Starting phenix.real_space_refine on Mon Aug 25 09:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g1s_29676/08_2025/8g1s_29676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g1s_29676/08_2025/8g1s_29676.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 { model { file = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2025/8g1s_29676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2025/8g1s_29676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2025/8g1s_29676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2025/8g1s_29676.map" } 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= 0.002 sd= 0.057 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: 6 Type Number sf(0) Gaussians P 92 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16476 2.51 5 N 4747 2.21 5 O 5366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26788 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Inner-chain residues flagged as termini: ['pdbres=" DG A 26 "'] Classifications: {'DNA': 18} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 17} Chain: "B" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 609 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "G" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 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: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 13, 'rna3p': 33} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.18 Number of scatterers: 26788 At special positions: 0 Unit cell: (137, 154, 162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 92 15.00 Mg 1 11.99 O 5366 8.00 N 4747 7.00 C 16476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 837.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 43 sheets defined 36.7% alpha, 12.1% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.601A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.713A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.894A pdb=" N LEU H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) 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 'H' and resid 228 through 232 Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.972A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.618A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 removed outlier: 3.518A pdb=" N ARG I 245 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 242 through 246' Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.026A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 removed outlier: 4.022A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 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 Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 519 through 526 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 607 through 614 removed outlier: 4.036A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 685 Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.773A pdb=" N SER I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 819 through 825 removed outlier: 3.987A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 865 removed outlier: 4.288A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.652A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I 978 " --> pdb=" O ARG I 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.349A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.532A pdb=" N MET I1131 " --> pdb=" O LYS I1127 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.527A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.532A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 removed outlier: 3.600A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1309 Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 28 through 33 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.546A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.641A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 229 Processing helix chain 'J' and resid 233 through 238 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 265 through 286 Processing helix chain 'J' and resid 288 through 309 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 389 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.524A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 434 removed outlier: 3.545A pdb=" N ILE J 434 " --> pdb=" O ARG J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.561A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.550A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.616A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.505A pdb=" N GLY J 613 " --> pdb=" O TYR J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.788A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 647 through 670 removed outlier: 3.964A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.744A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.528A pdb=" N VAL J 839 " --> pdb=" O LEU J 835 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.769A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 4.077A 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 1313 Processing helix chain 'J' and resid 1314 through 1316 No H-bonds generated for 'chain 'J' and resid 1314 through 1316' Processing helix chain 'J' and resid 1319 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.566A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 15 Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.519A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.668A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AA5, first strand: chain 'G' and resid 180 through 182 removed outlier: 6.571A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 16 removed outlier: 4.189A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 31 through 32 removed outlier: 3.816A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.583A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.937A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.649A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.258A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.672A pdb=" N ILE I 177 " --> pdb=" O GLY I 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 250 through 251 removed outlier: 4.379A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.786A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.961A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 599 through 606 removed outlier: 5.235A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 718 removed outlier: 6.552A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP I 781 " --> pdb=" O ALA I 718 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.763A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1096 through 1098 removed outlier: 3.556A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 838 removed outlier: 6.441A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.788A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1065 through 1066 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.692A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.302A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'J' and resid 356 through 357 removed outlier: 6.107A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 547 through 556 removed outlier: 3.653A pdb=" N GLU J 556 " --> pdb=" O VAL J 564 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.882A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.603A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.795A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE J 985 " --> pdb=" O SER J 957 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU J1009 " --> pdb=" O ILE J 958 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1034 through 1036 Processing sheet with id=AE5, first strand: chain 'J' and resid 1046 through 1047 removed outlier: 3.635A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1161 through 1162 Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.297A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4499 1.31 - 1.44: 6988 1.44 - 1.56: 15532 1.56 - 1.69: 183 1.69 - 1.81: 184 Bond restraints: 27386 Sorted by residual: bond pdb=" CA ARG J 425 " pdb=" C ARG J 425 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.25e-02 6.40e+03 2.16e+01 bond pdb=" C ARG J 425 " pdb=" O ARG J 425 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" CA ARG J 425 " pdb=" CB ARG J 425 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.58e-02 4.01e+03 1.22e+01 bond pdb=" CD ARG J 425 " pdb=" NE ARG J 425 " ideal model delta sigma weight residual 1.458 1.428 0.030 1.40e-02 5.10e+03 4.67e+00 bond pdb=" C GLY J1360 " pdb=" O GLY J1360 " ideal model delta sigma weight residual 1.236 1.247 -0.011 5.30e-03 3.56e+04 4.44e+00 ... (remaining 27381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 36745 1.79 - 3.57: 591 3.57 - 5.36: 70 5.36 - 7.14: 8 7.14 - 8.93: 2 Bond angle restraints: 37416 Sorted by residual: angle pdb=" N VAL I1254 " pdb=" CA VAL I1254 " pdb=" C VAL I1254 " ideal model delta sigma weight residual 112.29 108.01 4.28 9.40e-01 1.13e+00 2.07e+01 angle pdb=" NE ARG J 425 " pdb=" CZ ARG J 425 " pdb=" NH1 ARG J 425 " ideal model delta sigma weight residual 121.50 118.04 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" C GLY I 45 " pdb=" N GLN I 46 " pdb=" CA GLN I 46 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C GLN I1257 " pdb=" N PRO I1258 " pdb=" CA PRO I1258 " ideal model delta sigma weight residual 119.84 123.42 -3.58 1.25e+00 6.40e-01 8.21e+00 angle pdb=" CA ARG J 425 " pdb=" CB ARG J 425 " pdb=" CG ARG J 425 " ideal model delta sigma weight residual 114.10 108.39 5.71 2.00e+00 2.50e-01 8.14e+00 ... (remaining 37411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 16085 33.49 - 66.98: 595 66.98 - 100.47: 46 100.47 - 133.96: 0 133.96 - 167.45: 5 Dihedral angle restraints: 16731 sinusoidal: 7628 harmonic: 9103 Sorted by residual: dihedral pdb=" O4' C R 17 " pdb=" C1' C R 17 " pdb=" N1 C R 17 " pdb=" C2 C R 17 " ideal model delta sinusoidal sigma weight residual 200.00 55.70 144.30 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual 200.00 57.62 142.38 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" CA GLU J1343 " pdb=" C GLU J1343 " pdb=" N LEU J1344 " pdb=" CA LEU J1344 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 16728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2970 0.035 - 0.070: 924 0.070 - 0.105: 327 0.105 - 0.140: 83 0.140 - 0.175: 5 Chirality restraints: 4309 Sorted by residual: chirality pdb=" CA ARG J 425 " pdb=" N ARG J 425 " pdb=" C ARG J 425 " pdb=" CB ARG J 425 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" C1' G R 46 " pdb=" O4' G R 46 " pdb=" C2' G R 46 " pdb=" N9 G R 46 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C1' C R 17 " pdb=" O4' C R 17 " pdb=" C2' C R 17 " pdb=" N1 C R 17 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 4306 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 424 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASN J 424 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN J 424 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG J 425 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 46 " -0.031 2.00e-02 2.50e+03 1.32e-02 5.26e+00 pdb=" N9 G R 46 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G R 46 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G R 46 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G R 46 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G R 46 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G R 46 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G R 46 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G R 46 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G R 46 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G R 46 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G R 46 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO J 359 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " -0.025 5.00e-02 4.00e+02 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 308 2.58 - 3.16: 23528 3.16 - 3.74: 44403 3.74 - 4.32: 59592 4.32 - 4.90: 95788 Nonbonded interactions: 223619 Sorted by model distance: nonbonded pdb=" NZ LYS I1306 " pdb=" O2' C R 17 " model vdw 2.004 3.120 nonbonded pdb=" N1 DG A 26 " pdb=" OE2 GLU I 541 " model vdw 2.049 3.120 nonbonded pdb=" OP1 DT B 19 " pdb=" CG LYS I1262 " model vdw 2.055 3.440 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1401 " model vdw 2.087 2.170 nonbonded pdb=" OH TYR I 123 " pdb=" OE2 GLU I 126 " model vdw 2.182 3.040 ... (remaining 223614 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 8 through 158 or resid 170 through 234)) selection = (chain 'H' and resid 8 through 234) } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.080 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27386 Z= 0.146 Angle : 0.579 8.927 37416 Z= 0.330 Chirality : 0.040 0.175 4309 Planarity : 0.004 0.046 4556 Dihedral : 16.068 167.451 10875 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.59 % Rotamer: Outliers : 1.07 % Allowed : 7.11 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.15), residues: 3152 helix: -0.07 (0.16), residues: 1087 sheet: -2.43 (0.27), residues: 365 loop : -1.82 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 101 TYR 0.013 0.001 TYR I1281 PHE 0.012 0.001 PHE J 260 TRP 0.012 0.001 TRP J 580 HIS 0.003 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00286 (27386) covalent geometry : angle 0.57896 (37416) hydrogen bonds : bond 0.18961 ( 1024) hydrogen bonds : angle 7.06155 ( 2838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 551 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8576 (t0) cc_final: 0.8335 (t0) REVERT: G 75 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8343 (tm-30) REVERT: G 194 GLN cc_start: 0.7245 (pp30) cc_final: 0.6959 (pp30) REVERT: H 100 LEU cc_start: 0.9175 (mp) cc_final: 0.8967 (mt) REVERT: H 185 TYR cc_start: 0.8681 (p90) cc_final: 0.8331 (p90) REVERT: I 84 GLU cc_start: 0.7882 (tp30) cc_final: 0.7393 (mm-30) REVERT: I 523 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6526 (mm-30) REVERT: I 568 ASN cc_start: 0.8396 (p0) cc_final: 0.8094 (p0) REVERT: I 654 ASP cc_start: 0.7373 (m-30) cc_final: 0.6939 (m-30) REVERT: I 739 ASP cc_start: 0.8279 (p0) cc_final: 0.7993 (p0) REVERT: I 820 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7732 (tm-30) REVERT: I 1018 TYR cc_start: 0.6946 (t80) cc_final: 0.6276 (m-80) REVERT: I 1023 HIS cc_start: 0.8008 (t-90) cc_final: 0.7770 (t-90) REVERT: I 1085 MET cc_start: 0.8727 (mmt) cc_final: 0.8494 (mmt) REVERT: I 1098 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8864 (mm) REVERT: I 1180 MET cc_start: 0.8903 (tpp) cc_final: 0.8386 (tpp) REVERT: I 1305 TYR cc_start: 0.8776 (t80) cc_final: 0.8548 (t80) REVERT: J 267 ASP cc_start: 0.8376 (p0) cc_final: 0.7891 (t70) REVERT: J 298 MET cc_start: 0.8439 (ptt) cc_final: 0.8189 (ptp) REVERT: J 698 MET cc_start: 0.9097 (mmm) cc_final: 0.8714 (tpp) REVERT: J 833 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6451 (mt-10) REVERT: J 1121 LEU cc_start: 0.8639 (tp) cc_final: 0.8358 (mp) REVERT: K 8 ASP cc_start: 0.8414 (p0) cc_final: 0.7936 (p0) REVERT: K 47 THR cc_start: 0.9204 (m) cc_final: 0.8953 (m) outliers start: 29 outliers final: 6 residues processed: 574 average time/residue: 0.2145 time to fit residues: 187.6602 Evaluate side-chains 322 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 315 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 462 ASN I 519 ASN I 604 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN I1220 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN J 504 GLN J 736 GLN J1010 GLN ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084693 restraints weight = 63895.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087207 restraints weight = 35979.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087920 restraints weight = 22430.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088485 restraints weight = 19635.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088546 restraints weight = 17308.699| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27386 Z= 0.156 Angle : 0.629 9.130 37416 Z= 0.327 Chirality : 0.043 0.189 4309 Planarity : 0.005 0.049 4556 Dihedral : 15.878 169.443 4682 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 2.59 % Allowed : 14.14 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 3152 helix: 0.00 (0.16), residues: 1106 sheet: -2.42 (0.26), residues: 378 loop : -1.70 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I1106 TYR 0.026 0.002 TYR G 185 PHE 0.015 0.001 PHE I 253 TRP 0.013 0.001 TRP J 580 HIS 0.009 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00358 (27386) covalent geometry : angle 0.62852 (37416) hydrogen bonds : bond 0.04625 ( 1024) hydrogen bonds : angle 5.37392 ( 2838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 382 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8753 (t0) cc_final: 0.8331 (t0) REVERT: G 75 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 142 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7596 (mtm) REVERT: H 100 LEU cc_start: 0.8978 (mp) cc_final: 0.8767 (mt) REVERT: H 185 TYR cc_start: 0.8782 (p90) cc_final: 0.8408 (p90) REVERT: I 84 GLU cc_start: 0.8113 (tp30) cc_final: 0.7528 (mm-30) REVERT: I 163 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8202 (tptt) REVERT: I 504 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7712 (tm-30) REVERT: I 788 SER cc_start: 0.8941 (m) cc_final: 0.8353 (p) REVERT: I 820 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7803 (tm-30) REVERT: I 1018 TYR cc_start: 0.7109 (t80) cc_final: 0.6373 (m-80) REVERT: I 1098 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8731 (mm) REVERT: I 1141 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (tt) REVERT: I 1180 MET cc_start: 0.9010 (tpp) cc_final: 0.8350 (tpp) REVERT: I 1274 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7509 (mm-30) REVERT: I 1304 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8156 (ttm) REVERT: J 157 GLN cc_start: 0.7636 (mt0) cc_final: 0.7245 (pp30) REVERT: J 329 ASP cc_start: 0.8500 (m-30) cc_final: 0.8105 (m-30) REVERT: J 709 ARG cc_start: 0.6855 (tpt90) cc_final: 0.6632 (tmt-80) REVERT: J 833 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6529 (mt-10) REVERT: J 1121 LEU cc_start: 0.8687 (tp) cc_final: 0.8367 (mp) REVERT: J 1317 GLU cc_start: 0.7773 (pm20) cc_final: 0.7317 (tm-30) REVERT: K 51 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8030 (mt) outliers start: 70 outliers final: 29 residues processed: 429 average time/residue: 0.1807 time to fit residues: 126.5208 Evaluate side-chains 338 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 252 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 287 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN I 513 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I 965 GLN I1061 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080836 restraints weight = 63620.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083240 restraints weight = 33101.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084799 restraints weight = 21940.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085779 restraints weight = 17115.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086248 restraints weight = 14804.263| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27386 Z= 0.202 Angle : 0.627 9.765 37416 Z= 0.325 Chirality : 0.043 0.168 4309 Planarity : 0.004 0.058 4556 Dihedral : 15.950 169.298 4682 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 3.55 % Allowed : 15.85 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.15), residues: 3152 helix: 0.06 (0.16), residues: 1117 sheet: -2.36 (0.26), residues: 363 loop : -1.70 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 529 TYR 0.020 0.002 TYR I1281 PHE 0.015 0.002 PHE J1319 TRP 0.009 0.001 TRP I 807 HIS 0.006 0.001 HIS J 364 Details of bonding type rmsd covalent geometry : bond 0.00459 (27386) covalent geometry : angle 0.62688 (37416) hydrogen bonds : bond 0.04324 ( 1024) hydrogen bonds : angle 5.12853 ( 2838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 343 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7696 (tp30) cc_final: 0.7139 (tt0) REVERT: G 41 ASN cc_start: 0.8777 (t0) cc_final: 0.8366 (t0) REVERT: G 75 GLN cc_start: 0.9333 (tm-30) cc_final: 0.8309 (tm-30) REVERT: G 80 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7946 (tm-30) REVERT: G 142 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8099 (mtm) REVERT: G 185 TYR cc_start: 0.8916 (p90) cc_final: 0.8659 (p90) REVERT: H 185 TYR cc_start: 0.8849 (p90) cc_final: 0.8561 (p90) REVERT: I 84 GLU cc_start: 0.8422 (tp30) cc_final: 0.7757 (mm-30) REVERT: I 163 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8175 (tppt) REVERT: I 262 TYR cc_start: 0.6330 (m-80) cc_final: 0.5535 (m-80) REVERT: I 315 MET cc_start: 0.8144 (mmm) cc_final: 0.7577 (mmm) REVERT: I 562 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8483 (tp30) REVERT: I 611 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8325 (tt0) REVERT: I 788 SER cc_start: 0.9009 (m) cc_final: 0.8467 (p) REVERT: I 820 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7970 (tm-30) REVERT: I 882 ILE cc_start: 0.8614 (mp) cc_final: 0.8120 (tt) REVERT: I 1018 TYR cc_start: 0.7476 (t80) cc_final: 0.6446 (m-80) REVERT: I 1180 MET cc_start: 0.9060 (tpp) cc_final: 0.8405 (tpp) REVERT: I 1274 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7716 (mm-30) REVERT: J 157 GLN cc_start: 0.7743 (mt0) cc_final: 0.7471 (tm-30) REVERT: J 267 ASP cc_start: 0.8678 (p0) cc_final: 0.8038 (t70) REVERT: J 298 MET cc_start: 0.8744 (ptt) cc_final: 0.8532 (ptp) REVERT: J 329 ASP cc_start: 0.8641 (m-30) cc_final: 0.8121 (m-30) REVERT: J 709 ARG cc_start: 0.7140 (tpt90) cc_final: 0.6929 (tmt-80) REVERT: J 1121 LEU cc_start: 0.8743 (tp) cc_final: 0.8367 (mp) REVERT: K 8 ASP cc_start: 0.8466 (p0) cc_final: 0.7686 (p0) REVERT: K 51 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8245 (mt) REVERT: K 72 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8343 (tp40) REVERT: K 75 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7701 (tm-30) outliers start: 96 outliers final: 47 residues processed: 414 average time/residue: 0.1699 time to fit residues: 116.2067 Evaluate side-chains 359 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 310 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 31 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 15 optimal weight: 0.0040 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 526 HIS ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1314 GLN J 364 HIS ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.084022 restraints weight = 63776.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086272 restraints weight = 35187.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087011 restraints weight = 21907.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087294 restraints weight = 20268.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087283 restraints weight = 18311.029| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27386 Z= 0.144 Angle : 0.586 8.368 37416 Z= 0.304 Chirality : 0.042 0.169 4309 Planarity : 0.004 0.055 4556 Dihedral : 15.838 165.520 4677 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.63 % Allowed : 17.03 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.15), residues: 3152 helix: 0.24 (0.16), residues: 1114 sheet: -2.21 (0.27), residues: 333 loop : -1.56 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 123 TYR 0.016 0.001 TYR I1281 PHE 0.016 0.001 PHE I 337 TRP 0.009 0.001 TRP I 807 HIS 0.008 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00331 (27386) covalent geometry : angle 0.58622 (37416) hydrogen bonds : bond 0.03972 ( 1024) hydrogen bonds : angle 4.91168 ( 2838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 363 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7578 (tp30) cc_final: 0.7052 (tt0) REVERT: G 41 ASN cc_start: 0.8797 (t0) cc_final: 0.8211 (t0) REVERT: G 75 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8316 (tm-30) REVERT: G 185 TYR cc_start: 0.8823 (p90) cc_final: 0.8599 (p90) REVERT: H 185 TYR cc_start: 0.8790 (p90) cc_final: 0.8536 (p90) REVERT: I 84 GLU cc_start: 0.8025 (tp30) cc_final: 0.7506 (mm-30) REVERT: I 262 TYR cc_start: 0.6322 (m-80) cc_final: 0.5590 (m-80) REVERT: I 395 TYR cc_start: 0.7777 (t80) cc_final: 0.7525 (t80) REVERT: I 504 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7722 (tm-30) REVERT: I 611 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8201 (tt0) REVERT: I 693 LEU cc_start: 0.8675 (tp) cc_final: 0.8375 (mp) REVERT: I 820 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7870 (tm-30) REVERT: I 882 ILE cc_start: 0.8575 (mp) cc_final: 0.8156 (tt) REVERT: I 1018 TYR cc_start: 0.7480 (t80) cc_final: 0.6389 (m-80) REVERT: I 1180 MET cc_start: 0.9003 (tpp) cc_final: 0.8094 (tpp) REVERT: J 157 GLN cc_start: 0.7711 (mt0) cc_final: 0.7358 (tm-30) REVERT: J 267 ASP cc_start: 0.8538 (p0) cc_final: 0.7872 (t70) REVERT: J 298 MET cc_start: 0.8667 (ptt) cc_final: 0.8424 (ptp) REVERT: J 301 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8018 (mm-30) REVERT: J 329 ASP cc_start: 0.8489 (m-30) cc_final: 0.8054 (m-30) REVERT: J 414 GLU cc_start: 0.8271 (tp30) cc_final: 0.8018 (tm-30) REVERT: J 460 ASP cc_start: 0.7871 (m-30) cc_final: 0.7663 (t0) REVERT: J 534 GLU cc_start: 0.8518 (tt0) cc_final: 0.8290 (tt0) REVERT: J 581 MET cc_start: 0.8314 (mtm) cc_final: 0.7871 (mtm) REVERT: J 697 MET cc_start: 0.8837 (ttp) cc_final: 0.8611 (ttp) REVERT: J 743 MET cc_start: 0.8747 (tpp) cc_final: 0.8544 (tpp) REVERT: J 1121 LEU cc_start: 0.8721 (tp) cc_final: 0.8370 (mp) REVERT: J 1317 GLU cc_start: 0.7808 (pm20) cc_final: 0.7438 (tp30) REVERT: K 28 ARG cc_start: 0.7735 (mmt90) cc_final: 0.7449 (mmt180) REVERT: K 72 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8214 (tp-100) REVERT: K 75 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7887 (tm-30) REVERT: K 76 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7235 (mt-10) outliers start: 98 outliers final: 58 residues processed: 432 average time/residue: 0.1710 time to fit residues: 122.4295 Evaluate side-chains 368 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 96 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN H 132 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I1061 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084262 restraints weight = 63769.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086890 restraints weight = 34666.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087456 restraints weight = 20904.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087687 restraints weight = 19700.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087732 restraints weight = 17837.213| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27386 Z= 0.141 Angle : 0.594 13.023 37416 Z= 0.304 Chirality : 0.042 0.167 4309 Planarity : 0.004 0.059 4556 Dihedral : 15.760 164.436 4677 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.55 % Allowed : 18.14 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.15), residues: 3152 helix: 0.36 (0.16), residues: 1112 sheet: -2.23 (0.26), residues: 361 loop : -1.49 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 312 TYR 0.021 0.001 TYR J 140 PHE 0.012 0.001 PHE J1325 TRP 0.008 0.001 TRP I 807 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00327 (27386) covalent geometry : angle 0.59406 (37416) hydrogen bonds : bond 0.03869 ( 1024) hydrogen bonds : angle 4.79557 ( 2838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 340 time to evaluate : 1.020 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 29 GLU cc_start: 0.7599 (tp30) cc_final: 0.7049 (tt0) REVERT: G 41 ASN cc_start: 0.8819 (t0) cc_final: 0.8139 (t0) REVERT: G 75 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8231 (tm-30) REVERT: G 142 MET cc_start: 0.8120 (mtp) cc_final: 0.7585 (mtm) REVERT: H 185 TYR cc_start: 0.8766 (p90) cc_final: 0.8552 (p90) REVERT: I 84 GLU cc_start: 0.8000 (tp30) cc_final: 0.7457 (mm-30) REVERT: I 262 TYR cc_start: 0.6308 (m-80) cc_final: 0.6050 (m-10) REVERT: I 315 MET cc_start: 0.7921 (mmm) cc_final: 0.7344 (mmm) REVERT: I 492 MET cc_start: 0.9227 (pmm) cc_final: 0.9015 (pmm) REVERT: I 568 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.8930 (p0) REVERT: I 693 LEU cc_start: 0.8688 (tp) cc_final: 0.8385 (mp) REVERT: I 788 SER cc_start: 0.8915 (m) cc_final: 0.8338 (p) REVERT: I 816 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8894 (mt) REVERT: I 820 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7851 (tm-30) REVERT: I 882 ILE cc_start: 0.8537 (mp) cc_final: 0.8149 (tt) REVERT: I 1018 TYR cc_start: 0.7518 (t80) cc_final: 0.6383 (m-80) REVERT: I 1180 MET cc_start: 0.9012 (tpp) cc_final: 0.8070 (tpp) REVERT: I 1290 MET cc_start: 0.8692 (mmt) cc_final: 0.8380 (mmt) REVERT: J 157 GLN cc_start: 0.7678 (mt0) cc_final: 0.7389 (tm-30) REVERT: J 241 VAL cc_start: 0.9458 (t) cc_final: 0.9249 (m) REVERT: J 267 ASP cc_start: 0.8469 (p0) cc_final: 0.7715 (t70) REVERT: J 329 ASP cc_start: 0.8485 (m-30) cc_final: 0.8033 (m-30) REVERT: J 414 GLU cc_start: 0.8272 (tp30) cc_final: 0.8014 (tm-30) REVERT: J 415 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.9047 (p) REVERT: J 479 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7590 (tm-30) REVERT: J 534 GLU cc_start: 0.8506 (tt0) cc_final: 0.8269 (tt0) REVERT: J 581 MET cc_start: 0.8332 (mtm) cc_final: 0.7907 (mtm) REVERT: J 697 MET cc_start: 0.8861 (ttp) cc_final: 0.8651 (ttp) REVERT: J 743 MET cc_start: 0.8709 (tpp) cc_final: 0.8461 (tpp) REVERT: K 72 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8290 (tp40) REVERT: K 75 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7843 (tm-30) REVERT: K 76 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7277 (mt-10) outliers start: 96 outliers final: 56 residues processed: 411 average time/residue: 0.1684 time to fit residues: 115.8325 Evaluate side-chains 365 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 149 optimal weight: 5.9990 chunk 284 optimal weight: 0.0970 chunk 162 optimal weight: 0.5980 chunk 292 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 186 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I 965 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085987 restraints weight = 63572.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087940 restraints weight = 34485.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088786 restraints weight = 22749.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089046 restraints weight = 20777.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088902 restraints weight = 18109.228| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27386 Z= 0.128 Angle : 0.586 9.845 37416 Z= 0.300 Chirality : 0.042 0.177 4309 Planarity : 0.004 0.054 4556 Dihedral : 15.649 163.006 4677 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.41 % Allowed : 18.99 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 3152 helix: 0.43 (0.16), residues: 1125 sheet: -2.11 (0.26), residues: 362 loop : -1.43 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 312 TYR 0.028 0.001 TYR G 185 PHE 0.010 0.001 PHE I 405 TRP 0.012 0.001 TRP J 115 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00294 (27386) covalent geometry : angle 0.58612 (37416) hydrogen bonds : bond 0.03703 ( 1024) hydrogen bonds : angle 4.68546 ( 2838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 349 time to evaluate : 0.877 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: G 29 GLU cc_start: 0.7589 (tp30) cc_final: 0.7053 (tt0) REVERT: G 35 PHE cc_start: 0.7819 (m-80) cc_final: 0.7589 (m-80) REVERT: G 41 ASN cc_start: 0.8753 (t0) cc_final: 0.8096 (t0) REVERT: G 75 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8264 (tm-30) REVERT: G 142 MET cc_start: 0.8100 (mtp) cc_final: 0.7561 (mtm) REVERT: G 186 ASN cc_start: 0.8308 (m-40) cc_final: 0.7950 (m-40) REVERT: H 41 ASN cc_start: 0.7998 (t0) cc_final: 0.7606 (t0) REVERT: H 185 TYR cc_start: 0.8713 (p90) cc_final: 0.8490 (p90) REVERT: I 84 GLU cc_start: 0.7984 (tp30) cc_final: 0.7494 (mm-30) REVERT: I 262 TYR cc_start: 0.6341 (m-80) cc_final: 0.6136 (m-10) REVERT: I 563 THR cc_start: 0.9363 (m) cc_final: 0.8984 (p) REVERT: I 568 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (p0) REVERT: I 611 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8208 (tt0) REVERT: I 693 LEU cc_start: 0.8675 (tp) cc_final: 0.8423 (mp) REVERT: I 816 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8689 (mt) REVERT: I 820 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7890 (tm-30) REVERT: I 882 ILE cc_start: 0.8586 (mp) cc_final: 0.8196 (tt) REVERT: I 1018 TYR cc_start: 0.7548 (t80) cc_final: 0.6313 (m-80) REVERT: I 1085 MET cc_start: 0.8809 (mmm) cc_final: 0.8421 (mmp) REVERT: I 1180 MET cc_start: 0.8950 (tpp) cc_final: 0.8256 (tpp) REVERT: I 1274 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7619 (mm-30) REVERT: I 1290 MET cc_start: 0.8706 (mmt) cc_final: 0.8446 (mmt) REVERT: J 241 VAL cc_start: 0.9377 (t) cc_final: 0.9173 (m) REVERT: J 329 ASP cc_start: 0.8441 (m-30) cc_final: 0.7938 (m-30) REVERT: J 415 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.8995 (p) REVERT: J 460 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: J 479 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7521 (tm-30) REVERT: J 534 GLU cc_start: 0.8490 (tt0) cc_final: 0.8245 (tt0) REVERT: J 581 MET cc_start: 0.8323 (mtm) cc_final: 0.7875 (mtm) REVERT: J 697 MET cc_start: 0.8846 (ttp) cc_final: 0.8635 (ttp) REVERT: J 1317 GLU cc_start: 0.7835 (pm20) cc_final: 0.7404 (tp30) REVERT: K 28 ARG cc_start: 0.7577 (mmt90) cc_final: 0.7369 (mmt90) REVERT: K 72 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8349 (tp40) REVERT: K 75 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7940 (tm-30) outliers start: 92 outliers final: 61 residues processed: 418 average time/residue: 0.1694 time to fit residues: 117.5604 Evaluate side-chains 374 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 309 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 65 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 319 optimal weight: 40.0000 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 168 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1259 GLN ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086475 restraints weight = 63847.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088837 restraints weight = 34860.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089481 restraints weight = 21281.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089832 restraints weight = 19615.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089885 restraints weight = 17778.960| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27386 Z= 0.122 Angle : 0.587 8.855 37416 Z= 0.300 Chirality : 0.042 0.186 4309 Planarity : 0.004 0.055 4556 Dihedral : 15.604 162.993 4677 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.18 % Allowed : 19.70 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.15), residues: 3152 helix: 0.52 (0.16), residues: 1119 sheet: -1.98 (0.26), residues: 362 loop : -1.38 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 312 TYR 0.025 0.001 TYR G 185 PHE 0.019 0.001 PHE J1325 TRP 0.012 0.001 TRP J 236 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00283 (27386) covalent geometry : angle 0.58685 (37416) hydrogen bonds : bond 0.03632 ( 1024) hydrogen bonds : angle 4.62223 ( 2838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 345 time to evaluate : 1.121 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 29 GLU cc_start: 0.7622 (tp30) cc_final: 0.7076 (tt0) REVERT: G 41 ASN cc_start: 0.8775 (t0) cc_final: 0.8079 (t0) REVERT: G 75 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8280 (tm-30) REVERT: G 142 MET cc_start: 0.8209 (mtp) cc_final: 0.7674 (mtm) REVERT: G 186 ASN cc_start: 0.8349 (m-40) cc_final: 0.7990 (m-40) REVERT: H 41 ASN cc_start: 0.8105 (t0) cc_final: 0.7658 (t0) REVERT: H 185 TYR cc_start: 0.8696 (p90) cc_final: 0.8478 (p90) REVERT: I 14 ASP cc_start: 0.7702 (t0) cc_final: 0.7440 (t0) REVERT: I 84 GLU cc_start: 0.8086 (tp30) cc_final: 0.7541 (mm-30) REVERT: I 315 MET cc_start: 0.7850 (mmm) cc_final: 0.7340 (mmp) REVERT: I 563 THR cc_start: 0.9401 (m) cc_final: 0.8957 (p) REVERT: I 611 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8200 (tt0) REVERT: I 693 LEU cc_start: 0.8644 (tp) cc_final: 0.8411 (mp) REVERT: I 788 SER cc_start: 0.8925 (m) cc_final: 0.8373 (p) REVERT: I 816 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8694 (mt) REVERT: I 820 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7851 (tm-30) REVERT: I 882 ILE cc_start: 0.8604 (mp) cc_final: 0.8194 (tt) REVERT: I 1018 TYR cc_start: 0.7645 (t80) cc_final: 0.6318 (m-80) REVERT: I 1180 MET cc_start: 0.8946 (tpp) cc_final: 0.8279 (tpp) REVERT: I 1272 GLU cc_start: 0.7483 (tt0) cc_final: 0.7275 (tt0) REVERT: J 329 ASP cc_start: 0.8497 (m-30) cc_final: 0.7998 (m-30) REVERT: J 460 ASP cc_start: 0.7698 (m-30) cc_final: 0.7373 (m-30) REVERT: J 479 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7687 (tm-30) REVERT: J 534 GLU cc_start: 0.8548 (tt0) cc_final: 0.8303 (tt0) REVERT: J 581 MET cc_start: 0.8306 (mtm) cc_final: 0.7888 (mtm) REVERT: J 709 ARG cc_start: 0.6847 (tpt90) cc_final: 0.6644 (tmt-80) REVERT: J 1189 MET cc_start: 0.8635 (mmm) cc_final: 0.8313 (mmm) REVERT: J 1317 GLU cc_start: 0.7967 (pm20) cc_final: 0.7416 (tp30) REVERT: J 1325 PHE cc_start: 0.8821 (t80) cc_final: 0.8595 (t80) REVERT: J 1366 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7742 (m-70) REVERT: K 72 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8336 (tp40) REVERT: K 75 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 86 outliers final: 63 residues processed: 407 average time/residue: 0.1711 time to fit residues: 115.6967 Evaluate side-chains 382 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 317 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 49 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 193 optimal weight: 0.0040 chunk 46 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.113436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083859 restraints weight = 64353.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086269 restraints weight = 35249.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086939 restraints weight = 21621.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087152 restraints weight = 20186.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087173 restraints weight = 18228.666| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27386 Z= 0.183 Angle : 0.639 9.724 37416 Z= 0.324 Chirality : 0.043 0.232 4309 Planarity : 0.004 0.054 4556 Dihedral : 15.622 162.340 4677 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.30 % Allowed : 20.70 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 3152 helix: 0.38 (0.16), residues: 1126 sheet: -1.95 (0.26), residues: 384 loop : -1.38 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I1033 TYR 0.033 0.001 TYR I 262 PHE 0.031 0.001 PHE J1319 TRP 0.011 0.001 TRP J 580 HIS 0.006 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00424 (27386) covalent geometry : angle 0.63862 (37416) hydrogen bonds : bond 0.03858 ( 1024) hydrogen bonds : angle 4.69180 ( 2838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 319 time to evaluate : 1.116 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 29 GLU cc_start: 0.7654 (tp30) cc_final: 0.7085 (tt0) REVERT: G 41 ASN cc_start: 0.8830 (t0) cc_final: 0.8571 (t0) REVERT: G 75 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8285 (tm-30) REVERT: G 186 ASN cc_start: 0.8345 (m-40) cc_final: 0.7980 (m-40) REVERT: H 185 TYR cc_start: 0.8764 (p90) cc_final: 0.8552 (p90) REVERT: I 84 GLU cc_start: 0.8138 (tp30) cc_final: 0.7688 (mm-30) REVERT: I 315 MET cc_start: 0.7876 (mmm) cc_final: 0.7284 (mmm) REVERT: I 568 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8875 (p0) REVERT: I 693 LEU cc_start: 0.8720 (tp) cc_final: 0.8410 (mp) REVERT: I 788 SER cc_start: 0.9038 (m) cc_final: 0.8503 (p) REVERT: I 816 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8945 (mt) REVERT: I 820 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7925 (tm-30) REVERT: I 882 ILE cc_start: 0.8693 (mp) cc_final: 0.8257 (tt) REVERT: I 965 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7893 (pt0) REVERT: I 1018 TYR cc_start: 0.7682 (t80) cc_final: 0.6330 (m-80) REVERT: I 1180 MET cc_start: 0.8900 (tpp) cc_final: 0.8559 (tpp) REVERT: J 329 ASP cc_start: 0.8569 (m-30) cc_final: 0.8088 (m-30) REVERT: J 460 ASP cc_start: 0.7998 (m-30) cc_final: 0.7569 (m-30) REVERT: J 534 GLU cc_start: 0.8600 (tt0) cc_final: 0.8260 (tt0) REVERT: J 697 MET cc_start: 0.8905 (ttp) cc_final: 0.8645 (ttp) REVERT: J 709 ARG cc_start: 0.6911 (tpt90) cc_final: 0.6681 (tmt-80) REVERT: J 1098 GLN cc_start: 0.6369 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: J 1189 MET cc_start: 0.8636 (mmm) cc_final: 0.8345 (mmm) REVERT: J 1317 GLU cc_start: 0.7958 (pm20) cc_final: 0.7476 (tp30) REVERT: J 1366 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7886 (m-70) REVERT: K 11 GLU cc_start: 0.7940 (pm20) cc_final: 0.7263 (pm20) outliers start: 89 outliers final: 65 residues processed: 386 average time/residue: 0.1647 time to fit residues: 106.4964 Evaluate side-chains 369 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 300 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 218 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 519 ASN I 568 ASN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085353 restraints weight = 64236.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087327 restraints weight = 35303.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089048 restraints weight = 22296.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088967 restraints weight = 19566.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088939 restraints weight = 17536.665| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27386 Z= 0.138 Angle : 0.627 10.061 37416 Z= 0.317 Chirality : 0.042 0.203 4309 Planarity : 0.004 0.054 4556 Dihedral : 15.560 162.150 4677 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.48 % Allowed : 21.51 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 3152 helix: 0.37 (0.16), residues: 1124 sheet: -1.94 (0.25), residues: 392 loop : -1.34 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I1033 TYR 0.028 0.001 TYR H 177 PHE 0.027 0.001 PHE J1319 TRP 0.017 0.001 TRP J 115 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00322 (27386) covalent geometry : angle 0.62704 (37416) hydrogen bonds : bond 0.03720 ( 1024) hydrogen bonds : angle 4.65182 ( 2838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 332 time to evaluate : 1.090 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 29 GLU cc_start: 0.7634 (tp30) cc_final: 0.7055 (tt0) REVERT: G 41 ASN cc_start: 0.8778 (t0) cc_final: 0.8539 (t0) REVERT: G 75 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8277 (tm-30) REVERT: G 142 MET cc_start: 0.8239 (mtp) cc_final: 0.7854 (mtm) REVERT: G 186 ASN cc_start: 0.8381 (m-40) cc_final: 0.7989 (m-40) REVERT: H 17 GLU cc_start: 0.8561 (pp20) cc_final: 0.8223 (pp20) REVERT: I 84 GLU cc_start: 0.8196 (tp30) cc_final: 0.7669 (mm-30) REVERT: I 262 TYR cc_start: 0.6167 (m-10) cc_final: 0.5945 (m-80) REVERT: I 315 MET cc_start: 0.7894 (mmm) cc_final: 0.7388 (mmp) REVERT: I 370 MET cc_start: 0.8531 (mmm) cc_final: 0.8217 (mmm) REVERT: I 519 ASN cc_start: 0.8330 (m-40) cc_final: 0.8078 (m110) REVERT: I 568 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8389 (p0) REVERT: I 693 LEU cc_start: 0.8662 (tp) cc_final: 0.8422 (mp) REVERT: I 788 SER cc_start: 0.8816 (m) cc_final: 0.8435 (p) REVERT: I 816 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8723 (mt) REVERT: I 820 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7893 (tm-30) REVERT: I 882 ILE cc_start: 0.8672 (mp) cc_final: 0.8222 (tt) REVERT: I 965 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7868 (pt0) REVERT: I 1018 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: I 1180 MET cc_start: 0.8879 (tpp) cc_final: 0.8551 (tpp) REVERT: J 329 ASP cc_start: 0.8518 (m-30) cc_final: 0.8018 (m-30) REVERT: J 460 ASP cc_start: 0.7993 (m-30) cc_final: 0.7738 (m-30) REVERT: J 473 THR cc_start: 0.8307 (p) cc_final: 0.7952 (p) REVERT: J 534 GLU cc_start: 0.8613 (tt0) cc_final: 0.8277 (tt0) REVERT: J 623 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7889 (mm-40) REVERT: J 1098 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: J 1189 MET cc_start: 0.8665 (mmm) cc_final: 0.8396 (mmm) REVERT: J 1317 GLU cc_start: 0.7991 (pm20) cc_final: 0.7449 (tp30) REVERT: J 1366 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7841 (m-70) REVERT: K 11 GLU cc_start: 0.7980 (pm20) cc_final: 0.7346 (pm20) REVERT: K 72 GLN cc_start: 0.8538 (tp40) cc_final: 0.8275 (tp40) outliers start: 67 outliers final: 58 residues processed: 381 average time/residue: 0.1723 time to fit residues: 109.0824 Evaluate side-chains 372 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 188 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 287 optimal weight: 0.0050 chunk 42 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 150 HIS ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085242 restraints weight = 64209.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088404 restraints weight = 34720.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088786 restraints weight = 20466.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089328 restraints weight = 18544.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089401 restraints weight = 16687.141| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27386 Z= 0.135 Angle : 0.627 9.182 37416 Z= 0.317 Chirality : 0.042 0.189 4309 Planarity : 0.004 0.059 4556 Dihedral : 15.512 162.171 4677 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.48 % Allowed : 21.84 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.15), residues: 3152 helix: 0.34 (0.16), residues: 1125 sheet: -1.84 (0.26), residues: 379 loop : -1.32 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I1033 TYR 0.039 0.001 TYR H 185 PHE 0.026 0.001 PHE J1319 TRP 0.016 0.001 TRP J 115 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00316 (27386) covalent geometry : angle 0.62707 (37416) hydrogen bonds : bond 0.03681 ( 1024) hydrogen bonds : angle 4.63065 ( 2838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 320 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7613 (tp30) cc_final: 0.7034 (tt0) REVERT: G 41 ASN cc_start: 0.8788 (t0) cc_final: 0.8543 (t0) REVERT: G 75 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8246 (tm-30) REVERT: G 142 MET cc_start: 0.8227 (mtp) cc_final: 0.7822 (mtm) REVERT: G 186 ASN cc_start: 0.8384 (m-40) cc_final: 0.8009 (m-40) REVERT: H 17 GLU cc_start: 0.8611 (pp20) cc_final: 0.8189 (pp20) REVERT: I 84 GLU cc_start: 0.8148 (tp30) cc_final: 0.7633 (mm-30) REVERT: I 291 TYR cc_start: 0.7886 (t80) cc_final: 0.7662 (t80) REVERT: I 315 MET cc_start: 0.7901 (mmm) cc_final: 0.7384 (mmp) REVERT: I 519 ASN cc_start: 0.8442 (m-40) cc_final: 0.8240 (m-40) REVERT: I 693 LEU cc_start: 0.8670 (tp) cc_final: 0.8401 (mp) REVERT: I 788 SER cc_start: 0.8910 (m) cc_final: 0.8440 (p) REVERT: I 816 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8755 (mt) REVERT: I 820 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7879 (tm-30) REVERT: I 882 ILE cc_start: 0.8646 (mp) cc_final: 0.8188 (tt) REVERT: I 965 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7877 (pt0) REVERT: I 1018 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: I 1180 MET cc_start: 0.8871 (tpp) cc_final: 0.8468 (tpp) REVERT: J 329 ASP cc_start: 0.8504 (m-30) cc_final: 0.8003 (m-30) REVERT: J 460 ASP cc_start: 0.8143 (m-30) cc_final: 0.7897 (m-30) REVERT: J 473 THR cc_start: 0.8356 (p) cc_final: 0.7888 (p) REVERT: J 534 GLU cc_start: 0.8550 (tt0) cc_final: 0.8211 (tt0) REVERT: J 623 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7781 (mm-40) REVERT: J 1098 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: J 1189 MET cc_start: 0.8624 (mmm) cc_final: 0.8358 (mmm) REVERT: J 1317 GLU cc_start: 0.7978 (pm20) cc_final: 0.7441 (tp30) REVERT: J 1366 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7804 (m-70) REVERT: K 11 GLU cc_start: 0.7906 (pm20) cc_final: 0.7298 (pm20) outliers start: 67 outliers final: 61 residues processed: 369 average time/residue: 0.1652 time to fit residues: 102.4741 Evaluate side-chains 376 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 311 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1018 TYR Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 275 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 320 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 315 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 594 GLN ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.083119 restraints weight = 64306.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085661 restraints weight = 35534.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085981 restraints weight = 21602.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086423 restraints weight = 20749.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086432 restraints weight = 18603.601| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27386 Z= 0.196 Angle : 0.661 9.282 37416 Z= 0.335 Chirality : 0.043 0.194 4309 Planarity : 0.004 0.066 4556 Dihedral : 15.566 161.334 4677 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.74 % Allowed : 21.81 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3152 helix: 0.26 (0.16), residues: 1119 sheet: -2.00 (0.25), residues: 395 loop : -1.31 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1033 TYR 0.032 0.002 TYR H 185 PHE 0.026 0.002 PHE J1325 TRP 0.014 0.001 TRP J 115 HIS 0.005 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00452 (27386) covalent geometry : angle 0.66086 (37416) hydrogen bonds : bond 0.03940 ( 1024) hydrogen bonds : angle 4.73187 ( 2838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4642.38 seconds wall clock time: 81 minutes 38.45 seconds (4898.45 seconds total)