Starting phenix.real_space_refine on Mon Sep 14 19:48:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psw_20466/09_2026/6psw_20466_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psw_20466/09_2026/6psw_20466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6psw_20466/09_2026/6psw_20466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psw_20466/09_2026/6psw_20466.map" model { file = "/net/cci-nas-00/data/ceres_data/6psw_20466/09_2026/6psw_20466_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psw_20466/09_2026/6psw_20466_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 3 6.06 5 P 124 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20127 2.51 5 N 5780 2.21 5 O 6524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.04s 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: 32695 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10571 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 10460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10460 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3854 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 2 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 66} Chain: "O" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1270 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "P" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1272 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14460 SG CYS J 70 76.872 99.753 110.158 1.00 33.15 S ATOM 14474 SG CYS J 72 77.146 102.675 111.995 1.00 38.61 S ATOM 14582 SG CYS J 85 74.415 101.147 113.335 1.00 42.93 S ATOM 14606 SG CYS J 88 73.523 100.283 110.077 1.00 47.24 S ATOM 20288 SG CYS J 814 73.930 38.981 83.279 1.00 26.40 S ATOM 20853 SG CYS J 888 73.547 42.857 82.747 1.00 23.18 S ATOM 20925 SG CYS J 898 75.066 40.229 80.222 1.00 16.65 S ATOM 29825 SG CYS N 40 53.649 54.250 22.072 1.00 73.58 S ATOM 29984 SG CYS N 61 56.367 55.850 24.356 1.00 81.89 S Time building chain proxies: 6.78, per 1000 atoms: 0.21 Number of scatterers: 32695 At special positions: 0 Unit cell: (163.8, 156, 166.4, 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 3 29.99 S 136 16.00 P 124 15.00 Mg 1 11.99 O 6524 8.00 N 5780 7.00 C 20127 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 6 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 54 sheets defined 42.9% alpha, 12.6% beta 48 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.736A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'G' and resid 161 through 165 removed outlier: 4.511A pdb=" N ASP G 164 " --> pdb=" O SER G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.126A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.813A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.112A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.655A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 165 through 169 removed outlier: 4.244A pdb=" N GLY I 168 " --> pdb=" O HIS I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.880A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 removed outlier: 3.553A pdb=" N ILE I 220 " --> pdb=" O THR I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.626A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 4.033A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 479 removed outlier: 4.314A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.455A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.506A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 544 removed outlier: 3.882A pdb=" N GLY I 544 " --> pdb=" O GLU I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.840A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.639A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.519A pdb=" N LEU I 946 " --> pdb=" O ASP I 942 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA I 977 " --> pdb=" O SER I 973 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.881A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.650A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.813A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.627A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.591A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.528A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1299 through 1310 removed outlier: 3.955A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE I1308 " --> pdb=" O MET I1304 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.512A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.585A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.884A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 192 removed outlier: 3.533A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 4.061A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.657A pdb=" N LEU J 249 " --> pdb=" O PRO J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.872A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.644A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 515 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 580 Processing helix chain 'J' and resid 588 through 593 Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.028A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.535A pdb=" N ASP J 643 " --> pdb=" O GLY J 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 670 removed outlier: 4.679A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.798A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.571A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 790 removed outlier: 4.016A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 804 removed outlier: 3.561A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.675A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.530A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.683A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 4.114A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.590A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 4.052A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.071A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1323 removed outlier: 3.808A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.658A pdb=" N ALA J1336 " --> pdb=" O LEU J1332 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL J1337 " --> pdb=" O THR J1333 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 Processing helix chain 'J' and resid 1361 through 1374 removed outlier: 4.312A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.818A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.626A pdb=" N GLU K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 80 removed outlier: 3.724A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 removed outlier: 3.573A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 157 through 161 Processing helix chain 'L' and resid 215 through 233 Processing helix chain 'L' and resid 244 through 257 Processing helix chain 'L' and resid 262 through 290 Processing helix chain 'L' and resid 291 through 296 removed outlier: 3.812A pdb=" N CYS L 295 " --> pdb=" O CYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 316 through 321 removed outlier: 3.636A pdb=" N ALA L 321 " --> pdb=" O ASN L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 393 removed outlier: 4.046A pdb=" N ASN L 362 " --> pdb=" O VAL L 358 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.884A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 4.925A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 482 through 487 removed outlier: 3.904A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 511 through 515 removed outlier: 3.988A pdb=" N GLU L 515 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.596A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.572A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 removed outlier: 3.714A pdb=" N ALA L 556 " --> pdb=" O THR L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 580 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 604 through 611 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 263 through 273 removed outlier: 3.789A pdb=" N ALA M 267 " --> pdb=" O THR M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 282 Processing helix chain 'M' and resid 285 through 291 removed outlier: 3.633A pdb=" N LEU M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 310 removed outlier: 4.018A pdb=" N LEU M 300 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 27 removed outlier: 3.908A pdb=" N ALA N 8 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE N 27 " --> pdb=" O ILE N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 52 removed outlier: 3.547A pdb=" N PHE N 52 " --> pdb=" O ARG N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 70 Processing sheet with id=AA1, first strand: chain 'G' and resid 24 through 31 removed outlier: 5.232A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.552A pdb=" N VAL G 146 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.685A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 16 through 17 removed outlier: 3.976A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA H 184 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 50 through 60 removed outlier: 6.234A pdb=" N MET H 51 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY H 151 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 50 through 60 removed outlier: 6.234A pdb=" N MET H 51 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY H 151 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'H' and resid 110 through 111 removed outlier: 3.776A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.742A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 58 through 60 removed outlier: 7.105A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.149A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.785A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.958A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.700A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.339A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.599A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 633 through 636 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.605A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.951A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 7.066A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE I1096 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 834 through 840 removed outlier: 3.520A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD6, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD9, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE1, first strand: chain 'I' and resid 1336 through 1339 Processing sheet with id=AE2, first strand: chain 'J' and resid 104 through 112 removed outlier: 10.675A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE4, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.255A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE7, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.833A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.734A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 956 through 957 removed outlier: 3.803A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 959 through 961 Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AF4, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AF5, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 4.493A pdb=" N ALA J1097 " --> pdb=" O ILE J1080 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1046 through 1051 Processing sheet with id=AF7, first strand: chain 'J' and resid 1156 through 1157 removed outlier: 3.986A pdb=" N ASP J1208 " --> pdb=" O ALA J1157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.085A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1293 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 9.50 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10748 1.34 - 1.46: 7481 1.46 - 1.59: 14726 1.59 - 1.72: 251 1.72 - 1.84: 239 Bond restraints: 33445 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.842 -0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.712 -0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.694 -0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 33440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 43617 1.99 - 3.98: 1882 3.98 - 5.98: 170 5.98 - 7.97: 31 7.97 - 9.96: 9 Bond angle restraints: 45709 Sorted by residual: angle pdb=" O4' DT P 34 " pdb=" C4' DT P 34 " pdb=" C3' DT P 34 " ideal model delta sigma weight residual 106.00 101.61 4.39 6.00e-01 2.78e+00 5.35e+01 angle pdb=" N ILE N 27 " pdb=" CA ILE N 27 " pdb=" C ILE N 27 " ideal model delta sigma weight residual 106.21 113.68 -7.47 1.07e+00 8.73e-01 4.87e+01 angle pdb=" C THR L 94 " pdb=" N THR L 95 " pdb=" CA THR L 95 " ideal model delta sigma weight residual 122.56 113.32 9.24 1.50e+00 4.44e-01 3.79e+01 angle pdb=" O4' DT O 22 " pdb=" C4' DT O 22 " pdb=" C3' DT O 22 " ideal model delta sigma weight residual 106.00 102.66 3.34 6.00e-01 2.78e+00 3.09e+01 angle pdb=" O4' DC O 74 " pdb=" C4' DC O 74 " pdb=" C3' DC O 74 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.89e+01 ... (remaining 45704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 19187 32.36 - 64.71: 1134 64.71 - 97.07: 78 97.07 - 129.42: 5 129.42 - 161.78: 5 Dihedral angle restraints: 20409 sinusoidal: 9372 harmonic: 11037 Sorted by residual: dihedral pdb=" CA PHE I 545 " pdb=" C PHE I 545 " pdb=" N GLU I 546 " pdb=" CA GLU I 546 " ideal model delta harmonic sigma weight residual -180.00 -127.47 -52.53 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 139.27 40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA VAL I 442 " pdb=" C VAL I 442 " pdb=" N ASP I 443 " pdb=" CA ASP I 443 " ideal model delta harmonic sigma weight residual -180.00 -145.49 -34.51 0 5.00e+00 4.00e-02 4.76e+01 ... (remaining 20406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4167 0.060 - 0.119: 959 0.119 - 0.179: 87 0.179 - 0.239: 8 0.239 - 0.298: 3 Chirality restraints: 5224 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.83 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASP I 516 " pdb=" N ASP I 516 " pdb=" C ASP I 516 " pdb=" CB ASP I 516 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5221 not shown) Planarity restraints: 5525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 974 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ARG I 974 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG I 974 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE I 975 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 375 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C ALA L 375 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA L 375 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS L 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET H 51 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO H 52 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 52 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 52 " 0.041 5.00e-02 4.00e+02 ... (remaining 5522 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 370 2.57 - 3.15: 30080 3.15 - 3.73: 51344 3.73 - 4.32: 73007 4.32 - 4.90: 115999 Nonbonded interactions: 270800 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.987 2.170 nonbonded pdb=" OH TYR I 346 " pdb=" OD1 ASN I 437 " model vdw 2.023 3.040 nonbonded pdb=" OG1 THR I 216 " pdb=" OE1 GLN I 219 " model vdw 2.026 3.040 nonbonded pdb=" O ASN J 962 " pdb=" OG1 THR J 980 " model vdw 2.059 3.040 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.063 3.040 ... (remaining 270795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 6 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 228 or (resid 229 through 230 and \ (name N or name CA or name C or name O or name CB )) or resid 231 through 232 o \ r (resid 233 through 234 and (name N or name CA or name C or name O or name CB ) \ ))) } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 40.900 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.008 0.310 33454 Z= 0.437 Angle : 0.977 64.649 45715 Z= 0.586 Chirality : 0.049 0.298 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.871 161.776 13291 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 42.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.43 % Favored : 88.38 % Rotamer: Outliers : 0.40 % Allowed : 10.91 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -4.03 (0.11), residues: 3805 helix: -1.94 (0.11), residues: 1474 sheet: -3.31 (0.21), residues: 382 loop : -3.18 (0.12), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 842 TYR 0.024 0.002 TYR I 810 PHE 0.026 0.002 PHE J1325 TRP 0.034 0.002 TRP I 807 HIS 0.008 0.002 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.43 (33445) covalent geometry : angle 0.91171 / 0.58 (45709) hydrogen bonds : bond 0.14986 / 10.40 ( 1396) hydrogen bonds : angle 7.41680 / 5.04 ( 3858) metal coordination : bond 0.09948 / 6.45 ( 9) metal coordination : angle 30.72869 / 14.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 597 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8417 (tttt) REVERT: H 58 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5874 (tt0) REVERT: H 74 VAL cc_start: 0.7236 (t) cc_final: 0.6382 (m) REVERT: H 83 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8128 (mt) REVERT: H 200 LYS cc_start: 0.8866 (tttt) cc_final: 0.8592 (tttp) REVERT: I 36 GLN cc_start: 0.8021 (tp40) cc_final: 0.7591 (tp40) REVERT: I 40 GLU cc_start: 0.7788 (tt0) cc_final: 0.7512 (tt0) REVERT: I 50 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6732 (tt0) REVERT: I 277 LEU cc_start: 0.3754 (mt) cc_final: 0.3483 (mp) REVERT: I 793 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7649 (mm-30) REVERT: I 1331 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8079 (mtm180) REVERT: J 295 GLU cc_start: 0.8006 (tp30) cc_final: 0.7570 (tp30) REVERT: J 337 ARG cc_start: 0.8501 (mmt-90) cc_final: 0.8293 (mmt90) REVERT: J 555 TYR cc_start: 0.8271 (m-10) cc_final: 0.7846 (m-80) REVERT: J 707 ILE cc_start: 0.8006 (pt) cc_final: 0.7658 (tt) REVERT: J 715 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7274 (mptt) REVERT: J 749 LYS cc_start: 0.8358 (ptmt) cc_final: 0.8148 (mtpt) REVERT: J 785 ASP cc_start: 0.8320 (t0) cc_final: 0.8088 (t0) REVERT: J 991 THR cc_start: 0.6370 (p) cc_final: 0.6088 (p) REVERT: J 1020 TRP cc_start: 0.5491 (p90) cc_final: 0.5276 (p90) REVERT: J 1132 LYS cc_start: 0.4773 (OUTLIER) cc_final: 0.1955 (mtpt) REVERT: J 1349 GLU cc_start: 0.7702 (mp0) cc_final: 0.7271 (mt-10) REVERT: K 55 GLU cc_start: 0.6775 (pp20) cc_final: 0.6409 (pp20) REVERT: K 56 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7701 (mm-30) REVERT: L 136 GLU cc_start: 0.5627 (mt-10) cc_final: 0.3996 (mm-30) REVERT: L 143 TYR cc_start: 0.5490 (t80) cc_final: 0.4630 (t80) REVERT: L 276 MET cc_start: 0.6904 (mpp) cc_final: 0.6510 (mpp) REVERT: L 277 MET cc_start: 0.6646 (tpt) cc_final: 0.6387 (tmm) REVERT: L 297 MET cc_start: 0.1451 (ttm) cc_final: 0.0500 (mtp) REVERT: L 576 VAL cc_start: 0.7664 (t) cc_final: 0.7462 (t) REVERT: M 316 MET cc_start: 0.3865 (tpt) cc_final: 0.1676 (tmm) REVERT: N 9 TYR cc_start: 0.7758 (t80) cc_final: 0.7463 (t80) REVERT: N 65 GLN cc_start: 0.6948 (tt0) cc_final: 0.6471 (tp40) outliers start: 13 outliers final: 9 residues processed: 609 average time/residue: 0.2516 time to fit residues: 235.4691 Evaluate side-chains 387 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 376 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS H 84 ASN H 128 HIS I 69 GLN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 832 HIS I 834 GLN I 932 GLN I1116 HIS I1135 GLN I1220 GLN J 157 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN J 560 ASN J 680 ASN J 720 ASN J 865 HIS ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 910 ASN J 951 GLN J1023 HIS J1108 GLN J1249 ASN K 15 ASN L 227 GLN L 258 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS N 28 ASN N 30 HIS N 71 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115243 restraints weight = 56069.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115907 restraints weight = 50949.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116241 restraints weight = 40058.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116655 restraints weight = 32903.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116798 restraints weight = 29032.103| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33454 Z= 0.176 Angle : 0.797 24.644 45715 Z= 0.410 Chirality : 0.049 0.361 5224 Planarity : 0.006 0.079 5525 Dihedral : 19.142 160.097 5749 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 2.99 % Allowed : 15.83 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.08 % 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: -3.00 (0.12), residues: 3805 helix: -0.93 (0.12), residues: 1509 sheet: -2.62 (0.24), residues: 358 loop : -2.81 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 322 TYR 0.024 0.002 TYR L 148 PHE 0.029 0.002 PHE I 906 TRP 0.013 0.002 TRP I 807 HIS 0.013 0.001 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (33445) covalent geometry : angle 0.78390 / 0.41 (45709) hydrogen bonds : bond 0.05338 / 3.59 ( 1396) hydrogen bonds : angle 5.84225 / 4.03 ( 3858) metal coordination : bond 0.00884 / 0.44 ( 9) metal coordination : angle 12.79166 / 7.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 491 time to evaluate : 1.184 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: G 35 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: G 68 TYR cc_start: 0.8819 (m-80) cc_final: 0.8067 (m-80) REVERT: G 145 LYS cc_start: 0.8973 (tmmt) cc_final: 0.8169 (tttt) REVERT: H 32 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: I 36 GLN cc_start: 0.7967 (tp40) cc_final: 0.7323 (tp40) REVERT: I 50 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6582 (tt0) REVERT: I 88 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7741 (ttm-80) REVERT: I 119 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6384 (tt0) REVERT: I 208 ILE cc_start: 0.8223 (tt) cc_final: 0.7945 (tt) REVERT: I 470 ARG cc_start: 0.8315 (ptp90) cc_final: 0.8028 (ttp-170) REVERT: I 609 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7264 (tp) REVERT: I 705 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: I 741 MET cc_start: 0.7738 (ttp) cc_final: 0.7349 (ttp) REVERT: I 825 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6926 (mt-10) REVERT: I 974 ARG cc_start: 0.7631 (mmp80) cc_final: 0.7277 (mmp-170) REVERT: I 1137 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: I 1296 ASP cc_start: 0.8106 (t70) cc_final: 0.7762 (t0) REVERT: I 1331 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7845 (mtm180) REVERT: J 151 MET cc_start: 0.5801 (mpp) cc_final: 0.5432 (mpp) REVERT: J 158 GLN cc_start: 0.7047 (tt0) cc_final: 0.6456 (tp40) REVERT: J 165 TYR cc_start: 0.8199 (t80) cc_final: 0.7989 (t80) REVERT: J 295 GLU cc_start: 0.8257 (tp30) cc_final: 0.7689 (tp30) REVERT: J 339 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8101 (mtp180) REVERT: J 555 TYR cc_start: 0.8351 (m-10) cc_final: 0.7985 (m-80) REVERT: J 715 LYS cc_start: 0.7299 (mtpp) cc_final: 0.7063 (mptt) REVERT: J 785 ASP cc_start: 0.8567 (t0) cc_final: 0.8243 (t0) REVERT: J 805 GLN cc_start: 0.8459 (pm20) cc_final: 0.8127 (pp30) REVERT: J 918 ILE cc_start: 0.8829 (pt) cc_final: 0.8266 (mt) REVERT: J 1132 LYS cc_start: 0.4280 (OUTLIER) cc_final: 0.2181 (mmmt) REVERT: J 1349 GLU cc_start: 0.7788 (mp0) cc_final: 0.7025 (mt-10) REVERT: K 68 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7707 (tp30) REVERT: L 105 MET cc_start: 0.8373 (ppp) cc_final: 0.8156 (ppp) REVERT: L 148 TYR cc_start: 0.2373 (t80) cc_final: 0.2022 (t80) REVERT: L 161 LEU cc_start: 0.5858 (tt) cc_final: 0.5506 (tp) REVERT: L 273 MET cc_start: 0.6990 (mmm) cc_final: 0.6454 (mmm) REVERT: L 277 MET cc_start: 0.6948 (tpt) cc_final: 0.6250 (tmm) REVERT: L 297 MET cc_start: 0.0876 (ttm) cc_final: 0.0292 (mtp) REVERT: M 316 MET cc_start: 0.3718 (tpt) cc_final: 0.1537 (tmm) REVERT: N 9 TYR cc_start: 0.7751 (t80) cc_final: 0.7331 (t80) REVERT: N 17 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6778 (mmt) REVERT: N 65 GLN cc_start: 0.7010 (tt0) cc_final: 0.6489 (tp-100) outliers start: 98 outliers final: 48 residues processed: 559 average time/residue: 0.2118 time to fit residues: 189.9522 Evaluate side-chains 446 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 391 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 37 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 348 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 226 optimal weight: 0.2980 chunk 147 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 366 optimal weight: 40.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 93 GLN I 69 GLN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1249 ASN L 258 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN N 30 HIS N 68 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.150470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114473 restraints weight = 55953.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115026 restraints weight = 51957.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115348 restraints weight = 40889.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115799 restraints weight = 33280.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115910 restraints weight = 29454.711| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33454 Z= 0.185 Angle : 0.729 20.165 45715 Z= 0.378 Chirality : 0.047 0.352 5224 Planarity : 0.005 0.081 5525 Dihedral : 18.940 162.243 5747 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 4.03 % Allowed : 17.57 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.08 % 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: -2.48 (0.13), residues: 3805 helix: -0.43 (0.13), residues: 1504 sheet: -2.40 (0.24), residues: 367 loop : -2.55 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 233 TYR 0.024 0.002 TYR L 137 PHE 0.021 0.002 PHE I 545 TRP 0.011 0.001 TRP J 580 HIS 0.012 0.001 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (33445) covalent geometry : angle 0.71842 / 0.38 (45709) hydrogen bonds : bond 0.04898 / 3.28 ( 1396) hydrogen bonds : angle 5.49216 / 3.80 ( 3858) metal coordination : bond 0.00857 / 0.39 ( 9) metal coordination : angle 10.97452 / 6.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 407 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: G 68 TYR cc_start: 0.8864 (m-80) cc_final: 0.8165 (m-80) REVERT: G 145 LYS cc_start: 0.8949 (tmmt) cc_final: 0.8166 (ttpt) REVERT: H 147 GLN cc_start: 0.7583 (tt0) cc_final: 0.7158 (mt0) REVERT: H 211 ILE cc_start: 0.8859 (tp) cc_final: 0.8551 (pt) REVERT: I 50 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6610 (tt0) REVERT: I 119 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6542 (tt0) REVERT: I 219 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: I 609 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7547 (tp) REVERT: I 704 MET cc_start: 0.8076 (mmm) cc_final: 0.7841 (tpp) REVERT: I 741 MET cc_start: 0.7696 (ttp) cc_final: 0.7304 (ttp) REVERT: I 974 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7308 (mmp-170) REVERT: I 1072 ASN cc_start: 0.8247 (p0) cc_final: 0.7790 (p0) REVERT: I 1137 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: I 1319 MET cc_start: 0.6859 (ttm) cc_final: 0.6285 (tpp) REVERT: I 1331 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7952 (mtm180) REVERT: J 151 MET cc_start: 0.5958 (mpp) cc_final: 0.5551 (mpp) REVERT: J 368 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8673 (tt) REVERT: J 443 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7078 (mp0) REVERT: J 555 TYR cc_start: 0.8345 (m-10) cc_final: 0.7979 (m-80) REVERT: J 715 LYS cc_start: 0.7174 (mtpp) cc_final: 0.6899 (mptt) REVERT: J 785 ASP cc_start: 0.8521 (t0) cc_final: 0.8177 (m-30) REVERT: J 805 GLN cc_start: 0.8550 (pm20) cc_final: 0.8206 (pp30) REVERT: J 918 ILE cc_start: 0.8848 (pt) cc_final: 0.8267 (mt) REVERT: J 1132 LYS cc_start: 0.4104 (OUTLIER) cc_final: 0.3411 (mmtt) REVERT: J 1349 GLU cc_start: 0.7869 (mp0) cc_final: 0.7144 (mt-10) REVERT: J 1368 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.5634 (m-30) REVERT: K 11 GLU cc_start: 0.6552 (tp30) cc_final: 0.6352 (tp30) REVERT: K 56 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7811 (mm-30) REVERT: K 68 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7607 (tp30) REVERT: L 105 MET cc_start: 0.8339 (ppp) cc_final: 0.8079 (ppp) REVERT: L 277 MET cc_start: 0.6886 (tpt) cc_final: 0.6307 (tmm) REVERT: M 316 MET cc_start: 0.3158 (tpt) cc_final: 0.1761 (tmm) REVERT: N 9 TYR cc_start: 0.7799 (t80) cc_final: 0.7313 (t80) REVERT: N 17 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6675 (mmt) REVERT: N 65 GLN cc_start: 0.7308 (tt0) cc_final: 0.6604 (tp-100) outliers start: 132 outliers final: 72 residues processed: 506 average time/residue: 0.2179 time to fit residues: 180.0238 Evaluate side-chains 447 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 367 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 37 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 139 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 315 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110650 restraints weight = 56403.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111462 restraints weight = 53877.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111709 restraints weight = 40195.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112121 restraints weight = 33407.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112268 restraints weight = 29755.830| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 33454 Z= 0.311 Angle : 0.815 18.535 45715 Z= 0.421 Chirality : 0.050 0.352 5224 Planarity : 0.006 0.090 5525 Dihedral : 18.970 160.770 5743 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.38 % Favored : 90.51 % Rotamer: Outliers : 5.16 % Allowed : 19.22 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -2.40 (0.13), residues: 3805 helix: -0.38 (0.13), residues: 1488 sheet: -2.40 (0.24), residues: 381 loop : -2.46 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 67 TYR 0.021 0.002 TYR J 772 PHE 0.025 0.002 PHE I 545 TRP 0.013 0.002 TRP L 433 HIS 0.011 0.002 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 (33445) covalent geometry : angle 0.80726 / 0.42 (45709) hydrogen bonds : bond 0.05245 / 3.53 ( 1396) hydrogen bonds : angle 5.55503 / 3.85 ( 3858) metal coordination : bond 0.01447 / 0.73 ( 9) metal coordination : angle 9.92940 / 5.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 369 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: G 204 GLU cc_start: 0.7732 (tt0) cc_final: 0.7360 (mt-10) REVERT: H 147 GLN cc_start: 0.7498 (tt0) cc_final: 0.7118 (mt0) REVERT: H 211 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8460 (pt) REVERT: I 50 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6657 (tt0) REVERT: I 88 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: I 119 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: I 219 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: I 704 MET cc_start: 0.8183 (mmm) cc_final: 0.7896 (tpp) REVERT: I 741 MET cc_start: 0.7682 (ttp) cc_final: 0.7179 (ttp) REVERT: I 974 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7193 (mmp-170) REVERT: I 1024 GLU cc_start: 0.8085 (pp20) cc_final: 0.6916 (mm-30) REVERT: I 1072 ASN cc_start: 0.8116 (p0) cc_final: 0.7764 (p0) REVERT: I 1137 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: I 1296 ASP cc_start: 0.8239 (t70) cc_final: 0.7732 (t0) REVERT: I 1304 MET cc_start: 0.8466 (tpp) cc_final: 0.8230 (tpt) REVERT: I 1331 ARG cc_start: 0.8356 (ttm170) cc_final: 0.8004 (mtm180) REVERT: J 78 LEU cc_start: 0.7975 (tp) cc_final: 0.7761 (tt) REVERT: J 151 MET cc_start: 0.5938 (mpp) cc_final: 0.5688 (mpp) REVERT: J 368 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8848 (tt) REVERT: J 443 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7124 (mp0) REVERT: J 555 TYR cc_start: 0.8424 (m-10) cc_final: 0.7907 (m-80) REVERT: J 715 LYS cc_start: 0.7492 (mtpp) cc_final: 0.7015 (mptt) REVERT: J 895 CYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8576 (p) REVERT: J 918 ILE cc_start: 0.8929 (pt) cc_final: 0.8314 (mt) REVERT: J 1132 LYS cc_start: 0.3917 (OUTLIER) cc_final: 0.3473 (mmtt) REVERT: J 1292 LEU cc_start: 0.8005 (mm) cc_final: 0.7786 (mp) REVERT: J 1349 GLU cc_start: 0.7896 (mp0) cc_final: 0.7254 (mt-10) REVERT: J 1368 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.5933 (m-30) REVERT: L 105 MET cc_start: 0.8382 (ppp) cc_final: 0.8090 (ppp) REVERT: L 277 MET cc_start: 0.6700 (tpt) cc_final: 0.6185 (tmm) REVERT: L 329 LYS cc_start: 0.6229 (mtpt) cc_final: 0.5017 (mmtp) REVERT: L 390 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8341 (tp) REVERT: M 316 MET cc_start: 0.3197 (tpt) cc_final: 0.1799 (tmm) REVERT: N 9 TYR cc_start: 0.7911 (t80) cc_final: 0.7266 (t80) REVERT: N 65 GLN cc_start: 0.7182 (tt0) cc_final: 0.6395 (tp-100) REVERT: N 66 GLU cc_start: 0.7836 (mm-30) cc_final: 0.6950 (pt0) outliers start: 169 outliers final: 121 residues processed: 492 average time/residue: 0.2133 time to fit residues: 171.8920 Evaluate side-chains 472 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 341 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 760 ASN Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1328 THR Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 359 LYS Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 428 SER Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 37 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 279 optimal weight: 0.2980 chunk 349 optimal weight: 3.9990 chunk 325 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 341 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 69 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN N 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113546 restraints weight = 55789.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114523 restraints weight = 52018.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114770 restraints weight = 38122.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115164 restraints weight = 32053.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115310 restraints weight = 28508.307| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33454 Z= 0.172 Angle : 0.709 16.768 45715 Z= 0.367 Chirality : 0.046 0.354 5224 Planarity : 0.005 0.082 5525 Dihedral : 18.802 161.685 5741 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.64 % Rotamer: Outliers : 4.52 % Allowed : 21.14 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -2.10 (0.13), residues: 3805 helix: -0.10 (0.13), residues: 1492 sheet: -2.15 (0.25), residues: 376 loop : -2.34 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1174 TYR 0.020 0.002 TYR J 679 PHE 0.021 0.002 PHE I 545 TRP 0.012 0.001 TRP J 580 HIS 0.013 0.001 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (33445) covalent geometry : angle 0.70148 / 0.37 (45709) hydrogen bonds : bond 0.04619 / 3.09 ( 1396) hydrogen bonds : angle 5.30366 / 3.67 ( 3858) metal coordination : bond 0.00784 / 0.36 ( 9) metal coordination : angle 8.82206 / 4.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 389 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: G 137 ASN cc_start: 0.6429 (p0) cc_final: 0.6164 (p0) REVERT: G 204 GLU cc_start: 0.7694 (tt0) cc_final: 0.7370 (mt-10) REVERT: H 147 GLN cc_start: 0.7444 (tt0) cc_final: 0.7049 (mt0) REVERT: H 211 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8470 (pt) REVERT: I 50 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6595 (tt0) REVERT: I 88 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7814 (ttm110) REVERT: I 119 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: I 219 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: I 515 MET cc_start: 0.8750 (ttp) cc_final: 0.8538 (ttt) REVERT: I 704 MET cc_start: 0.8084 (mmm) cc_final: 0.7802 (tpp) REVERT: I 711 ASP cc_start: 0.6803 (m-30) cc_final: 0.6594 (m-30) REVERT: I 741 MET cc_start: 0.7645 (ttp) cc_final: 0.7155 (ttp) REVERT: I 974 ARG cc_start: 0.7622 (mmp80) cc_final: 0.7177 (mmp-170) REVERT: I 987 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.3900 (mp0) REVERT: I 1024 GLU cc_start: 0.7960 (pp20) cc_final: 0.6870 (mm-30) REVERT: I 1025 PHE cc_start: 0.7754 (t80) cc_final: 0.7544 (t80) REVERT: I 1137 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: I 1296 ASP cc_start: 0.8152 (t0) cc_final: 0.7646 (t0) REVERT: I 1304 MET cc_start: 0.8439 (tpp) cc_final: 0.8224 (tpt) REVERT: I 1319 MET cc_start: 0.6879 (ttm) cc_final: 0.6273 (tpp) REVERT: I 1331 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7899 (mtm180) REVERT: J 78 LEU cc_start: 0.7876 (tp) cc_final: 0.7648 (tt) REVERT: J 151 MET cc_start: 0.5589 (mpp) cc_final: 0.5343 (mpp) REVERT: J 368 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8775 (tt) REVERT: J 555 TYR cc_start: 0.8364 (m-10) cc_final: 0.7864 (m-80) REVERT: J 715 LYS cc_start: 0.7268 (mtpp) cc_final: 0.7040 (mppt) REVERT: J 770 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8063 (mm) REVERT: J 785 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: J 918 ILE cc_start: 0.8825 (pt) cc_final: 0.8259 (mt) REVERT: J 1132 LYS cc_start: 0.3886 (OUTLIER) cc_final: 0.3473 (mmtt) REVERT: J 1188 GLU cc_start: 0.6756 (tp30) cc_final: 0.6482 (tp30) REVERT: J 1260 MET cc_start: 0.8382 (ttm) cc_final: 0.8123 (ttm) REVERT: J 1341 ARG cc_start: 0.7089 (ttt-90) cc_final: 0.6758 (ttt-90) REVERT: J 1349 GLU cc_start: 0.7969 (mp0) cc_final: 0.7356 (mt-10) REVERT: J 1368 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6010 (m-30) REVERT: J 1372 ARG cc_start: 0.6347 (mmp80) cc_final: 0.5859 (mtm-85) REVERT: L 105 MET cc_start: 0.8371 (ppp) cc_final: 0.8061 (ppp) REVERT: L 276 MET cc_start: 0.6984 (mtt) cc_final: 0.6692 (mtt) REVERT: L 277 MET cc_start: 0.6714 (tpt) cc_final: 0.6170 (tmm) REVERT: M 316 MET cc_start: 0.3205 (tpt) cc_final: 0.1809 (tmm) REVERT: N 9 TYR cc_start: 0.7838 (t80) cc_final: 0.7252 (t80) REVERT: N 65 GLN cc_start: 0.7378 (tt0) cc_final: 0.6489 (tp-100) REVERT: N 66 GLU cc_start: 0.7877 (mm-30) cc_final: 0.6954 (pt0) outliers start: 148 outliers final: 97 residues processed: 497 average time/residue: 0.2143 time to fit residues: 173.8522 Evaluate side-chains 460 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 352 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 182 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 284 optimal weight: 0.3980 chunk 153 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 79 optimal weight: 0.0770 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN J 594 GLN ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 GLN M 268 ASN N 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.150858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114561 restraints weight = 55651.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115145 restraints weight = 51909.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115502 restraints weight = 39664.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115955 restraints weight = 32851.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116108 restraints weight = 29137.208| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33454 Z= 0.156 Angle : 0.684 14.196 45715 Z= 0.354 Chirality : 0.045 0.352 5224 Planarity : 0.005 0.077 5525 Dihedral : 18.619 162.099 5741 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.07 % Favored : 91.85 % Rotamer: Outliers : 4.95 % Allowed : 21.36 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.86 (0.13), residues: 3805 helix: 0.10 (0.13), residues: 1507 sheet: -2.05 (0.25), residues: 366 loop : -2.21 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 67 TYR 0.019 0.002 TYR J 679 PHE 0.018 0.002 PHE I1187 TRP 0.011 0.001 TRP J1020 HIS 0.014 0.001 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (33445) covalent geometry : angle 0.67838 / 0.35 (45709) hydrogen bonds : bond 0.04381 / 2.92 ( 1396) hydrogen bonds : angle 5.14381 / 3.57 ( 3858) metal coordination : bond 0.00717 / 0.33 ( 9) metal coordination : angle 7.52622 / 4.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 385 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: G 68 TYR cc_start: 0.8872 (m-80) cc_final: 0.8157 (m-80) REVERT: G 137 ASN cc_start: 0.6388 (p0) cc_final: 0.6071 (p0) REVERT: G 145 LYS cc_start: 0.8871 (tmmt) cc_final: 0.8054 (ttpt) REVERT: G 204 GLU cc_start: 0.7684 (tt0) cc_final: 0.7389 (mt-10) REVERT: H 147 GLN cc_start: 0.7437 (tt0) cc_final: 0.7035 (mt0) REVERT: H 211 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8476 (pt) REVERT: I 50 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6537 (tt0) REVERT: I 88 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: I 119 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6536 (tt0) REVERT: I 219 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: I 515 MET cc_start: 0.8761 (ttp) cc_final: 0.8542 (ttt) REVERT: I 741 MET cc_start: 0.7729 (ttp) cc_final: 0.7230 (ttp) REVERT: I 800 MET cc_start: 0.7967 (mtm) cc_final: 0.7653 (mtp) REVERT: I 974 ARG cc_start: 0.7628 (mmp80) cc_final: 0.7242 (mmp-170) REVERT: I 987 GLU cc_start: 0.4700 (OUTLIER) cc_final: 0.3987 (mp0) REVERT: I 1024 GLU cc_start: 0.7989 (pp20) cc_final: 0.6907 (mm-30) REVERT: I 1025 PHE cc_start: 0.7818 (t80) cc_final: 0.7608 (t80) REVERT: I 1137 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: I 1296 ASP cc_start: 0.8235 (t0) cc_final: 0.7753 (t0) REVERT: I 1304 MET cc_start: 0.8473 (tpp) cc_final: 0.8078 (tpt) REVERT: I 1319 MET cc_start: 0.6917 (ttm) cc_final: 0.6420 (tpp) REVERT: I 1331 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7865 (mtm180) REVERT: J 334 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7473 (tptm) REVERT: J 368 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8622 (tt) REVERT: J 555 TYR cc_start: 0.8347 (m-10) cc_final: 0.7836 (m-80) REVERT: J 715 LYS cc_start: 0.7269 (mtpp) cc_final: 0.6921 (mptt) REVERT: J 770 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7911 (mm) REVERT: J 785 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: J 895 CYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8402 (p) REVERT: J 918 ILE cc_start: 0.8826 (pt) cc_final: 0.8296 (mt) REVERT: J 1040 MET cc_start: 0.4916 (mtp) cc_final: 0.4454 (ptp) REVERT: J 1132 LYS cc_start: 0.4011 (OUTLIER) cc_final: 0.3550 (mmtt) REVERT: J 1260 MET cc_start: 0.8386 (ttm) cc_final: 0.8090 (ttm) REVERT: J 1341 ARG cc_start: 0.7108 (ttt-90) cc_final: 0.6785 (ttt-90) REVERT: J 1349 GLU cc_start: 0.7976 (mp0) cc_final: 0.7340 (mt-10) REVERT: J 1368 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6008 (m-30) REVERT: J 1372 ARG cc_start: 0.6251 (mmp80) cc_final: 0.5845 (mtm-85) REVERT: K 56 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7770 (mm-30) REVERT: L 105 MET cc_start: 0.8375 (ppp) cc_final: 0.8064 (ppp) REVERT: L 277 MET cc_start: 0.6763 (tpt) cc_final: 0.6275 (tmm) REVERT: L 390 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8431 (tp) REVERT: L 425 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: M 316 MET cc_start: 0.3168 (tpt) cc_final: 0.1793 (tmm) REVERT: N 9 TYR cc_start: 0.7776 (t80) cc_final: 0.7225 (t80) REVERT: N 65 GLN cc_start: 0.7406 (tt0) cc_final: 0.6489 (tp-100) REVERT: N 66 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7026 (pt0) outliers start: 162 outliers final: 107 residues processed: 506 average time/residue: 0.2128 time to fit residues: 176.0272 Evaluate side-chains 477 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 355 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 37 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 290 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 8 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113701 restraints weight = 56164.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114383 restraints weight = 52983.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114727 restraints weight = 39372.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115120 restraints weight = 32902.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115245 restraints weight = 29643.829| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33454 Z= 0.185 Angle : 0.697 13.188 45715 Z= 0.361 Chirality : 0.046 0.348 5224 Planarity : 0.005 0.085 5525 Dihedral : 18.543 161.497 5739 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.72 % Rotamer: Outliers : 5.19 % Allowed : 21.81 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.76 (0.13), residues: 3805 helix: 0.17 (0.13), residues: 1505 sheet: -2.01 (0.25), residues: 388 loop : -2.14 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 67 TYR 0.025 0.002 TYR L 430 PHE 0.016 0.002 PHE I 545 TRP 0.011 0.001 TRP L 315 HIS 0.013 0.001 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (33445) covalent geometry : angle 0.69172 / 0.36 (45709) hydrogen bonds : bond 0.04410 / 2.94 ( 1396) hydrogen bonds : angle 5.12083 / 3.55 ( 3858) metal coordination : bond 0.00878 / 0.42 ( 9) metal coordination : angle 7.27504 / 4.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 369 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: G 68 TYR cc_start: 0.8910 (m-80) cc_final: 0.8138 (m-80) REVERT: G 137 ASN cc_start: 0.6426 (p0) cc_final: 0.6134 (p0) REVERT: G 145 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8135 (ttpt) REVERT: G 204 GLU cc_start: 0.7717 (tt0) cc_final: 0.7443 (mt-10) REVERT: H 147 GLN cc_start: 0.7446 (tt0) cc_final: 0.7107 (mt0) REVERT: H 211 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (pt) REVERT: I 50 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6562 (tt0) REVERT: I 119 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: I 515 MET cc_start: 0.8779 (ttp) cc_final: 0.8552 (ttt) REVERT: I 711 ASP cc_start: 0.6611 (m-30) cc_final: 0.6293 (m-30) REVERT: I 741 MET cc_start: 0.7752 (ttp) cc_final: 0.7211 (ttp) REVERT: I 800 MET cc_start: 0.8094 (mtm) cc_final: 0.7752 (mtp) REVERT: I 974 ARG cc_start: 0.7627 (mmp80) cc_final: 0.7165 (mmp-170) REVERT: I 987 GLU cc_start: 0.4510 (OUTLIER) cc_final: 0.3734 (mp0) REVERT: I 1024 GLU cc_start: 0.8050 (pp20) cc_final: 0.6982 (mm-30) REVERT: I 1137 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: I 1177 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7838 (ttm170) REVERT: I 1304 MET cc_start: 0.8473 (tpp) cc_final: 0.8072 (tpt) REVERT: I 1319 MET cc_start: 0.6924 (ttm) cc_final: 0.6481 (tpp) REVERT: I 1331 ARG cc_start: 0.8285 (ttm170) cc_final: 0.7891 (mtm180) REVERT: J 78 LEU cc_start: 0.7886 (tp) cc_final: 0.7618 (tt) REVERT: J 334 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7595 (tptm) REVERT: J 368 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8798 (tt) REVERT: J 505 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7722 (t0) REVERT: J 555 TYR cc_start: 0.8294 (m-10) cc_final: 0.7789 (m-80) REVERT: J 715 LYS cc_start: 0.7430 (mtpp) cc_final: 0.7004 (mptt) REVERT: J 770 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8015 (mm) REVERT: J 785 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: J 895 CYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8431 (p) REVERT: J 918 ILE cc_start: 0.8863 (pt) cc_final: 0.8327 (mt) REVERT: J 1132 LYS cc_start: 0.4032 (OUTLIER) cc_final: 0.3598 (mmtt) REVERT: J 1260 MET cc_start: 0.8426 (ttm) cc_final: 0.8193 (ttm) REVERT: J 1341 ARG cc_start: 0.7113 (ttt-90) cc_final: 0.6757 (ttt-90) REVERT: J 1349 GLU cc_start: 0.7987 (mp0) cc_final: 0.7339 (mt-10) REVERT: J 1368 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6051 (m-30) REVERT: J 1372 ARG cc_start: 0.6228 (mmp80) cc_final: 0.5793 (mtm-85) REVERT: K 64 LEU cc_start: 0.8367 (mt) cc_final: 0.8049 (mp) REVERT: L 105 MET cc_start: 0.8403 (ppp) cc_final: 0.8081 (ppp) REVERT: L 277 MET cc_start: 0.6741 (tpt) cc_final: 0.6275 (tmm) REVERT: L 369 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7113 (mt-10) REVERT: L 390 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8425 (tp) REVERT: L 425 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: M 316 MET cc_start: 0.3188 (tpt) cc_final: 0.1801 (tmm) REVERT: N 4 GLU cc_start: 0.6981 (mp0) cc_final: 0.6630 (mt-10) REVERT: N 9 TYR cc_start: 0.7811 (t80) cc_final: 0.7160 (t80) REVERT: N 65 GLN cc_start: 0.7405 (tt0) cc_final: 0.6487 (tp-100) REVERT: N 66 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7058 (pt0) outliers start: 170 outliers final: 124 residues processed: 497 average time/residue: 0.2116 time to fit residues: 172.8161 Evaluate side-chains 486 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 346 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 428 SER Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 37 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 302 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 298 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 235 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN ** J 936 HIS ** 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 = 0.3924 r_free = 0.3924 target = 0.152484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116136 restraints weight = 55853.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117012 restraints weight = 52146.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117360 restraints weight = 37852.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117785 restraints weight = 31568.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117904 restraints weight = 28139.063| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33454 Z= 0.131 Angle : 0.660 11.715 45715 Z= 0.343 Chirality : 0.044 0.348 5224 Planarity : 0.005 0.073 5525 Dihedral : 18.365 161.977 5739 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 3.97 % Allowed : 22.88 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.03 % Twisted Proline : 0.66 % Twisted General : 0.08 % 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: -1.54 (0.13), residues: 3805 helix: 0.37 (0.13), residues: 1496 sheet: -1.80 (0.26), residues: 363 loop : -2.03 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 67 TYR 0.020 0.001 TYR J 679 PHE 0.017 0.001 PHE I 230 TRP 0.009 0.001 TRP I 807 HIS 0.081 0.002 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (33445) covalent geometry : angle 0.65620 / 0.34 (45709) hydrogen bonds : bond 0.04113 / 2.73 ( 1396) hydrogen bonds : angle 4.97830 / 3.45 ( 3858) metal coordination : bond 0.00514 / 0.23 ( 9) metal coordination : angle 6.24581 / 3.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 384 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: G 68 TYR cc_start: 0.8860 (m-80) cc_final: 0.8081 (m-80) REVERT: G 145 LYS cc_start: 0.8856 (tmmt) cc_final: 0.8547 (tmtt) REVERT: G 204 GLU cc_start: 0.7571 (tt0) cc_final: 0.7282 (mt-10) REVERT: H 147 GLN cc_start: 0.7451 (tt0) cc_final: 0.7136 (mt0) REVERT: H 211 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8523 (pt) REVERT: I 50 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6667 (tt0) REVERT: I 108 GLU cc_start: 0.2803 (tm-30) cc_final: 0.2500 (tm-30) REVERT: I 119 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6375 (tt0) REVERT: I 515 MET cc_start: 0.8746 (ttp) cc_final: 0.8511 (ttt) REVERT: I 711 ASP cc_start: 0.6470 (m-30) cc_final: 0.6195 (m-30) REVERT: I 741 MET cc_start: 0.7745 (ttp) cc_final: 0.7298 (ttp) REVERT: I 800 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7783 (mtp) REVERT: I 987 GLU cc_start: 0.4661 (OUTLIER) cc_final: 0.3992 (mp0) REVERT: I 1024 GLU cc_start: 0.8090 (pp20) cc_final: 0.7301 (mm-30) REVERT: I 1137 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: I 1170 MET cc_start: 0.7724 (mmp) cc_final: 0.7436 (mmm) REVERT: I 1177 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7832 (ttm170) REVERT: I 1296 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7709 (t0) REVERT: I 1304 MET cc_start: 0.8442 (tpp) cc_final: 0.8071 (tpt) REVERT: I 1319 MET cc_start: 0.6887 (ttm) cc_final: 0.6558 (tpp) REVERT: I 1331 ARG cc_start: 0.8310 (ttm170) cc_final: 0.7879 (mtm180) REVERT: J 334 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7532 (tptm) REVERT: J 505 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7801 (t0) REVERT: J 555 TYR cc_start: 0.8222 (m-10) cc_final: 0.7726 (m-80) REVERT: J 715 LYS cc_start: 0.7354 (mtpp) cc_final: 0.6973 (mptt) REVERT: J 770 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7866 (mm) REVERT: J 895 CYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (p) REVERT: J 918 ILE cc_start: 0.8811 (pt) cc_final: 0.8301 (mt) REVERT: J 1040 MET cc_start: 0.4917 (mtp) cc_final: 0.4413 (ptp) REVERT: J 1132 LYS cc_start: 0.3980 (OUTLIER) cc_final: 0.3555 (mmtt) REVERT: J 1189 MET cc_start: 0.6579 (mmm) cc_final: 0.6358 (ttt) REVERT: J 1260 MET cc_start: 0.8407 (ttm) cc_final: 0.8182 (ttm) REVERT: J 1341 ARG cc_start: 0.7032 (ttt-90) cc_final: 0.6792 (ttt-90) REVERT: J 1344 LEU cc_start: 0.8422 (mp) cc_final: 0.7436 (mm) REVERT: J 1349 GLU cc_start: 0.7954 (mp0) cc_final: 0.7249 (mt-10) REVERT: K 64 LEU cc_start: 0.8422 (mt) cc_final: 0.8048 (mp) REVERT: L 105 MET cc_start: 0.8402 (ppp) cc_final: 0.8090 (ppp) REVERT: L 277 MET cc_start: 0.6717 (tpt) cc_final: 0.6290 (tmm) REVERT: L 390 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8398 (tp) REVERT: L 425 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: M 262 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4795 (tt) REVERT: M 316 MET cc_start: 0.2953 (tpt) cc_final: 0.1552 (tmm) REVERT: N 4 GLU cc_start: 0.6940 (mp0) cc_final: 0.6382 (mt-10) REVERT: N 9 TYR cc_start: 0.7580 (t80) cc_final: 0.6995 (t80) REVERT: N 46 GLU cc_start: 0.5673 (tp30) cc_final: 0.5188 (pm20) REVERT: N 65 GLN cc_start: 0.7339 (tt0) cc_final: 0.6368 (tp-100) outliers start: 130 outliers final: 94 residues processed: 480 average time/residue: 0.2131 time to fit residues: 167.3250 Evaluate side-chains 474 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 365 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 37 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 28 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 278 optimal weight: 30.0000 chunk 209 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 198 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 139 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN J 157 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114886 restraints weight = 55869.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115675 restraints weight = 51811.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115893 restraints weight = 40525.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116335 restraints weight = 33350.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116529 restraints weight = 29340.701| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33454 Z= 0.167 Angle : 0.676 15.563 45715 Z= 0.349 Chirality : 0.045 0.342 5224 Planarity : 0.005 0.075 5525 Dihedral : 18.311 161.327 5737 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.91 % Favored : 92.04 % Rotamer: Outliers : 4.06 % Allowed : 22.88 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -1.50 (0.13), residues: 3805 helix: 0.36 (0.13), residues: 1503 sheet: -1.79 (0.26), residues: 379 loop : -1.98 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 67 TYR 0.019 0.001 TYR J 679 PHE 0.016 0.001 PHE I 545 TRP 0.017 0.001 TRP J1020 HIS 0.004 0.001 HIS J1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (33445) covalent geometry : angle 0.67215 / 0.35 (45709) hydrogen bonds : bond 0.04187 / 2.78 ( 1396) hydrogen bonds : angle 4.97047 / 3.45 ( 3858) metal coordination : bond 0.00769 / 0.37 ( 9) metal coordination : angle 6.15179 / 3.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 360 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: G 68 TYR cc_start: 0.8957 (m-80) cc_final: 0.8213 (m-80) REVERT: G 204 GLU cc_start: 0.7747 (tt0) cc_final: 0.7478 (mt-10) REVERT: H 147 GLN cc_start: 0.7486 (tt0) cc_final: 0.7169 (mt0) REVERT: H 211 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8545 (pt) REVERT: I 50 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6694 (tt0) REVERT: I 108 GLU cc_start: 0.3414 (tm-30) cc_final: 0.3179 (tm-30) REVERT: I 119 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6370 (tt0) REVERT: I 515 MET cc_start: 0.8791 (ttp) cc_final: 0.8537 (ttt) REVERT: I 711 ASP cc_start: 0.6514 (m-30) cc_final: 0.6290 (m-30) REVERT: I 741 MET cc_start: 0.7698 (ttp) cc_final: 0.7333 (ttp) REVERT: I 800 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7809 (mtp) REVERT: I 987 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4013 (mp0) REVERT: I 1024 GLU cc_start: 0.8081 (pp20) cc_final: 0.7233 (mm-30) REVERT: I 1137 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: I 1177 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7864 (ttm170) REVERT: I 1296 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7711 (t0) REVERT: I 1304 MET cc_start: 0.8466 (tpp) cc_final: 0.8092 (tpt) REVERT: I 1319 MET cc_start: 0.6950 (ttm) cc_final: 0.6588 (tpp) REVERT: I 1331 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7918 (mtm180) REVERT: J 334 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7589 (tptm) REVERT: J 368 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8686 (tt) REVERT: J 466 MET cc_start: 0.8431 (mtt) cc_final: 0.8154 (mtm) REVERT: J 505 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7820 (t0) REVERT: J 555 TYR cc_start: 0.8241 (m-10) cc_final: 0.7751 (m-80) REVERT: J 715 LYS cc_start: 0.7400 (mtpp) cc_final: 0.6992 (mptt) REVERT: J 770 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7894 (mm) REVERT: J 895 CYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8524 (p) REVERT: J 918 ILE cc_start: 0.8856 (pt) cc_final: 0.8341 (mt) REVERT: J 1040 MET cc_start: 0.4937 (mtp) cc_final: 0.4422 (ptp) REVERT: J 1078 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6466 (mt) REVERT: J 1132 LYS cc_start: 0.3988 (OUTLIER) cc_final: 0.3513 (mmtt) REVERT: J 1260 MET cc_start: 0.8447 (ttm) cc_final: 0.8188 (ttm) REVERT: J 1341 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.6775 (ttt-90) REVERT: J 1344 LEU cc_start: 0.8542 (mp) cc_final: 0.7942 (mm) REVERT: J 1349 GLU cc_start: 0.7884 (mp0) cc_final: 0.7221 (mt-10) REVERT: J 1368 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: K 55 GLU cc_start: 0.6580 (pp20) cc_final: 0.6216 (pp20) REVERT: K 56 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7545 (mm-30) REVERT: K 68 GLU cc_start: 0.7843 (tp30) cc_final: 0.7536 (tp30) REVERT: L 105 MET cc_start: 0.8435 (ppp) cc_final: 0.8127 (ppp) REVERT: L 277 MET cc_start: 0.6709 (tpt) cc_final: 0.6287 (tmm) REVERT: L 297 MET cc_start: 0.1968 (mtp) cc_final: 0.1322 (ptp) REVERT: L 390 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8478 (tp) REVERT: L 425 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: M 316 MET cc_start: 0.2545 (tpt) cc_final: 0.1448 (tmm) REVERT: N 4 GLU cc_start: 0.6957 (mp0) cc_final: 0.6481 (mt-10) REVERT: N 9 TYR cc_start: 0.7592 (t80) cc_final: 0.7027 (t80) REVERT: N 46 GLU cc_start: 0.5751 (tp30) cc_final: 0.5201 (pm20) REVERT: N 65 GLN cc_start: 0.7384 (tt0) cc_final: 0.6441 (tp-100) REVERT: N 66 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6883 (pt0) outliers start: 133 outliers final: 103 residues processed: 461 average time/residue: 0.2102 time to fit residues: 158.8058 Evaluate side-chains 467 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 347 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 30 HIS Chi-restraints excluded: chain N residue 37 CYS Chi-restraints excluded: chain N residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 281 optimal weight: 4.9990 chunk 225 optimal weight: 0.3980 chunk 275 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1080 ASN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 GLN N 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113622 restraints weight = 55921.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114519 restraints weight = 53507.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114920 restraints weight = 37719.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115326 restraints weight = 31754.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115424 restraints weight = 28707.297| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33454 Z= 0.201 Angle : 0.699 12.245 45715 Z= 0.362 Chirality : 0.045 0.337 5224 Planarity : 0.005 0.074 5525 Dihedral : 18.311 160.360 5737 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.15 % Favored : 91.77 % Rotamer: Outliers : 3.97 % Allowed : 23.13 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.05 % 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: -1.52 (0.13), residues: 3805 helix: 0.30 (0.13), residues: 1509 sheet: -1.81 (0.25), residues: 396 loop : -1.95 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 67 TYR 0.019 0.002 TYR J 679 PHE 0.017 0.002 PHE I 80 TRP 0.026 0.002 TRP J1020 HIS 0.023 0.001 HIS N 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (33445) covalent geometry : angle 0.69559 / 0.36 (45709) hydrogen bonds : bond 0.04287 / 2.85 ( 1396) hydrogen bonds : angle 4.99605 / 3.46 ( 3858) metal coordination : bond 0.00946 / 0.47 ( 9) metal coordination : angle 6.37409 / 3.51 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 348 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: G 204 GLU cc_start: 0.7737 (tt0) cc_final: 0.7480 (mt-10) REVERT: H 147 GLN cc_start: 0.7449 (tt0) cc_final: 0.7121 (mt0) REVERT: H 211 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8554 (pt) REVERT: I 50 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6705 (tt0) REVERT: I 515 MET cc_start: 0.8812 (ttp) cc_final: 0.8548 (ttt) REVERT: I 711 ASP cc_start: 0.6608 (m-30) cc_final: 0.6303 (m-30) REVERT: I 741 MET cc_start: 0.7691 (ttp) cc_final: 0.7427 (ttp) REVERT: I 800 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7794 (mtp) REVERT: I 987 GLU cc_start: 0.4660 (OUTLIER) cc_final: 0.4003 (mp0) REVERT: I 1066 MET cc_start: 0.7899 (mtp) cc_final: 0.7584 (mtp) REVERT: I 1137 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: I 1177 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7858 (ttm170) REVERT: I 1296 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7605 (t0) REVERT: I 1304 MET cc_start: 0.8481 (tpp) cc_final: 0.8105 (tpt) REVERT: I 1319 MET cc_start: 0.6987 (ttm) cc_final: 0.6564 (tpp) REVERT: I 1331 ARG cc_start: 0.8332 (ttm170) cc_final: 0.7929 (mtm180) REVERT: J 334 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7627 (tptm) REVERT: J 466 MET cc_start: 0.8434 (mtt) cc_final: 0.8163 (mtm) REVERT: J 505 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7804 (t0) REVERT: J 555 TYR cc_start: 0.8258 (m-10) cc_final: 0.7768 (m-80) REVERT: J 715 LYS cc_start: 0.7569 (mtpp) cc_final: 0.7056 (mptt) REVERT: J 770 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7897 (mm) REVERT: J 895 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8530 (p) REVERT: J 918 ILE cc_start: 0.8804 (pt) cc_final: 0.8296 (mt) REVERT: J 1040 MET cc_start: 0.4815 (mtp) cc_final: 0.4293 (ptp) REVERT: J 1078 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6422 (mt) REVERT: J 1132 LYS cc_start: 0.4007 (OUTLIER) cc_final: 0.3553 (mmtt) REVERT: J 1341 ARG cc_start: 0.7048 (ttt-90) cc_final: 0.6796 (ttt-90) REVERT: J 1344 LEU cc_start: 0.8537 (mp) cc_final: 0.7727 (mm) REVERT: J 1349 GLU cc_start: 0.7918 (mp0) cc_final: 0.7244 (mt-10) REVERT: J 1368 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.5819 (m-30) REVERT: K 56 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7672 (mm-30) REVERT: K 68 GLU cc_start: 0.7793 (tp30) cc_final: 0.7535 (tp30) REVERT: K 74 GLU cc_start: 0.7831 (pt0) cc_final: 0.7471 (pt0) REVERT: L 105 MET cc_start: 0.8456 (ppp) cc_final: 0.8136 (ppp) REVERT: L 277 MET cc_start: 0.6707 (tpt) cc_final: 0.6282 (tmm) REVERT: L 297 MET cc_start: 0.2074 (mtp) cc_final: 0.1299 (ptp) REVERT: L 390 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8392 (tp) REVERT: L 425 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6292 (m-80) REVERT: M 316 MET cc_start: 0.2445 (tpt) cc_final: 0.1551 (tmm) REVERT: N 9 TYR cc_start: 0.7730 (t80) cc_final: 0.7106 (t80) REVERT: N 46 GLU cc_start: 0.5755 (tp30) cc_final: 0.5245 (pm20) REVERT: N 65 GLN cc_start: 0.7394 (tt0) cc_final: 0.6464 (tp-100) REVERT: N 66 GLU cc_start: 0.7833 (mm-30) cc_final: 0.6912 (pt0) outliers start: 130 outliers final: 107 residues processed: 444 average time/residue: 0.2096 time to fit residues: 152.9490 Evaluate side-chains 463 residues out of total 3283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 340 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 987 GLU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1137 GLU Chi-restraints excluded: chain I residue 1145 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 679 TYR Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1078 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1132 LYS Chi-restraints excluded: chain J residue 1149 ARG Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 265 GLN Chi-restraints excluded: chain L residue 316 PHE Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 428 SER Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 37 CYS Chi-restraints excluded: chain N residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 149 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 384 optimal weight: 40.0000 chunk 354 optimal weight: 20.0000 chunk 237 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1080 ASN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114697 restraints weight = 55987.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115707 restraints weight = 53227.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116084 restraints weight = 37551.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116427 restraints weight = 32158.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116536 restraints weight = 28831.411| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33454 Z= 0.162 Angle : 0.675 12.893 45715 Z= 0.349 Chirality : 0.044 0.334 5224 Planarity : 0.005 0.074 5525 Dihedral : 18.230 160.180 5737 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.96 % Favored : 91.98 % Rotamer: Outliers : 3.94 % Allowed : 23.25 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.05 % Twisted Proline : 0.66 % Twisted General : 0.03 % 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: -1.44 (0.13), residues: 3805 helix: 0.34 (0.13), residues: 1514 sheet: -1.75 (0.25), residues: 393 loop : -1.89 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 67 TYR 0.019 0.001 TYR J 679 PHE 0.018 0.001 PHE I 545 TRP 0.018 0.001 TRP J1020 HIS 0.005 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (33445) covalent geometry : angle 0.67110 / 0.35 (45709) hydrogen bonds : bond 0.04143 / 2.75 ( 1396) hydrogen bonds : angle 4.93511 / 3.42 ( 3858) metal coordination : bond 0.00770 / 0.36 ( 9) metal coordination : angle 6.09056 / 3.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5291.90 seconds wall clock time: 92 minutes 49.97 seconds (5569.97 seconds total)