REVERT: D 211 GLU cc_start: 0.7993 (pp20) cc_final: 0.7462 (pp20) REVERT: D 215 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8108 (mmtt) REVERT: D 219 LYS cc_start: 0.8341 (mttt) cc_final: 0.7911 (mttt) REVERT: D 221 ILE cc_start: 0.8531 (tp) cc_final: 0.8310 (tp) REVERT: D 222 LYS cc_start: 0.8300 (mptt) cc_final: 0.7921 (mptt) REVERT: D 233 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7852 (mmtm) REVERT: D 236 TRP cc_start: 0.8787 (m-10) cc_final: 0.8541 (m-10) REVERT: D 237 MET cc_start: 0.7816 (tpp) cc_final: 0.7141 (tpp) REVERT: D 241 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7783 (p) REVERT: D 248 ASP cc_start: 0.7693 (m-30) cc_final: 0.7279 (p0) REVERT: D 294 ASN cc_start: 0.8161 (t0) cc_final: 0.6605 (t0) REVERT: D 295 GLU cc_start: 0.7995 (tt0) cc_final: 0.7450 (tt0) REVERT: D 297 ARG cc_start: 0.8296 (tmm-80) cc_final: 0.7762 (tmm-80) REVERT: D 298 MET cc_start: 0.7631 (mmp) cc_final: 0.6542 (mmt) REVERT: D 301 GLU cc_start: 0.7809 (tp30) cc_final: 0.7305 (tm-30) REVERT: D 330 MET cc_start: 0.7366 (ttt) cc_final: 0.7165 (ttt) REVERT: D 378 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7840 (mmmm) REVERT: D 399 LYS cc_start: 0.8316 (mppt) cc_final: 0.7613 (mmtm) REVERT: D 400 MET cc_start: 0.8176 (mtm) cc_final: 0.7934 (mtm) REVERT: D 402 GLU cc_start: 0.7378 (pp20) cc_final: 0.6699 (pp20) REVERT: D 403 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7383 (ttm110) REVERT: D 418 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6964 (mm-30) REVERT: D 432 LEU cc_start: 0.8362 (mm) cc_final: 0.7922 (mm) REVERT: D 454 CYS cc_start: 0.7348 (p) cc_final: 0.6989 (m) REVERT: D 462 ASP cc_start: 0.7340 (m-30) cc_final: 0.7065 (m-30) REVERT: D 479 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7440 (tm-30) REVERT: D 506 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7969 (p) REVERT: D 511 TYR cc_start: 0.7719 (t80) cc_final: 0.7020 (t80) REVERT: D 531 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7937 (ttmm) REVERT: D 556 GLU cc_start: 0.6728 (tp30) cc_final: 0.6232 (tm-30) REVERT: D 566 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7646 (mtpp) REVERT: D 587 LEU cc_start: 0.8177 (mm) cc_final: 0.7916 (mt) REVERT: D 604 MET cc_start: 0.7471 (tmm) cc_final: 0.7124 (tmm) REVERT: D 625 MET cc_start: 0.7739 (tmm) cc_final: 0.7404 (tmm) REVERT: D 644 MET cc_start: 0.8034 (mpp) cc_final: 0.7618 (mtm) REVERT: D 658 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 660 GLU cc_start: 0.7584 (tt0) cc_final: 0.7351 (tt0) REVERT: D 692 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7832 (ttm110) REVERT: D 697 MET cc_start: 0.7802 (tmm) cc_final: 0.7582 (tmm) REVERT: D 698 MET cc_start: 0.7536 (tpt) cc_final: 0.6976 (tmm) REVERT: D 703 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7478 (m) REVERT: D 715 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7918 (tppt) REVERT: D 722 ILE cc_start: 0.8434 (tp) cc_final: 0.8211 (tt) REVERT: D 724 MET cc_start: 0.7831 (ttp) cc_final: 0.7581 (mtp) REVERT: D 728 SER cc_start: 0.8351 (p) cc_final: 0.7892 (t) REVERT: D 739 GLN cc_start: 0.7876 (tt0) cc_final: 0.7429 (tp40) REVERT: D 757 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8329 (m) REVERT: D 780 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7917 (ttm170) REVERT: D 781 LYS cc_start: 0.8670 (tptp) cc_final: 0.8221 (tppt) REVERT: D 805 GLN cc_start: 0.7888 (pm20) cc_final: 0.7309 (pm20) REVERT: D 806 ASP cc_start: 0.7576 (p0) cc_final: 0.6629 (t0) REVERT: D 808 VAL cc_start: 0.8457 (t) cc_final: 0.8113 (p) REVERT: D 839 VAL cc_start: 0.8481 (t) cc_final: 0.8227 (p) REVERT: D 873 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7743 (mt-10) REVERT: D 877 VAL cc_start: 0.8193 (t) cc_final: 0.7931 (p) REVERT: D 883 ARG cc_start: 0.7272 (ttp80) cc_final: 0.6801 (ttp80) REVERT: D 898 CYS cc_start: 0.6445 (m) cc_final: 0.6142 (m) REVERT: D 964 LYS cc_start: 0.7608 (tppt) cc_final: 0.7402 (tppt) REVERT: D 992 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7733 (mmtt) REVERT: D 993 GLU cc_start: 0.5627 (mm-30) cc_final: 0.5191 (mm-30) REVERT: D 1040 MET cc_start: 0.6697 (tpp) cc_final: 0.3965 (mmt) REVERT: D 1095 MET cc_start: 0.6427 (pmm) cc_final: 0.6021 (pmm) REVERT: D 1144 LEU cc_start: 0.8454 (mt) cc_final: 0.8020 (mt) REVERT: D 1148 ARG cc_start: 0.7379 (ptp-170) cc_final: 0.6965 (ptm160) REVERT: D 1224 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7769 (mtm-85) REVERT: D 1236 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6967 (tm-30) REVERT: D 1247 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7799 (ttmt) REVERT: D 1334 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7304 (mm-30) REVERT: D 1342 ASP cc_start: 0.6977 (t0) cc_final: 0.5994 (p0) REVERT: D 1352 ILE cc_start: 0.8286 (tp) cc_final: 0.7910 (tt) REVERT: E 31 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7877 (tt0) REVERT: E 53 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6666 (mm-30) REVERT: E 55 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6741 (pm20) REVERT: E 59 ILE cc_start: 0.8123 (mp) cc_final: 0.7557 (mp) REVERT: E 68 GLU cc_start: 0.7912 (tp30) cc_final: 0.7645 (tp30) outliers start: 92 outliers final: 52 residues processed: 790 average time/residue: 0.2149 time to fit residues: 255.2609 Evaluate side-chains 797 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 734 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 55 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 290 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 162 optimal weight: 0.0470 chunk 313 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108959 restraints weight = 48885.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112774 restraints weight = 25302.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.115322 restraints weight = 15729.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117001 restraints weight = 11142.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118003 restraints weight = 8831.335| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26854 Z= 0.136 Angle : 0.668 12.059 36562 Z= 0.341 Chirality : 0.044 0.317 4184 Planarity : 0.005 0.073 4544 Dihedral : 14.241 171.881 4233 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.25 % Allowed : 20.16 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3164 helix: 0.70 (0.16), residues: 1057 sheet: -0.23 (0.27), residues: 337 loop : -1.56 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1369 TYR 0.016 0.001 TYR C 70 PHE 0.025 0.001 PHE C 224 TRP 0.032 0.002 TRP D 33 HIS 0.021 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (26848) covalent geometry : angle 0.66640 / 0.34 (36556) hydrogen bonds : bond 0.04290 / 4.63 ( 1030) hydrogen bonds : angle 4.55150 / 4.83 ( 2816) metal coordination : bond 0.00519 / 0.62 ( 6) metal coordination : angle 3.86847 / 6.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 762 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8023 (mtpp) REVERT: A 67 GLU cc_start: 0.7718 (tp30) cc_final: 0.7365 (tm-30) REVERT: A 80 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 120 ASP cc_start: 0.7453 (t0) cc_final: 0.7128 (p0) REVERT: A 153 VAL cc_start: 0.8598 (t) cc_final: 0.8311 (p) REVERT: A 206 GLU cc_start: 0.7382 (pp20) cc_final: 0.6779 (tm-30) REVERT: A 214 GLU cc_start: 0.7539 (pp20) cc_final: 0.7316 (tm-30) REVERT: B 33 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7460 (ttp80) REVERT: B 41 ASN cc_start: 0.8320 (m-40) cc_final: 0.8074 (m-40) REVERT: B 84 ASN cc_start: 0.7849 (t0) cc_final: 0.7472 (t0) REVERT: B 140 ILE cc_start: 0.8057 (tp) cc_final: 0.7352 (tp) REVERT: B 142 MET cc_start: 0.6317 (mmm) cc_final: 0.5773 (mmm) REVERT: B 174 ASP cc_start: 0.7185 (m-30) cc_final: 0.6561 (m-30) REVERT: C 7 GLU cc_start: 0.6701 (mp0) cc_final: 0.6313 (pm20) REVERT: C 8 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7290 (mttt) REVERT: C 124 MET cc_start: 0.7277 (ttp) cc_final: 0.6346 (tmm) REVERT: C 126 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6723 (tp30) REVERT: C 169 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7442 (tmtt) REVERT: C 177 ILE cc_start: 0.7824 (mm) cc_final: 0.7416 (tp) REVERT: C 191 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8097 (mtmm) REVERT: C 199 ASP cc_start: 0.7672 (t0) cc_final: 0.7445 (t0) REVERT: C 283 LYS cc_start: 0.8227 (tppt) cc_final: 0.7788 (tppt) REVERT: C 330 HIS cc_start: 0.7119 (m90) cc_final: 0.6758 (m-70) REVERT: C 334 GLU cc_start: 0.5688 (pp20) cc_final: 0.4610 (tp30) REVERT: C 392 GLU cc_start: 0.7554 (tp30) cc_final: 0.7105 (tp30) REVERT: C 427 ASP cc_start: 0.7770 (m-30) cc_final: 0.7518 (m-30) REVERT: C 447 HIS cc_start: 0.7525 (t70) cc_final: 0.7271 (t-170) REVERT: C 459 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7199 (mtm) REVERT: C 461 GLU cc_start: 0.7906 (tt0) cc_final: 0.7112 (tm-30) REVERT: C 519 ASN cc_start: 0.7850 (m110) cc_final: 0.7527 (m-40) REVERT: C 668 ILE cc_start: 0.8165 (mm) cc_final: 0.7949 (mt) REVERT: C 674 ASP cc_start: 0.7950 (t0) cc_final: 0.7535 (t0) REVERT: C 681 MET cc_start: 0.7247 (tpp) cc_final: 0.6795 (mtt) REVERT: C 737 ASN cc_start: 0.8611 (m-40) cc_final: 0.7576 (m110) REVERT: C 761 GLN cc_start: 0.7617 (mm110) cc_final: 0.7015 (mp10) REVERT: C 779 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7702 (ttm-80) REVERT: C 793 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6706 (mt-10) REVERT: C 825 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 853 ASP cc_start: 0.7932 (m-30) cc_final: 0.7599 (p0) REVERT: C 864 LYS cc_start: 0.7332 (mmtp) cc_final: 0.6959 (mmtp) REVERT: C 870 ILE cc_start: 0.8190 (mm) cc_final: 0.7959 (mm) REVERT: C 928 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8627 (m) REVERT: C 930 ASP cc_start: 0.7096 (t0) cc_final: 0.6772 (t0) REVERT: C 951 MET cc_start: 0.8242 (mtp) cc_final: 0.7824 (mtp) REVERT: C 952 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8166 (mm-40) REVERT: C 954 LYS cc_start: 0.8502 (mtmm) cc_final: 0.7564 (mtmt) REVERT: C 957 LYS cc_start: 0.8863 (pptt) cc_final: 0.8510 (pptt) REVERT: C 1022 LYS cc_start: 0.8231 (pptt) cc_final: 0.8000 (pptt) REVERT: C 1030 GLU cc_start: 0.8108 (tp30) cc_final: 0.7836 (tp30) REVERT: C 1073 LYS cc_start: 0.7387 (ptpp) cc_final: 0.6864 (ptpp) REVERT: C 1079 ILE cc_start: 0.8316 (mm) cc_final: 0.7210 (mt) REVERT: C 1095 ASP cc_start: 0.7436 (m-30) cc_final: 0.7119 (t0) REVERT: C 1131 MET cc_start: 0.7476 (tpp) cc_final: 0.7188 (tpp) REVERT: C 1142 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7820 (mtt-85) REVERT: C 1171 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7728 (ttp-170) REVERT: C 1178 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8256 (mmtt) REVERT: C 1200 LYS cc_start: 0.8220 (tptp) cc_final: 0.7973 (tptp) REVERT: C 1270 PHE cc_start: 0.7333 (t80) cc_final: 0.6114 (t80) REVERT: C 1274 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6779 (mm-30) REVERT: C 1279 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6895 (mm-30) REVERT: C 1287 LEU cc_start: 0.8185 (tt) cc_final: 0.7953 (tp) REVERT: C 1289 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 1290 MET cc_start: 0.7406 (tmm) cc_final: 0.7040 (tmm) REVERT: C 1304 MET cc_start: 0.7134 (tpt) cc_final: 0.6906 (tpp) REVERT: C 1321 GLU cc_start: 0.6952 (pm20) cc_final: 0.6502 (pp20) REVERT: C 1329 GLU cc_start: 0.7377 (tt0) cc_final: 0.6844 (mt-10) REVERT: D 21 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7091 (mmtp) REVERT: D 32 SER cc_start: 0.8705 (m) cc_final: 0.8434 (p) REVERT: D 35 PHE cc_start: 0.6817 (m-80) cc_final: 0.6554 (m-80) REVERT: D 50 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8610 (tmtt) REVERT: D 69 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7047 (tm-30) REVERT: D 84 ILE cc_start: 0.7889 (pt) cc_final: 0.7675 (mp) REVERT: D 115 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.8147 (m-10) REVERT: D 117 LEU cc_start: 0.7956 (mm) cc_final: 0.7655 (mm) REVERT: D 141 PHE cc_start: 0.7621 (m-10) cc_final: 0.7381 (m-10) REVERT: D 179 LYS cc_start: 0.8319 (mttt) cc_final: 0.7727 (mmmm) REVERT: D 183 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7507 (tm-30) REVERT: D 190 LYS cc_start: 0.7947 (ptpp) cc_final: 0.7339 (ptpp) REVERT: D 200 GLN cc_start: 0.8105 (pp30) cc_final: 0.7781 (pp30) REVERT: D 211 GLU cc_start: 0.8005 (pp20) cc_final: 0.7479 (pp20) REVERT: D 215 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8107 (mmtt) REVERT: D 219 LYS cc_start: 0.8338 (mttt) cc_final: 0.7917 (mttt) REVERT: D 221 ILE cc_start: 0.8542 (tp) cc_final: 0.8339 (tp) REVERT: D 222 LYS cc_start: 0.8324 (mptt) cc_final: 0.7936 (mptt) REVERT: D 233 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7990 (mmmm) REVERT: D 236 TRP cc_start: 0.8795 (m-10) cc_final: 0.8533 (m-10) REVERT: D 237 MET cc_start: 0.7831 (tpp) cc_final: 0.7161 (tpp) REVERT: D 241 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7773 (p) REVERT: D 248 ASP cc_start: 0.7705 (m-30) cc_final: 0.7263 (p0) REVERT: D 278 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7888 (ttm110) REVERT: D 294 ASN cc_start: 0.8152 (t0) cc_final: 0.6869 (t0) REVERT: D 295 GLU cc_start: 0.7983 (tt0) cc_final: 0.7450 (tt0) REVERT: D 297 ARG cc_start: 0.8310 (tmm-80) cc_final: 0.7770 (tmm-80) REVERT: D 298 MET cc_start: 0.7647 (mmp) cc_final: 0.6539 (mmt) REVERT: D 301 GLU cc_start: 0.7849 (tp30) cc_final: 0.7360 (tm-30) REVERT: D 311 ARG cc_start: 0.7359 (tpp80) cc_final: 0.7112 (tpp80) REVERT: D 339 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7395 (ttp-110) REVERT: D 378 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7768 (ttmm) REVERT: D 398 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8132 (mmmt) REVERT: D 399 LYS cc_start: 0.8391 (mppt) cc_final: 0.7690 (mmtm) REVERT: D 400 MET cc_start: 0.8228 (mtm) cc_final: 0.7947 (mtm) REVERT: D 402 GLU cc_start: 0.7078 (pp20) cc_final: 0.6752 (pp20) REVERT: D 403 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7260 (ttm110) REVERT: D 432 LEU cc_start: 0.8398 (mm) cc_final: 0.7960 (mm) REVERT: D 454 CYS cc_start: 0.7302 (p) cc_final: 0.6993 (m) REVERT: D 462 ASP cc_start: 0.7313 (m-30) cc_final: 0.7074 (m-30) REVERT: D 479 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7437 (tm-30) REVERT: D 506 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8009 (p) REVERT: D 511 TYR cc_start: 0.7712 (t80) cc_final: 0.7055 (t80) REVERT: D 531 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7922 (ttmm) REVERT: D 556 GLU cc_start: 0.6730 (tp30) cc_final: 0.6229 (tm-30) REVERT: D 566 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7654 (mtpp) REVERT: D 568 SER cc_start: 0.7740 (p) cc_final: 0.7528 (m) REVERT: D 587 LEU cc_start: 0.8212 (mm) cc_final: 0.7950 (mt) REVERT: D 604 MET cc_start: 0.7460 (tmm) cc_final: 0.7118 (tmm) REVERT: D 644 MET cc_start: 0.8044 (mpp) cc_final: 0.7618 (mtm) REVERT: D 658 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7954 (mm-30) REVERT: D 660 GLU cc_start: 0.7591 (tt0) cc_final: 0.7351 (tt0) REVERT: D 681 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7885 (ttpp) REVERT: D 697 MET cc_start: 0.7786 (tmm) cc_final: 0.7556 (tmm) REVERT: D 698 MET cc_start: 0.7516 (tpt) cc_final: 0.6966 (tmm) REVERT: D 703 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7495 (m) REVERT: D 715 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7926 (tppt) REVERT: D 722 ILE cc_start: 0.8422 (tp) cc_final: 0.8203 (tt) REVERT: D 724 MET cc_start: 0.7819 (ttp) cc_final: 0.7614 (mtp) REVERT: D 728 SER cc_start: 0.8320 (p) cc_final: 0.7878 (t) REVERT: D 739 GLN cc_start: 0.7895 (tt0) cc_final: 0.7442 (tp40) REVERT: D 757 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8300 (m) REVERT: D 780 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7905 (ttm170) REVERT: D 781 LYS cc_start: 0.8678 (tptp) cc_final: 0.8235 (tppt) REVERT: D 805 GLN cc_start: 0.7889 (pm20) cc_final: 0.7409 (pm20) REVERT: D 806 ASP cc_start: 0.7526 (p0) cc_final: 0.6626 (t0) REVERT: D 808 VAL cc_start: 0.8439 (t) cc_final: 0.8100 (p) REVERT: D 839 VAL cc_start: 0.8486 (t) cc_final: 0.8242 (p) REVERT: D 873 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 877 VAL cc_start: 0.8214 (t) cc_final: 0.7946 (p) REVERT: D 905 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6752 (mtt-85) REVERT: D 992 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7753 (mmtt) REVERT: D 993 GLU cc_start: 0.5624 (mm-30) cc_final: 0.5180 (mm-30) REVERT: D 1040 MET cc_start: 0.6551 (tpp) cc_final: 0.4079 (mmt) REVERT: D 1095 MET cc_start: 0.6461 (pmm) cc_final: 0.6086 (pmm) REVERT: D 1144 LEU cc_start: 0.8489 (mt) cc_final: 0.8011 (mt) REVERT: D 1148 ARG cc_start: 0.7376 (ptp-170) cc_final: 0.6981 (ptm160) REVERT: D 1224 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7778 (mtm-85) REVERT: D 1236 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: D 1247 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7834 (ttmt) REVERT: D 1334 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7319 (mm-30) REVERT: D 1352 ILE cc_start: 0.8301 (tp) cc_final: 0.7927 (tt) REVERT: E 31 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7725 (tt0) REVERT: E 53 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6713 (mm-30) REVERT: E 55 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6622 (pm20) REVERT: E 59 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7583 (mp) REVERT: E 68 GLU cc_start: 0.7933 (tp30) cc_final: 0.7658 (tp30) outliers start: 88 outliers final: 63 residues processed: 794 average time/residue: 0.2178 time to fit residues: 258.2308 Evaluate side-chains 822 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 747 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 319 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 580 GLN C 628 HIS ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 545 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103923 restraints weight = 48774.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107622 restraints weight = 25427.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110147 restraints weight = 15855.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111647 restraints weight = 11315.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112594 restraints weight = 9063.618| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26854 Z= 0.300 Angle : 0.786 11.605 36562 Z= 0.410 Chirality : 0.049 0.302 4184 Planarity : 0.006 0.065 4544 Dihedral : 14.447 174.484 4233 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.88 % Allowed : 20.75 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3164 helix: 0.23 (0.16), residues: 1072 sheet: -0.43 (0.27), residues: 367 loop : -1.72 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1341 TYR 0.026 0.003 TYR C1281 PHE 0.041 0.002 PHE C1025 TRP 0.053 0.003 TRP D 33 HIS 0.009 0.002 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.30 (26848) covalent geometry : angle 0.77949 / 0.41 (36556) hydrogen bonds : bond 0.05857 / 6.40 ( 1030) hydrogen bonds : angle 4.84473 / 5.29 ( 2816) metal coordination : bond 0.02861 / 2.71 ( 6) metal coordination : angle 7.90050 / 14.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 796 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8205 (mtpp) REVERT: A 80 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 97 GLU cc_start: 0.7312 (mp0) cc_final: 0.7103 (mp0) REVERT: A 118 ASP cc_start: 0.7737 (p0) cc_final: 0.7471 (p0) REVERT: A 206 GLU cc_start: 0.7408 (pp20) cc_final: 0.6691 (pp20) REVERT: B 60 GLU cc_start: 0.5982 (tp30) cc_final: 0.5544 (tp30) REVERT: B 84 ASN cc_start: 0.7989 (t0) cc_final: 0.7747 (t0) REVERT: B 142 MET cc_start: 0.6373 (mmm) cc_final: 0.6169 (mmm) REVERT: B 174 ASP cc_start: 0.7291 (m-30) cc_final: 0.6623 (m-30) REVERT: C 7 GLU cc_start: 0.6738 (mp0) cc_final: 0.6282 (pm20) REVERT: C 8 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7292 (mttt) REVERT: C 33 ASP cc_start: 0.6454 (p0) cc_final: 0.6236 (p0) REVERT: C 50 GLU cc_start: 0.6866 (tp30) cc_final: 0.6559 (tp30) REVERT: C 99 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7845 (tppt) REVERT: C 169 LYS cc_start: 0.7948 (tmtt) cc_final: 0.7459 (tmtt) REVERT: C 177 ILE cc_start: 0.8145 (mm) cc_final: 0.7746 (tp) REVERT: C 191 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8091 (mtmm) REVERT: C 197 ARG cc_start: 0.7393 (mtp-110) cc_final: 0.6982 (mtp85) REVERT: C 199 ASP cc_start: 0.7871 (t0) cc_final: 0.7665 (t0) REVERT: C 217 THR cc_start: 0.7085 (m) cc_final: 0.5945 (t) REVERT: C 334 GLU cc_start: 0.5870 (pp20) cc_final: 0.4249 (tm-30) REVERT: C 392 GLU cc_start: 0.7664 (tp30) cc_final: 0.7183 (tp30) REVERT: C 394 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7284 (ttm110) REVERT: C 427 ASP cc_start: 0.8009 (m-30) cc_final: 0.7766 (m-30) REVERT: C 447 HIS cc_start: 0.7712 (t70) cc_final: 0.7446 (t-170) REVERT: C 461 GLU cc_start: 0.7907 (tt0) cc_final: 0.7187 (tm-30) REVERT: C 491 ASP cc_start: 0.7035 (p0) cc_final: 0.6726 (p0) REVERT: C 524 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 554 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7921 (m170) REVERT: C 641 GLU cc_start: 0.7279 (pm20) cc_final: 0.6006 (pp20) REVERT: C 668 ILE cc_start: 0.8235 (mm) cc_final: 0.8026 (mt) REVERT: C 674 ASP cc_start: 0.8099 (t0) cc_final: 0.7724 (t0) REVERT: C 675 ASP cc_start: 0.7887 (t0) cc_final: 0.7343 (t70) REVERT: C 681 MET cc_start: 0.7293 (tpp) cc_final: 0.6915 (mtt) REVERT: C 737 ASN cc_start: 0.8670 (m-40) cc_final: 0.7624 (m-40) REVERT: C 761 GLN cc_start: 0.7426 (mm110) cc_final: 0.6899 (mp10) REVERT: C 779 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7840 (ttm-80) REVERT: C 793 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 814 ASP cc_start: 0.7166 (t0) cc_final: 0.6270 (t0) REVERT: C 825 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 835 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 853 ASP cc_start: 0.7962 (m-30) cc_final: 0.7436 (p0) REVERT: C 864 LYS cc_start: 0.7404 (mmtp) cc_final: 0.7159 (mmtp) REVERT: C 882 ILE cc_start: 0.8543 (mp) cc_final: 0.8303 (mm) REVERT: C 930 ASP cc_start: 0.7029 (t0) cc_final: 0.6627 (t0) REVERT: C 951 MET cc_start: 0.8282 (mtp) cc_final: 0.7652 (mtp) REVERT: C 954 LYS cc_start: 0.8538 (mtmm) cc_final: 0.7565 (mtmt) REVERT: C 957 LYS cc_start: 0.8956 (pptt) cc_final: 0.8541 (pptt) REVERT: C 1030 GLU cc_start: 0.8230 (tp30) cc_final: 0.8028 (tp30) REVERT: C 1073 LYS cc_start: 0.7428 (ptpp) cc_final: 0.6598 (ptpp) REVERT: C 1079 ILE cc_start: 0.8241 (mm) cc_final: 0.7937 (mt) REVERT: C 1095 ASP cc_start: 0.7499 (m-30) cc_final: 0.7124 (t0) REVERT: C 1122 LYS cc_start: 0.8111 (mmmm) cc_final: 0.7902 (mmmm) REVERT: C 1131 MET cc_start: 0.7493 (tpp) cc_final: 0.7191 (tpp) REVERT: C 1146 GLN cc_start: 0.8238 (tp40) cc_final: 0.7705 (tp40) REVERT: C 1164 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: C 1171 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7791 (ttp-170) REVERT: C 1178 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8298 (mmtt) REVERT: C 1251 TYR cc_start: 0.7819 (m-80) cc_final: 0.7584 (m-10) REVERT: C 1270 PHE cc_start: 0.7729 (t80) cc_final: 0.7497 (t80) REVERT: C 1274 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6740 (mm-30) REVERT: C 1279 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6321 (mm-30) REVERT: C 1287 LEU cc_start: 0.8208 (tt) cc_final: 0.7729 (tp) REVERT: C 1289 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 1303 LYS cc_start: 0.8083 (tppp) cc_final: 0.7678 (ttmm) REVERT: C 1304 MET cc_start: 0.7087 (tpt) cc_final: 0.6877 (tpp) REVERT: C 1329 GLU cc_start: 0.7450 (tt0) cc_final: 0.6988 (mt-10) REVERT: D 21 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7375 (mmmm) REVERT: D 32 SER cc_start: 0.8759 (m) cc_final: 0.8495 (p) REVERT: D 35 PHE cc_start: 0.6838 (m-80) cc_final: 0.6533 (m-80) REVERT: D 50 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8556 (tmtt) REVERT: D 66 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8046 (mmmm) REVERT: D 69 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7188 (tm-30) REVERT: D 102 MET cc_start: 0.7555 (mtp) cc_final: 0.7305 (mtm) REVERT: D 115 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: D 117 LEU cc_start: 0.8060 (mm) cc_final: 0.7615 (mm) REVERT: D 130 MET cc_start: 0.7592 (mmt) cc_final: 0.7350 (mmm) REVERT: D 141 PHE cc_start: 0.7652 (m-10) cc_final: 0.7367 (m-10) REVERT: D 179 LYS cc_start: 0.8422 (mttt) cc_final: 0.7686 (tttt) REVERT: D 183 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7382 (tm-30) REVERT: D 186 GLN cc_start: 0.7790 (tt0) cc_final: 0.7134 (tt0) REVERT: D 190 LYS cc_start: 0.8105 (ptpp) cc_final: 0.7437 (ptpp) REVERT: D 200 GLN cc_start: 0.8154 (pp30) cc_final: 0.7692 (pp30) REVERT: D 211 GLU cc_start: 0.8058 (pp20) cc_final: 0.7527 (pp20) REVERT: D 215 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8283 (mmtt) REVERT: D 221 ILE cc_start: 0.8610 (tp) cc_final: 0.8364 (tp) REVERT: D 222 LYS cc_start: 0.8404 (mptt) cc_final: 0.7987 (mptt) REVERT: D 233 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8107 (mmmm) REVERT: D 237 MET cc_start: 0.7874 (tpp) cc_final: 0.7611 (tpp) REVERT: D 248 ASP cc_start: 0.7630 (m-30) cc_final: 0.7270 (p0) REVERT: D 278 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7950 (ttm110) REVERT: D 294 ASN cc_start: 0.8232 (t0) cc_final: 0.6844 (t0) REVERT: D 295 GLU cc_start: 0.8035 (tt0) cc_final: 0.7593 (tt0) REVERT: D 297 ARG cc_start: 0.8250 (tmm-80) cc_final: 0.7687 (tmm-80) REVERT: D 298 MET cc_start: 0.7913 (mmp) cc_final: 0.6846 (mmt) REVERT: D 301 GLU cc_start: 0.7803 (tp30) cc_final: 0.7573 (tm-30) REVERT: D 330 MET cc_start: 0.7550 (ttt) cc_final: 0.7311 (ttt) REVERT: D 370 LYS cc_start: 0.7938 (tttm) cc_final: 0.7608 (tttt) REVERT: D 378 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8039 (mmmm) REVERT: D 398 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8006 (mmmt) REVERT: D 399 LYS cc_start: 0.8497 (mppt) cc_final: 0.7866 (mppt) REVERT: D 400 MET cc_start: 0.8327 (mtm) cc_final: 0.7764 (mtm) REVERT: D 402 GLU cc_start: 0.7334 (pp20) cc_final: 0.6973 (pp20) REVERT: D 403 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7487 (ttm110) REVERT: D 432 LEU cc_start: 0.8480 (mm) cc_final: 0.8215 (mm) REVERT: D 462 ASP cc_start: 0.7447 (m-30) cc_final: 0.7191 (m-30) REVERT: D 506 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8201 (p) REVERT: D 511 TYR cc_start: 0.7838 (t80) cc_final: 0.7296 (t80) REVERT: D 531 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7975 (ttmm) REVERT: D 547 ARG cc_start: 0.7460 (mpt-90) cc_final: 0.7065 (mpt-90) REVERT: D 566 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7731 (mtpp) REVERT: D 568 SER cc_start: 0.7775 (p) cc_final: 0.7556 (m) REVERT: D 604 MET cc_start: 0.7483 (tmm) cc_final: 0.7203 (tmm) REVERT: D 644 MET cc_start: 0.8076 (mpp) cc_final: 0.7562 (mtm) REVERT: D 658 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8313 (mm-30) REVERT: D 681 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7912 (ttpp) REVERT: D 698 MET cc_start: 0.7574 (tpt) cc_final: 0.7001 (tmm) REVERT: D 715 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7998 (ttmm) REVERT: D 724 MET cc_start: 0.7938 (ttp) cc_final: 0.7725 (mtp) REVERT: D 728 SER cc_start: 0.8400 (p) cc_final: 0.7902 (t) REVERT: D 739 GLN cc_start: 0.7966 (tt0) cc_final: 0.7466 (tp40) REVERT: D 757 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8274 (m) REVERT: D 781 LYS cc_start: 0.8738 (tptp) cc_final: 0.8345 (tppt) REVERT: D 789 LYS cc_start: 0.7946 (ptmm) cc_final: 0.7532 (tttm) REVERT: D 806 ASP cc_start: 0.7472 (p0) cc_final: 0.6620 (t0) REVERT: D 808 VAL cc_start: 0.8514 (t) cc_final: 0.8186 (p) REVERT: D 867 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 873 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7771 (mt-10) REVERT: D 877 VAL cc_start: 0.8189 (t) cc_final: 0.7988 (p) REVERT: D 905 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7017 (mtt-85) REVERT: D 964 LYS cc_start: 0.7631 (tppt) cc_final: 0.7398 (tppt) REVERT: D 992 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7851 (mmtt) REVERT: D 993 GLU cc_start: 0.5299 (mm-30) cc_final: 0.4846 (mm-30) REVERT: D 1095 MET cc_start: 0.6487 (pmm) cc_final: 0.6266 (pmm) REVERT: D 1148 ARG cc_start: 0.7381 (ptp-170) cc_final: 0.7096 (ptm160) REVERT: D 1224 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7777 (mtt180) REVERT: D 1244 GLN cc_start: 0.8253 (tt0) cc_final: 0.7514 (tm-30) REVERT: D 1247 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7681 (ttpt) REVERT: D 1334 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7468 (mm-30) REVERT: D 1352 ILE cc_start: 0.8428 (tp) cc_final: 0.8015 (tt) REVERT: D 1357 ILE cc_start: 0.7852 (mm) cc_final: 0.7226 (tt) REVERT: E 53 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6822 (mm-30) REVERT: E 55 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: E 59 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7742 (mp) REVERT: E 68 GLU cc_start: 0.7931 (tp30) cc_final: 0.7670 (tp30) outliers start: 105 outliers final: 70 residues processed: 838 average time/residue: 0.2122 time to fit residues: 268.3466 Evaluate side-chains 848 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 768 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 608 CYS Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 215 optimal weight: 0.7980 chunk 118 optimal weight: 0.0010 chunk 57 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 299 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 545 HIS D 951 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107397 restraints weight = 48860.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111206 restraints weight = 25197.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113764 restraints weight = 15651.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115356 restraints weight = 11135.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116164 restraints weight = 8868.979| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26854 Z= 0.146 Angle : 0.741 12.653 36562 Z= 0.375 Chirality : 0.046 0.296 4184 Planarity : 0.005 0.065 4544 Dihedral : 14.322 173.911 4233 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.14 % Allowed : 22.71 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3164 helix: 0.44 (0.16), residues: 1070 sheet: -0.37 (0.27), residues: 354 loop : -1.58 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1369 TYR 0.023 0.002 TYR C 70 PHE 0.036 0.001 PHE C1025 TRP 0.059 0.003 TRP D 33 HIS 0.010 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (26848) covalent geometry : angle 0.73641 / 0.37 (36556) hydrogen bonds : bond 0.04721 / 5.18 ( 1030) hydrogen bonds : angle 4.59025 / 4.97 ( 2816) metal coordination : bond 0.00965 / 1.11 ( 6) metal coordination : angle 6.72213 / 12.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 755 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8134 (mtpp) REVERT: A 80 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6791 (tm-30) REVERT: A 118 ASP cc_start: 0.7761 (p0) cc_final: 0.7500 (p0) REVERT: A 170 ARG cc_start: 0.5849 (ptt180) cc_final: 0.5616 (ptt-90) REVERT: A 206 GLU cc_start: 0.7158 (pp20) cc_final: 0.6753 (pp20) REVERT: B 60 GLU cc_start: 0.5923 (tp30) cc_final: 0.5496 (tp30) REVERT: B 84 ASN cc_start: 0.7982 (t0) cc_final: 0.7596 (t0) REVERT: B 140 ILE cc_start: 0.7872 (tp) cc_final: 0.7047 (tp) REVERT: B 142 MET cc_start: 0.6285 (mmm) cc_final: 0.5643 (mmm) REVERT: B 205 MET cc_start: 0.6975 (pmm) cc_final: 0.6719 (pmm) REVERT: C 8 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7235 (mttt) REVERT: C 22 LEU cc_start: 0.8687 (tt) cc_final: 0.8404 (mt) REVERT: C 33 ASP cc_start: 0.6325 (p0) cc_final: 0.6115 (p0) REVERT: C 50 GLU cc_start: 0.6770 (tp30) cc_final: 0.6540 (tp30) REVERT: C 99 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7815 (tppt) REVERT: C 124 MET cc_start: 0.7422 (ttp) cc_final: 0.6380 (tmm) REVERT: C 169 LYS cc_start: 0.8001 (tmtt) cc_final: 0.7517 (tmtt) REVERT: C 177 ILE cc_start: 0.7880 (mm) cc_final: 0.7588 (tp) REVERT: C 191 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8082 (mtmm) REVERT: C 199 ASP cc_start: 0.7767 (t0) cc_final: 0.7559 (t0) REVERT: C 217 THR cc_start: 0.7071 (m) cc_final: 0.5964 (t) REVERT: C 334 GLU cc_start: 0.5752 (pp20) cc_final: 0.4125 (tm-30) REVERT: C 392 GLU cc_start: 0.7598 (tp30) cc_final: 0.7132 (tp30) REVERT: C 394 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7291 (ttm110) REVERT: C 427 ASP cc_start: 0.7957 (m-30) cc_final: 0.7682 (m-30) REVERT: C 447 HIS cc_start: 0.7649 (t70) cc_final: 0.7345 (t-170) REVERT: C 461 GLU cc_start: 0.7898 (tt0) cc_final: 0.7190 (tm-30) REVERT: C 492 MET cc_start: 0.6677 (pmm) cc_final: 0.6408 (pmm) REVERT: C 554 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7785 (m170) REVERT: C 668 ILE cc_start: 0.8214 (mm) cc_final: 0.8012 (mt) REVERT: C 674 ASP cc_start: 0.8056 (t0) cc_final: 0.7707 (t0) REVERT: C 675 ASP cc_start: 0.7811 (t0) cc_final: 0.7344 (t70) REVERT: C 681 MET cc_start: 0.7272 (tpp) cc_final: 0.6884 (mtt) REVERT: C 737 ASN cc_start: 0.8634 (m-40) cc_final: 0.7721 (m-40) REVERT: C 761 GLN cc_start: 0.7515 (mm110) cc_final: 0.7040 (mp10) REVERT: C 775 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 779 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.7743 (ttm-80) REVERT: C 793 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6627 (mt-10) REVERT: C 814 ASP cc_start: 0.7038 (t0) cc_final: 0.6402 (t0) REVERT: C 825 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7518 (mm-30) REVERT: C 853 ASP cc_start: 0.7873 (m-30) cc_final: 0.7639 (p0) REVERT: C 864 LYS cc_start: 0.7372 (mmtp) cc_final: 0.6925 (mmtp) REVERT: C 930 ASP cc_start: 0.6993 (t0) cc_final: 0.6655 (t0) REVERT: C 951 MET cc_start: 0.8155 (mtp) cc_final: 0.7544 (mtp) REVERT: C 954 LYS cc_start: 0.8484 (mtmm) cc_final: 0.7495 (mtmt) REVERT: C 955 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7243 (tp-100) REVERT: C 957 LYS cc_start: 0.8920 (pptt) cc_final: 0.8487 (pptt) REVERT: C 1030 GLU cc_start: 0.8178 (tp30) cc_final: 0.7957 (tp30) REVERT: C 1073 LYS cc_start: 0.7346 (ptpp) cc_final: 0.6546 (ptpp) REVERT: C 1079 ILE cc_start: 0.8301 (mm) cc_final: 0.7668 (mt) REVERT: C 1095 ASP cc_start: 0.7451 (m-30) cc_final: 0.7082 (t0) REVERT: C 1122 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7876 (mmmm) REVERT: C 1142 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7788 (mtt-85) REVERT: C 1146 GLN cc_start: 0.8158 (tp40) cc_final: 0.7479 (tp40) REVERT: C 1164 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: C 1171 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7733 (ttp-170) REVERT: C 1178 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8260 (mmtt) REVERT: C 1274 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6855 (mm-30) REVERT: C 1279 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6949 (mm-30) REVERT: C 1289 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7567 (tt0) REVERT: C 1303 LYS cc_start: 0.7985 (tppp) cc_final: 0.7682 (ttmm) REVERT: C 1304 MET cc_start: 0.7037 (tpt) cc_final: 0.6650 (tpp) REVERT: D 21 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7265 (mmmm) REVERT: D 32 SER cc_start: 0.8679 (m) cc_final: 0.8408 (p) REVERT: D 35 PHE cc_start: 0.6701 (m-80) cc_final: 0.6437 (m-80) REVERT: D 50 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8585 (tmtt) REVERT: D 66 LYS cc_start: 0.8264 (mmmm) cc_final: 0.8025 (mmmm) REVERT: D 69 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7162 (tm-30) REVERT: D 102 MET cc_start: 0.7550 (mtp) cc_final: 0.7250 (mtm) REVERT: D 115 TRP cc_start: 0.8662 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: D 117 LEU cc_start: 0.8020 (mm) cc_final: 0.7529 (mm) REVERT: D 130 MET cc_start: 0.7628 (mmt) cc_final: 0.7408 (mmm) REVERT: D 141 PHE cc_start: 0.7672 (m-10) cc_final: 0.7414 (m-10) REVERT: D 179 LYS cc_start: 0.8404 (mttt) cc_final: 0.7778 (mmmm) REVERT: D 180 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6569 (ppp) REVERT: D 183 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 190 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7415 (ptpp) REVERT: D 200 GLN cc_start: 0.8135 (pp30) cc_final: 0.7797 (pp30) REVERT: D 211 GLU cc_start: 0.7988 (pp20) cc_final: 0.7460 (pp20) REVERT: D 215 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8089 (mmtt) REVERT: D 219 LYS cc_start: 0.8374 (mttt) cc_final: 0.7952 (mttt) REVERT: D 221 ILE cc_start: 0.8560 (tp) cc_final: 0.8312 (tp) REVERT: D 222 LYS cc_start: 0.8362 (mptt) cc_final: 0.7930 (mptt) REVERT: D 233 LYS cc_start: 0.8359 (mmmm) cc_final: 0.8020 (mmmm) REVERT: D 236 TRP cc_start: 0.8858 (m-10) cc_final: 0.8565 (m-10) REVERT: D 248 ASP cc_start: 0.7633 (m-30) cc_final: 0.7236 (p0) REVERT: D 278 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7916 (ttm110) REVERT: D 294 ASN cc_start: 0.8234 (t0) cc_final: 0.6913 (t0) REVERT: D 295 GLU cc_start: 0.7929 (tt0) cc_final: 0.7470 (tt0) REVERT: D 297 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7663 (tmm-80) REVERT: D 298 MET cc_start: 0.7827 (mmp) cc_final: 0.6670 (mmt) REVERT: D 301 GLU cc_start: 0.7798 (tp30) cc_final: 0.7438 (tm-30) REVERT: D 378 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7843 (mmmm) REVERT: D 398 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7878 (mmmt) REVERT: D 399 LYS cc_start: 0.8437 (mppt) cc_final: 0.7701 (mmtm) REVERT: D 400 MET cc_start: 0.8334 (mtm) cc_final: 0.7622 (mtm) REVERT: D 402 GLU cc_start: 0.7156 (pp20) cc_final: 0.6886 (pp20) REVERT: D 403 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7294 (ttm110) REVERT: D 432 LEU cc_start: 0.8422 (mm) cc_final: 0.8008 (mm) REVERT: D 462 ASP cc_start: 0.7287 (m-30) cc_final: 0.7033 (m-30) REVERT: D 479 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 506 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7994 (p) REVERT: D 511 TYR cc_start: 0.7786 (t80) cc_final: 0.6997 (t80) REVERT: D 531 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7927 (ttmm) REVERT: D 566 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7665 (mtpp) REVERT: D 604 MET cc_start: 0.7422 (tmm) cc_final: 0.7164 (tmm) REVERT: D 644 MET cc_start: 0.7987 (mpp) cc_final: 0.7514 (mtm) REVERT: D 681 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7879 (ttpp) REVERT: D 698 MET cc_start: 0.7564 (tpt) cc_final: 0.6760 (tmm) REVERT: D 715 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7895 (ttmm) REVERT: D 724 MET cc_start: 0.7888 (ttp) cc_final: 0.7493 (mtp) REVERT: D 728 SER cc_start: 0.8277 (p) cc_final: 0.7676 (m) REVERT: D 739 GLN cc_start: 0.8003 (tt0) cc_final: 0.7492 (tp40) REVERT: D 757 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8220 (m) REVERT: D 781 LYS cc_start: 0.8676 (tptp) cc_final: 0.8250 (tppt) REVERT: D 789 LYS cc_start: 0.7828 (ptmm) cc_final: 0.7453 (tttm) REVERT: D 805 GLN cc_start: 0.7889 (pm20) cc_final: 0.7445 (pm20) REVERT: D 806 ASP cc_start: 0.7491 (p0) cc_final: 0.6597 (t0) REVERT: D 808 VAL cc_start: 0.8518 (t) cc_final: 0.8195 (p) REVERT: D 839 VAL cc_start: 0.8626 (t) cc_final: 0.8334 (p) REVERT: D 867 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7453 (tm-30) REVERT: D 873 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7691 (mt-10) REVERT: D 877 VAL cc_start: 0.8263 (t) cc_final: 0.8047 (p) REVERT: D 964 LYS cc_start: 0.7641 (tppt) cc_final: 0.7420 (tppt) REVERT: D 992 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7851 (mmtt) REVERT: D 993 GLU cc_start: 0.5218 (mm-30) cc_final: 0.4782 (mm-30) REVERT: D 1040 MET cc_start: 0.6674 (tpp) cc_final: 0.4030 (mmm) REVERT: D 1101 LEU cc_start: 0.8790 (tp) cc_final: 0.7880 (pp) REVERT: D 1148 ARG cc_start: 0.7388 (ptp-170) cc_final: 0.7061 (ptm160) REVERT: D 1224 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7861 (mtm-85) REVERT: D 1244 GLN cc_start: 0.8165 (tt0) cc_final: 0.7426 (tm-30) REVERT: D 1334 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7349 (mm-30) REVERT: D 1352 ILE cc_start: 0.8373 (tp) cc_final: 0.7984 (tt) REVERT: E 53 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6815 (mm-30) REVERT: E 55 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: E 59 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7592 (mp) REVERT: E 68 GLU cc_start: 0.7899 (tp30) cc_final: 0.7633 (tp30) outliers start: 85 outliers final: 58 residues processed: 787 average time/residue: 0.2192 time to fit residues: 257.8783 Evaluate side-chains 807 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 740 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 82 optimal weight: 0.0570 chunk 231 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 192 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 510 GLN C 519 ASN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 545 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108417 restraints weight = 48701.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112245 restraints weight = 25098.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114833 restraints weight = 15551.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116459 restraints weight = 11017.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117165 restraints weight = 8779.636| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26854 Z= 0.137 Angle : 0.746 14.427 36562 Z= 0.372 Chirality : 0.046 0.566 4184 Planarity : 0.005 0.061 4544 Dihedral : 14.273 172.213 4233 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.99 % Allowed : 23.41 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3164 helix: 0.56 (0.16), residues: 1065 sheet: -0.25 (0.27), residues: 346 loop : -1.52 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1369 TYR 0.025 0.001 TYR D 165 PHE 0.033 0.001 PHE C1025 TRP 0.066 0.002 TRP D 33 HIS 0.048 0.002 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (26848) covalent geometry : angle 0.74174 / 0.37 (36556) hydrogen bonds : bond 0.04442 / 4.81 ( 1030) hydrogen bonds : angle 4.52472 / 4.88 ( 2816) metal coordination : bond 0.00756 / 0.76 ( 6) metal coordination : angle 6.27020 / 11.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 757 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8032 (mtpp) REVERT: A 68 TYR cc_start: 0.8566 (m-10) cc_final: 0.8074 (m-10) REVERT: A 80 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6779 (tm-30) REVERT: A 102 LEU cc_start: 0.8458 (tp) cc_final: 0.8053 (tp) REVERT: A 118 ASP cc_start: 0.7760 (p0) cc_final: 0.7491 (p0) REVERT: A 153 VAL cc_start: 0.8651 (t) cc_final: 0.8407 (p) REVERT: A 170 ARG cc_start: 0.5756 (ptt180) cc_final: 0.5514 (ptt-90) REVERT: A 206 GLU cc_start: 0.7092 (pp20) cc_final: 0.6720 (pp20) REVERT: B 60 GLU cc_start: 0.5907 (tp30) cc_final: 0.5491 (tp30) REVERT: B 84 ASN cc_start: 0.7930 (t0) cc_final: 0.7537 (t0) REVERT: B 140 ILE cc_start: 0.7757 (tp) cc_final: 0.6998 (tp) REVERT: B 142 MET cc_start: 0.6252 (mmm) cc_final: 0.5703 (mmm) REVERT: C 8 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7277 (mttt) REVERT: C 22 LEU cc_start: 0.8660 (tt) cc_final: 0.8367 (mt) REVERT: C 33 ASP cc_start: 0.6310 (p0) cc_final: 0.6093 (p0) REVERT: C 50 GLU cc_start: 0.6735 (tp30) cc_final: 0.6503 (tp30) REVERT: C 124 MET cc_start: 0.7395 (ttp) cc_final: 0.6425 (tmm) REVERT: C 169 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7517 (tmtt) REVERT: C 177 ILE cc_start: 0.7812 (mm) cc_final: 0.7559 (tp) REVERT: C 191 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8058 (mtmm) REVERT: C 199 ASP cc_start: 0.7727 (t0) cc_final: 0.7498 (t0) REVERT: C 215 TYR cc_start: 0.7546 (m-80) cc_final: 0.7167 (m-80) REVERT: C 217 THR cc_start: 0.7045 (m) cc_final: 0.5941 (t) REVERT: C 299 LYS cc_start: 0.7750 (ptmt) cc_final: 0.7143 (ptmm) REVERT: C 330 HIS cc_start: 0.7103 (m90) cc_final: 0.6648 (m-70) REVERT: C 334 GLU cc_start: 0.5704 (pp20) cc_final: 0.4665 (tp30) REVERT: C 392 GLU cc_start: 0.7558 (tp30) cc_final: 0.7111 (tp30) REVERT: C 394 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7270 (ttm110) REVERT: C 424 ASP cc_start: 0.7507 (m-30) cc_final: 0.7192 (m-30) REVERT: C 427 ASP cc_start: 0.7930 (m-30) cc_final: 0.7643 (m-30) REVERT: C 447 HIS cc_start: 0.7628 (t70) cc_final: 0.7324 (t-170) REVERT: C 461 GLU cc_start: 0.7882 (tt0) cc_final: 0.7186 (tm-30) REVERT: C 541 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7610 (mm-30) REVERT: C 554 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7726 (m170) REVERT: C 653 MET cc_start: 0.7264 (tpt) cc_final: 0.7026 (tpp) REVERT: C 668 ILE cc_start: 0.8202 (mm) cc_final: 0.7985 (mt) REVERT: C 674 ASP cc_start: 0.8000 (t0) cc_final: 0.7645 (t0) REVERT: C 675 ASP cc_start: 0.7799 (t0) cc_final: 0.7320 (t70) REVERT: C 681 MET cc_start: 0.7244 (tpp) cc_final: 0.6894 (mtt) REVERT: C 737 ASN cc_start: 0.8628 (m-40) cc_final: 0.7702 (m-40) REVERT: C 761 GLN cc_start: 0.7547 (mm110) cc_final: 0.7037 (mp10) REVERT: C 779 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7709 (ttm-80) REVERT: C 793 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6590 (mt-10) REVERT: C 825 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7498 (mm-30) REVERT: C 864 LYS cc_start: 0.7376 (mmtp) cc_final: 0.6944 (mmmm) REVERT: C 928 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8537 (m) REVERT: C 930 ASP cc_start: 0.7016 (t0) cc_final: 0.6716 (t0) REVERT: C 951 MET cc_start: 0.8214 (mtp) cc_final: 0.7563 (mtp) REVERT: C 954 LYS cc_start: 0.8488 (mtmm) cc_final: 0.7520 (mtmt) REVERT: C 955 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7223 (tp-100) REVERT: C 957 LYS cc_start: 0.8921 (pptt) cc_final: 0.8486 (pptt) REVERT: C 1079 ILE cc_start: 0.8277 (mm) cc_final: 0.7902 (mt) REVERT: C 1095 ASP cc_start: 0.7402 (m-30) cc_final: 0.7055 (t0) REVERT: C 1122 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7835 (mmmm) REVERT: C 1131 MET cc_start: 0.7566 (tpp) cc_final: 0.7210 (tpp) REVERT: C 1164 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: C 1171 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7721 (ttp-170) REVERT: C 1178 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8241 (mmtt) REVERT: C 1274 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6806 (mm-30) REVERT: C 1279 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6908 (mm-30) REVERT: C 1289 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7508 (tt0) REVERT: C 1303 LYS cc_start: 0.7976 (tppp) cc_final: 0.7631 (ttmm) REVERT: C 1332 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7658 (p) REVERT: C 1337 ILE cc_start: 0.7868 (tp) cc_final: 0.7547 (tt) REVERT: D 21 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7244 (mmmm) REVERT: D 35 PHE cc_start: 0.6643 (m-80) cc_final: 0.6408 (m-80) REVERT: D 50 LYS cc_start: 0.8915 (tmtt) cc_final: 0.8601 (tmtt) REVERT: D 66 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7965 (mmmm) REVERT: D 69 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7141 (tm-30) REVERT: D 102 MET cc_start: 0.7514 (mtp) cc_final: 0.7273 (mtm) REVERT: D 115 TRP cc_start: 0.8597 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: D 117 LEU cc_start: 0.7960 (mm) cc_final: 0.7544 (mm) REVERT: D 130 MET cc_start: 0.7572 (mmt) cc_final: 0.7356 (mmm) REVERT: D 141 PHE cc_start: 0.7656 (m-10) cc_final: 0.7408 (m-10) REVERT: D 179 LYS cc_start: 0.8355 (mttt) cc_final: 0.8022 (mmmm) REVERT: D 183 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7762 (tm-30) REVERT: D 190 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7382 (ptpp) REVERT: D 200 GLN cc_start: 0.8106 (pp30) cc_final: 0.7786 (pp30) REVERT: D 211 GLU cc_start: 0.8004 (pp20) cc_final: 0.7468 (pp20) REVERT: D 215 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8079 (mmtt) REVERT: D 219 LYS cc_start: 0.8364 (mttt) cc_final: 0.7942 (mttt) REVERT: D 221 ILE cc_start: 0.8546 (tp) cc_final: 0.8318 (tp) REVERT: D 222 LYS cc_start: 0.8360 (mptt) cc_final: 0.7926 (mptt) REVERT: D 233 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8010 (mmmm) REVERT: D 236 TRP cc_start: 0.8849 (m-10) cc_final: 0.8584 (m-10) REVERT: D 241 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7749 (p) REVERT: D 248 ASP cc_start: 0.7651 (m-30) cc_final: 0.7219 (p0) REVERT: D 278 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7880 (ttm110) REVERT: D 294 ASN cc_start: 0.8228 (t0) cc_final: 0.6912 (t0) REVERT: D 295 GLU cc_start: 0.7904 (tt0) cc_final: 0.7441 (tt0) REVERT: D 297 ARG cc_start: 0.8265 (tmm-80) cc_final: 0.7700 (tmm-80) REVERT: D 298 MET cc_start: 0.7792 (mmp) cc_final: 0.6647 (mmt) REVERT: D 301 GLU cc_start: 0.7799 (tp30) cc_final: 0.7412 (tm-30) REVERT: D 312 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7174 (mmm160) REVERT: D 370 LYS cc_start: 0.7883 (tttp) cc_final: 0.7667 (tttm) REVERT: D 378 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7777 (mmmm) REVERT: D 398 LYS cc_start: 0.8478 (mmtt) cc_final: 0.7948 (mmmt) REVERT: D 399 LYS cc_start: 0.8404 (mppt) cc_final: 0.7468 (mmtm) REVERT: D 400 MET cc_start: 0.8257 (mtm) cc_final: 0.7568 (mtm) REVERT: D 402 GLU cc_start: 0.7081 (pp20) cc_final: 0.6619 (pp20) REVERT: D 403 ARG cc_start: 0.7823 (ttm110) cc_final: 0.7175 (ttm110) REVERT: D 432 LEU cc_start: 0.8426 (mm) cc_final: 0.8016 (mm) REVERT: D 479 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7344 (tm-30) REVERT: D 506 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7937 (p) REVERT: D 511 TYR cc_start: 0.7723 (t80) cc_final: 0.6952 (t80) REVERT: D 525 MET cc_start: 0.7127 (ptp) cc_final: 0.6768 (ptp) REVERT: D 531 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7957 (ttmm) REVERT: D 566 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7684 (mtpp) REVERT: D 568 SER cc_start: 0.7684 (m) cc_final: 0.7306 (t) REVERT: D 604 MET cc_start: 0.7416 (tmm) cc_final: 0.7157 (tmm) REVERT: D 644 MET cc_start: 0.7987 (mpp) cc_final: 0.7515 (mtm) REVERT: D 681 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7903 (ttpp) REVERT: D 698 MET cc_start: 0.7622 (tpt) cc_final: 0.6915 (tmm) REVERT: D 715 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7762 (ttmm) REVERT: D 724 MET cc_start: 0.7863 (ttp) cc_final: 0.7490 (mtp) REVERT: D 728 SER cc_start: 0.8176 (p) cc_final: 0.7644 (m) REVERT: D 739 GLN cc_start: 0.8010 (tt0) cc_final: 0.7394 (tp40) REVERT: D 757 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8287 (m) REVERT: D 781 LYS cc_start: 0.8657 (tptp) cc_final: 0.8231 (tppt) REVERT: D 805 GLN cc_start: 0.7912 (pm20) cc_final: 0.7448 (pm20) REVERT: D 806 ASP cc_start: 0.7460 (p0) cc_final: 0.6608 (t0) REVERT: D 808 VAL cc_start: 0.8515 (t) cc_final: 0.8178 (p) REVERT: D 811 GLU cc_start: 0.7681 (tp30) cc_final: 0.7369 (tp30) REVERT: D 839 VAL cc_start: 0.8591 (t) cc_final: 0.8313 (p) REVERT: D 867 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 873 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 877 VAL cc_start: 0.8301 (t) cc_final: 0.8052 (p) REVERT: D 905 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6776 (mtt-85) REVERT: D 964 LYS cc_start: 0.7620 (tppt) cc_final: 0.7391 (tppt) REVERT: D 983 LYS cc_start: 0.7678 (pttm) cc_final: 0.7475 (mppt) REVERT: D 992 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7903 (mmtt) REVERT: D 993 GLU cc_start: 0.5636 (mm-30) cc_final: 0.5279 (mm-30) REVERT: D 1040 MET cc_start: 0.6692 (tpp) cc_final: 0.4034 (mmt) REVERT: D 1095 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6357 (pmm) REVERT: D 1101 LEU cc_start: 0.8834 (tp) cc_final: 0.7968 (pp) REVERT: D 1148 ARG cc_start: 0.7372 (ptp-170) cc_final: 0.7052 (ptm160) REVERT: D 1202 GLU cc_start: 0.6728 (mp0) cc_final: 0.5795 (mt-10) REVERT: D 1244 GLN cc_start: 0.8112 (tt0) cc_final: 0.7478 (tm-30) REVERT: D 1334 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7342 (mm-30) REVERT: D 1352 ILE cc_start: 0.8368 (tp) cc_final: 0.7979 (tt) REVERT: E 53 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6787 (mm-30) REVERT: E 55 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: E 59 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7619 (mp) REVERT: E 68 GLU cc_start: 0.7878 (tp30) cc_final: 0.7611 (tp30) outliers start: 81 outliers final: 55 residues processed: 789 average time/residue: 0.2162 time to fit residues: 256.2462 Evaluate side-chains 814 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 746 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 159 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 0.0770 chunk 175 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.136586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107116 restraints weight = 48543.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110739 restraints weight = 25921.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113062 restraints weight = 16403.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114687 restraints weight = 11881.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115690 restraints weight = 9523.632| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26854 Z= 0.161 Angle : 0.766 14.296 36562 Z= 0.384 Chirality : 0.047 0.450 4184 Planarity : 0.005 0.067 4544 Dihedral : 14.296 172.459 4233 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.88 % Allowed : 23.63 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3164 helix: 0.46 (0.16), residues: 1077 sheet: -0.38 (0.26), residues: 369 loop : -1.50 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1369 TYR 0.033 0.002 TYR D 165 PHE 0.029 0.001 PHE C1025 TRP 0.068 0.003 TRP D 33 HIS 0.015 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (26848) covalent geometry : angle 0.76141 / 0.38 (36556) hydrogen bonds : bond 0.04623 / 5.02 ( 1030) hydrogen bonds : angle 4.55287 / 4.93 ( 2816) metal coordination : bond 0.00901 / 1.01 ( 6) metal coordination : angle 6.64395 / 12.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 764 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8044 (mtpp) REVERT: A 68 TYR cc_start: 0.8584 (m-10) cc_final: 0.8125 (m-10) REVERT: A 80 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6820 (tm-30) REVERT: A 102 LEU cc_start: 0.8467 (tp) cc_final: 0.8072 (tp) REVERT: A 118 ASP cc_start: 0.7754 (p0) cc_final: 0.7482 (p0) REVERT: A 206 GLU cc_start: 0.7164 (pp20) cc_final: 0.6823 (pp20) REVERT: B 60 GLU cc_start: 0.6042 (tp30) cc_final: 0.5615 (tp30) REVERT: B 71 LYS cc_start: 0.7492 (mmmt) cc_final: 0.7250 (mmmt) REVERT: B 84 ASN cc_start: 0.8030 (t0) cc_final: 0.7634 (t0) REVERT: B 140 ILE cc_start: 0.7750 (tp) cc_final: 0.6985 (tp) REVERT: B 142 MET cc_start: 0.6019 (mmm) cc_final: 0.5522 (mmm) REVERT: B 188 GLU cc_start: 0.6790 (pm20) cc_final: 0.6221 (mp0) REVERT: B 193 GLU cc_start: 0.7223 (pm20) cc_final: 0.6866 (pm20) REVERT: C 8 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7239 (mttt) REVERT: C 22 LEU cc_start: 0.8640 (tt) cc_final: 0.8378 (mt) REVERT: C 33 ASP cc_start: 0.6330 (p0) cc_final: 0.6111 (p0) REVERT: C 50 GLU cc_start: 0.6769 (tp30) cc_final: 0.6467 (tp30) REVERT: C 99 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7878 (tppt) REVERT: C 124 MET cc_start: 0.7415 (ttp) cc_final: 0.6445 (tmm) REVERT: C 169 LYS cc_start: 0.7968 (tmtt) cc_final: 0.7543 (tmtt) REVERT: C 177 ILE cc_start: 0.7891 (mm) cc_final: 0.7581 (tp) REVERT: C 191 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8039 (mtmm) REVERT: C 199 ASP cc_start: 0.7810 (t0) cc_final: 0.7569 (t0) REVERT: C 215 TYR cc_start: 0.7559 (m-80) cc_final: 0.7294 (m-80) REVERT: C 217 THR cc_start: 0.7046 (m) cc_final: 0.5947 (t) REVERT: C 330 HIS cc_start: 0.7140 (m90) cc_final: 0.6688 (m-70) REVERT: C 334 GLU cc_start: 0.5697 (pp20) cc_final: 0.4066 (tm-30) REVERT: C 343 HIS cc_start: 0.6772 (m90) cc_final: 0.6542 (m90) REVERT: C 392 GLU cc_start: 0.7528 (tp30) cc_final: 0.7090 (tp30) REVERT: C 394 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7250 (ttm110) REVERT: C 427 ASP cc_start: 0.7928 (m-30) cc_final: 0.7651 (m-30) REVERT: C 447 HIS cc_start: 0.7640 (t70) cc_final: 0.7289 (t-170) REVERT: C 461 GLU cc_start: 0.7870 (tt0) cc_final: 0.7244 (tm-30) REVERT: C 491 ASP cc_start: 0.6904 (p0) cc_final: 0.6680 (p0) REVERT: C 504 GLU cc_start: 0.7435 (pp20) cc_final: 0.7052 (pp20) REVERT: C 541 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 641 GLU cc_start: 0.7145 (pm20) cc_final: 0.6093 (pp20) REVERT: C 674 ASP cc_start: 0.8041 (t0) cc_final: 0.7669 (t0) REVERT: C 675 ASP cc_start: 0.7833 (t0) cc_final: 0.7383 (t70) REVERT: C 737 ASN cc_start: 0.8632 (m-40) cc_final: 0.7714 (m-40) REVERT: C 761 GLN cc_start: 0.7426 (mm110) cc_final: 0.6982 (mp10) REVERT: C 779 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.7709 (ttm-80) REVERT: C 793 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6579 (mt-10) REVERT: C 825 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 864 LYS cc_start: 0.7338 (mmtp) cc_final: 0.6909 (mmmm) REVERT: C 886 LYS cc_start: 0.7464 (tmtt) cc_final: 0.7241 (tmtt) REVERT: C 930 ASP cc_start: 0.6997 (t0) cc_final: 0.6663 (t0) REVERT: C 951 MET cc_start: 0.8211 (mtp) cc_final: 0.7592 (mtp) REVERT: C 954 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7554 (mtmt) REVERT: C 955 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7209 (tp-100) REVERT: C 957 LYS cc_start: 0.8910 (pptt) cc_final: 0.8487 (pptt) REVERT: C 1053 TYR cc_start: 0.8128 (m-80) cc_final: 0.7314 (m-80) REVERT: C 1079 ILE cc_start: 0.8250 (mm) cc_final: 0.7886 (mt) REVERT: C 1095 ASP cc_start: 0.7391 (m-30) cc_final: 0.7049 (t0) REVERT: C 1122 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7861 (mmmm) REVERT: C 1164 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: C 1171 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7739 (ttp-170) REVERT: C 1178 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8273 (mmtt) REVERT: C 1216 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7351 (ttm-80) REVERT: C 1256 GLN cc_start: 0.7951 (mt0) cc_final: 0.7749 (mt0) REVERT: C 1274 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6791 (mm-30) REVERT: C 1279 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6943 (mm-30) REVERT: C 1289 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7482 (tt0) REVERT: C 1303 LYS cc_start: 0.8022 (tppp) cc_final: 0.7678 (ttmm) REVERT: C 1332 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7710 (p) REVERT: C 1337 ILE cc_start: 0.7889 (tp) cc_final: 0.7575 (tt) REVERT: D 21 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7578 (mmtt) REVERT: D 35 PHE cc_start: 0.6677 (m-80) cc_final: 0.6401 (m-80) REVERT: D 69 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 115 TRP cc_start: 0.8662 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: D 117 LEU cc_start: 0.7987 (mm) cc_final: 0.7537 (mm) REVERT: D 130 MET cc_start: 0.7539 (mmt) cc_final: 0.7323 (mmm) REVERT: D 141 PHE cc_start: 0.7622 (m-10) cc_final: 0.7361 (m-10) REVERT: D 179 LYS cc_start: 0.8308 (mttt) cc_final: 0.7952 (mmmm) REVERT: D 183 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7747 (tm-30) REVERT: D 190 LYS cc_start: 0.8019 (ptpp) cc_final: 0.7412 (ptpp) REVERT: D 200 GLN cc_start: 0.8104 (pp30) cc_final: 0.7743 (pp30) REVERT: D 211 GLU cc_start: 0.8004 (pp20) cc_final: 0.7471 (pp20) REVERT: D 215 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8171 (mmtt) REVERT: D 216 LYS cc_start: 0.8640 (tppt) cc_final: 0.8270 (mmmm) REVERT: D 221 ILE cc_start: 0.8545 (tp) cc_final: 0.8323 (tp) REVERT: D 222 LYS cc_start: 0.8364 (mptt) cc_final: 0.7921 (mptt) REVERT: D 233 LYS cc_start: 0.8348 (mmmm) cc_final: 0.8025 (mmmm) REVERT: D 236 TRP cc_start: 0.8863 (m-10) cc_final: 0.8609 (m-10) REVERT: D 241 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7720 (p) REVERT: D 278 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7881 (ttm110) REVERT: D 294 ASN cc_start: 0.8247 (t0) cc_final: 0.6910 (t0) REVERT: D 295 GLU cc_start: 0.7905 (tt0) cc_final: 0.7428 (tt0) REVERT: D 297 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7643 (tmm-80) REVERT: D 298 MET cc_start: 0.7796 (mmp) cc_final: 0.6658 (mmt) REVERT: D 301 GLU cc_start: 0.7788 (tp30) cc_final: 0.7497 (tm-30) REVERT: D 312 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.7157 (mmm160) REVERT: D 372 MET cc_start: 0.7817 (mtt) cc_final: 0.7545 (mtm) REVERT: D 398 LYS cc_start: 0.8440 (mmtt) cc_final: 0.7953 (mmmt) REVERT: D 399 LYS cc_start: 0.8387 (mppt) cc_final: 0.7707 (mmtm) REVERT: D 400 MET cc_start: 0.8209 (mtm) cc_final: 0.7620 (mtm) REVERT: D 402 GLU cc_start: 0.7135 (pp20) cc_final: 0.6843 (pp20) REVERT: D 403 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7271 (ttm110) REVERT: D 432 LEU cc_start: 0.8448 (mm) cc_final: 0.8024 (mm) REVERT: D 462 ASP cc_start: 0.7036 (m-30) cc_final: 0.6503 (m-30) REVERT: D 479 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7323 (tm-30) REVERT: D 506 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8038 (p) REVERT: D 511 TYR cc_start: 0.7762 (t80) cc_final: 0.7026 (t80) REVERT: D 531 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7948 (ttpp) REVERT: D 556 GLU cc_start: 0.6487 (tp30) cc_final: 0.6112 (tp30) REVERT: D 566 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7605 (mtpp) REVERT: D 568 SER cc_start: 0.7626 (m) cc_final: 0.7202 (t) REVERT: D 604 MET cc_start: 0.7412 (tmm) cc_final: 0.7153 (tmm) REVERT: D 644 MET cc_start: 0.8000 (mpp) cc_final: 0.7558 (mtm) REVERT: D 681 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8030 (ttpt) REVERT: D 698 MET cc_start: 0.7469 (tpt) cc_final: 0.6801 (tmm) REVERT: D 724 MET cc_start: 0.7834 (ttp) cc_final: 0.7506 (mtp) REVERT: D 728 SER cc_start: 0.8163 (p) cc_final: 0.7672 (m) REVERT: D 739 GLN cc_start: 0.8005 (tt0) cc_final: 0.7424 (tp40) REVERT: D 765 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6975 (tm-30) REVERT: D 781 LYS cc_start: 0.8644 (tptp) cc_final: 0.8224 (tppt) REVERT: D 789 LYS cc_start: 0.7822 (ptmm) cc_final: 0.7478 (tttm) REVERT: D 805 GLN cc_start: 0.7924 (pm20) cc_final: 0.7515 (pm20) REVERT: D 806 ASP cc_start: 0.7423 (p0) cc_final: 0.6597 (t0) REVERT: D 808 VAL cc_start: 0.8532 (t) cc_final: 0.8210 (p) REVERT: D 811 GLU cc_start: 0.7683 (tp30) cc_final: 0.7418 (tp30) REVERT: D 839 VAL cc_start: 0.8618 (t) cc_final: 0.8352 (p) REVERT: D 867 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 877 VAL cc_start: 0.8267 (t) cc_final: 0.8021 (p) REVERT: D 964 LYS cc_start: 0.7647 (tppt) cc_final: 0.7419 (tppt) REVERT: D 992 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7781 (mmtt) REVERT: D 993 GLU cc_start: 0.5166 (mm-30) cc_final: 0.4755 (mm-30) REVERT: D 1040 MET cc_start: 0.6707 (tpp) cc_final: 0.4031 (mmt) REVERT: D 1095 MET cc_start: 0.6713 (pmm) cc_final: 0.6270 (pmm) REVERT: D 1101 LEU cc_start: 0.8866 (tp) cc_final: 0.8029 (pp) REVERT: D 1148 ARG cc_start: 0.7316 (ptp-170) cc_final: 0.6955 (ptm160) REVERT: D 1202 GLU cc_start: 0.6612 (mp0) cc_final: 0.5685 (mt-10) REVERT: D 1244 GLN cc_start: 0.8007 (tt0) cc_final: 0.7450 (tm-30) REVERT: D 1291 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8151 (mm-30) REVERT: D 1334 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7320 (mm-30) REVERT: D 1352 ILE cc_start: 0.8423 (tp) cc_final: 0.8018 (tt) REVERT: E 53 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6760 (mm-30) REVERT: E 55 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6584 (pm20) REVERT: E 59 ILE cc_start: 0.8199 (mp) cc_final: 0.7627 (mp) REVERT: E 68 GLU cc_start: 0.7830 (tp30) cc_final: 0.7591 (tp30) outliers start: 78 outliers final: 67 residues processed: 797 average time/residue: 0.2143 time to fit residues: 256.2070 Evaluate side-chains 824 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 750 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 517 GLN Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 55 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 302 optimal weight: 0.0010 chunk 3 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 147 optimal weight: 0.0770 chunk 142 optimal weight: 0.0040 chunk 266 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109549 restraints weight = 48639.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113387 restraints weight = 25184.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115997 restraints weight = 15679.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117673 restraints weight = 11129.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118808 restraints weight = 8818.498| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26854 Z= 0.139 Angle : 0.778 14.307 36562 Z= 0.386 Chirality : 0.046 0.426 4184 Planarity : 0.005 0.100 4544 Dihedral : 14.237 171.896 4233 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.66 % Allowed : 24.37 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3164 helix: 0.52 (0.16), residues: 1072 sheet: -0.28 (0.27), residues: 358 loop : -1.42 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1369 TYR 0.034 0.001 TYR D 165 PHE 0.024 0.001 PHE C1025 TRP 0.056 0.002 TRP D 33 HIS 0.026 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (26848) covalent geometry : angle 0.77441 / 0.39 (36556) hydrogen bonds : bond 0.04210 / 4.56 ( 1030) hydrogen bonds : angle 4.48200 / 4.84 ( 2816) metal coordination : bond 0.00577 / 0.66 ( 6) metal coordination : angle 5.83831 / 10.74 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5957.91 seconds wall clock time: 103 minutes 21.63 seconds (6201.63 seconds total)