Starting phenix.real_space_refine on Mon Jun 23 08:45:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g1s_29676/06_2025/8g1s_29676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g1s_29676/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g1s_29676/06_2025/8g1s_29676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g1s_29676/06_2025/8g1s_29676.map" model { file = "/net/cci-nas-00/data/ceres_data/8g1s_29676/06_2025/8g1s_29676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g1s_29676/06_2025/8g1s_29676.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.67s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.10, per 1000 atoms: 0.56 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: 7.15 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 10.75 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: 14.94 Time building geometry restraints manager: 8.34 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 73.490 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.110 ------------------------------------------------------------------------------- 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 : 17.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 TRP 0.012 0.001 TRP J 580 HIS 0.003 0.001 HIS G 23 PHE 0.012 0.001 PHE J 260 TYR 0.013 0.001 TYR I1281 ARG 0.005 0.001 ARG J 101 Details of bonding type rmsd hydrogen bonds : bond 0.18961 ( 1024) hydrogen bonds : angle 7.06155 ( 2838) covalent geometry : bond 0.00286 (27386) covalent geometry : angle 0.57896 (37416) *********************** 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 : 2.823 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: 0.6340 time to fit residues: 567.0502 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 : 3.751 ------------------------------------------------------------------------------- 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 271 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 343 HIS I 462 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN ** J1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083752 restraints weight = 63654.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086020 restraints weight = 34488.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087535 restraints weight = 23465.212| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27386 Z= 0.164 Angle : 0.632 9.388 37416 Z= 0.329 Chirality : 0.043 0.185 4309 Planarity : 0.005 0.050 4556 Dihedral : 15.886 169.580 4682 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 2.92 % Allowed : 13.99 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 3152 helix: -0.02 (0.16), residues: 1108 sheet: -2.44 (0.25), residues: 378 loop : -1.71 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 580 HIS 0.009 0.001 HIS I 343 PHE 0.015 0.002 PHE I 253 TYR 0.025 0.002 TYR G 185 ARG 0.006 0.001 ARG I1106 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 1024) hydrogen bonds : angle 5.38852 ( 2838) covalent geometry : bond 0.00375 (27386) covalent geometry : angle 0.63241 (37416) *********************** 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 460 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 381 time to evaluate : 3.052 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: 0.8762 (t0) cc_final: 0.8325 (t0) REVERT: G 75 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8417 (tm-30) REVERT: G 142 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: H 100 LEU cc_start: 0.8938 (mp) cc_final: 0.8728 (mt) REVERT: H 185 TYR cc_start: 0.8802 (p90) cc_final: 0.8417 (p90) REVERT: I 84 GLU cc_start: 0.8139 (tp30) cc_final: 0.7559 (mm-30) REVERT: I 163 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8191 (tppt) REVERT: I 504 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7716 (tm-30) REVERT: I 562 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8464 (tp30) REVERT: I 611 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8269 (tt0) REVERT: I 788 SER cc_start: 0.8957 (m) cc_final: 0.8369 (p) REVERT: I 820 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7818 (tm-30) REVERT: I 1018 TYR cc_start: 0.7178 (t80) cc_final: 0.6370 (m-80) REVERT: I 1098 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8819 (mm) REVERT: I 1141 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9046 (tt) REVERT: I 1180 MET cc_start: 0.8972 (tpp) cc_final: 0.8335 (tpp) REVERT: I 1274 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7528 (mm-30) REVERT: I 1290 MET cc_start: 0.8633 (mmt) cc_final: 0.8424 (mmt) REVERT: I 1304 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8112 (ttm) REVERT: J 157 GLN cc_start: 0.7528 (mt0) cc_final: 0.7214 (pp30) REVERT: J 329 ASP cc_start: 0.8531 (m-30) cc_final: 0.8137 (m-30) REVERT: J 698 MET cc_start: 0.9076 (mmm) cc_final: 0.8803 (tpp) REVERT: J 709 ARG cc_start: 0.6862 (tpt90) cc_final: 0.6633 (tmt-80) REVERT: J 833 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6537 (mt-10) REVERT: J 1121 LEU cc_start: 0.8710 (tp) cc_final: 0.8368 (mp) REVERT: J 1317 GLU cc_start: 0.7784 (pm20) cc_final: 0.7341 (tm-30) REVERT: K 63 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9116 (mm) outliers start: 79 outliers final: 33 residues processed: 432 average time/residue: 0.3734 time to fit residues: 262.5734 Evaluate side-chains 346 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 2.716 ------------------------------------------------------------------------------- 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 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 54 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 176 ILE 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 1295 SER 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 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 171 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 275 optimal weight: 30.0000 chunk 167 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** ** J 736 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 = 0.3710 r_free = 0.3710 target = 0.111344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080424 restraints weight = 62998.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.082776 restraints weight = 32830.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084275 restraints weight = 21802.893| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2439 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= 0.218 Angle : 0.640 10.170 37416 Z= 0.332 Chirality : 0.044 0.172 4309 Planarity : 0.005 0.060 4556 Dihedral : 15.970 169.198 4682 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.86 % Rotamer: Outliers : 3.52 % Allowed : 16.14 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 3152 helix: 0.01 (0.16), residues: 1117 sheet: -2.41 (0.26), residues: 363 loop : -1.73 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 807 HIS 0.006 0.001 HIS J 364 PHE 0.016 0.002 PHE J 620 TYR 0.019 0.002 TYR I1281 ARG 0.004 0.000 ARG I 529 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 1024) hydrogen bonds : angle 5.17565 ( 2838) covalent geometry : bond 0.00500 (27386) covalent geometry : angle 0.63956 (37416) *********************** 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 435 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 340 time to evaluate : 3.044 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: 0.7723 (tp30) cc_final: 0.7145 (tt0) REVERT: G 35 PHE cc_start: 0.8088 (m-80) cc_final: 0.7813 (m-80) REVERT: G 41 ASN cc_start: 0.8827 (t0) cc_final: 0.8430 (t0) REVERT: G 75 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8335 (tm-30) REVERT: G 142 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: H 185 TYR cc_start: 0.8875 (p90) cc_final: 0.8567 (p90) REVERT: I 84 GLU cc_start: 0.8426 (tp30) cc_final: 0.7769 (mm-30) REVERT: I 562 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8490 (tp30) REVERT: I 611 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8338 (tt0) REVERT: I 644 LEU cc_start: 0.8702 (mp) cc_final: 0.8494 (tp) REVERT: I 788 SER cc_start: 0.9021 (m) cc_final: 0.8512 (p) REVERT: I 820 GLU cc_start: 0.8640 (tm-30) cc_final: 0.7979 (tm-30) REVERT: I 882 ILE cc_start: 0.8553 (mp) cc_final: 0.8049 (tt) REVERT: I 1018 TYR cc_start: 0.7525 (t80) cc_final: 0.6444 (m-80) REVERT: I 1073 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8847 (pttp) REVERT: I 1180 MET cc_start: 0.9079 (tpp) cc_final: 0.8423 (tpp) REVERT: I 1274 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7753 (mm-30) REVERT: I 1281 TYR cc_start: 0.8228 (m-80) cc_final: 0.7967 (m-10) REVERT: J 157 GLN cc_start: 0.7760 (mt0) cc_final: 0.7475 (tm-30) REVERT: J 197 GLU cc_start: 0.8539 (tp30) cc_final: 0.8330 (tp30) REVERT: J 267 ASP cc_start: 0.8674 (p0) cc_final: 0.8054 (t70) REVERT: J 298 MET cc_start: 0.8760 (ptt) cc_final: 0.8552 (ptp) REVERT: J 301 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7684 (mm-30) REVERT: J 329 ASP cc_start: 0.8657 (m-30) cc_final: 0.8165 (m-30) REVERT: J 698 MET cc_start: 0.9193 (mmm) cc_final: 0.8855 (tpp) REVERT: J 1121 LEU cc_start: 0.8704 (tp) cc_final: 0.8504 (tp) REVERT: K 8 ASP cc_start: 0.8473 (p0) cc_final: 0.7545 (p0) REVERT: K 55 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7591 (mt-10) REVERT: K 72 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8361 (tp40) outliers start: 95 outliers final: 47 residues processed: 412 average time/residue: 0.3785 time to fit residues: 256.0472 Evaluate side-chains 354 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 2.947 ------------------------------------------------------------------------------- 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 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 1073 LYS 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 145 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 43 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 272 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 215 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 343 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 526 HIS I 568 ASN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1314 GLN J 364 HIS ** J 736 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.114972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085300 restraints weight = 64086.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087933 restraints weight = 34849.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088503 restraints weight = 20860.354| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27386 Z= 0.125 Angle : 0.582 8.231 37416 Z= 0.302 Chirality : 0.042 0.165 4309 Planarity : 0.004 0.054 4556 Dihedral : 15.810 165.013 4677 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.00 % Allowed : 17.36 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3152 helix: 0.32 (0.16), residues: 1108 sheet: -2.24 (0.27), residues: 343 loop : -1.55 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 807 HIS 0.008 0.001 HIS I 343 PHE 0.017 0.001 PHE I 337 TYR 0.024 0.001 TYR G 185 ARG 0.009 0.000 ARG J 312 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 1024) hydrogen bonds : angle 4.85670 ( 2838) covalent geometry : bond 0.00286 (27386) covalent geometry : angle 0.58198 (37416) *********************** 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 451 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 370 time to evaluate : 2.649 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: 0.7608 (tp30) cc_final: 0.7073 (tt0) REVERT: G 41 ASN cc_start: 0.8746 (t0) cc_final: 0.8417 (t0) REVERT: G 75 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 194 GLN cc_start: 0.7749 (pm20) cc_final: 0.7510 (pm20) REVERT: H 41 ASN cc_start: 0.8106 (t0) cc_final: 0.7740 (t0) REVERT: H 185 TYR cc_start: 0.8769 (p90) cc_final: 0.8492 (p90) REVERT: I 14 ASP cc_start: 0.7909 (t0) cc_final: 0.7708 (t0) REVERT: I 84 GLU cc_start: 0.8100 (tp30) cc_final: 0.7522 (mm-30) REVERT: I 262 TYR cc_start: 0.6384 (m-10) cc_final: 0.6152 (m-10) REVERT: I 315 MET cc_start: 0.8020 (mmm) cc_final: 0.7445 (mmm) REVERT: I 395 TYR cc_start: 0.7823 (t80) cc_final: 0.7588 (t80) REVERT: I 492 MET cc_start: 0.9204 (pmm) cc_final: 0.9004 (pmm) REVERT: I 504 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7770 (tm-30) REVERT: I 568 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8868 (p0) REVERT: I 693 LEU cc_start: 0.8683 (tp) cc_final: 0.8380 (mp) REVERT: I 820 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7882 (tm-30) REVERT: I 882 ILE cc_start: 0.8580 (mp) cc_final: 0.8165 (tt) REVERT: I 1018 TYR cc_start: 0.7491 (t80) cc_final: 0.6389 (m-80) REVERT: I 1098 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8654 (mm) REVERT: I 1180 MET cc_start: 0.8999 (tpp) cc_final: 0.8047 (tpp) REVERT: I 1290 MET cc_start: 0.8709 (mmt) cc_final: 0.8484 (mmt) REVERT: J 267 ASP cc_start: 0.8592 (p0) cc_final: 0.7906 (t70) REVERT: J 298 MET cc_start: 0.8670 (ptt) cc_final: 0.8402 (ptp) REVERT: J 329 ASP cc_start: 0.8555 (m-30) cc_final: 0.8022 (m-30) REVERT: J 414 GLU cc_start: 0.8281 (tp30) cc_final: 0.7997 (tm-30) REVERT: J 534 GLU cc_start: 0.8552 (tt0) cc_final: 0.8334 (tt0) REVERT: J 581 MET cc_start: 0.8346 (mtm) cc_final: 0.7856 (mtm) REVERT: J 697 MET cc_start: 0.8887 (ttp) cc_final: 0.8678 (ttp) REVERT: J 743 MET cc_start: 0.8735 (tpp) cc_final: 0.8529 (tpp) REVERT: J 1121 LEU cc_start: 0.8659 (tp) cc_final: 0.8305 (mp) REVERT: J 1189 MET cc_start: 0.8517 (mmm) cc_final: 0.8268 (mmm) REVERT: J 1317 GLU cc_start: 0.7832 (pm20) cc_final: 0.7381 (tp30) REVERT: K 11 GLU cc_start: 0.7896 (pm20) cc_final: 0.7454 (pm20) REVERT: K 72 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8338 (tp40) REVERT: K 75 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7880 (tm-30) REVERT: K 76 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7418 (mt-10) outliers start: 81 outliers final: 44 residues processed: 430 average time/residue: 0.3575 time to fit residues: 252.2627 Evaluate side-chains 356 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 205 MET 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 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 282 VAL Chi-restraints excluded: chain I residue 287 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 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 1097 VAL Chi-restraints excluded: chain I residue 1098 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 1295 SER Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 356 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 251 optimal weight: 0.5980 chunk 237 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 736 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.115590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085745 restraints weight = 63759.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088509 restraints weight = 35139.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088866 restraints weight = 21668.421| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3107 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= 0.122 Angle : 0.590 13.026 37416 Z= 0.302 Chirality : 0.042 0.201 4309 Planarity : 0.004 0.057 4556 Dihedral : 15.734 163.445 4677 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.04 % Allowed : 19.03 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 3152 helix: 0.39 (0.16), residues: 1114 sheet: -2.13 (0.27), residues: 342 loop : -1.51 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 115 HIS 0.004 0.001 HIS I 330 PHE 0.025 0.001 PHE J1319 TYR 0.027 0.001 TYR J 140 ARG 0.008 0.000 ARG I1033 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1024) hydrogen bonds : angle 4.72802 ( 2838) covalent geometry : bond 0.00280 (27386) covalent geometry : angle 0.59015 (37416) *********************** 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 444 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 362 time to evaluate : 2.868 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: 0.7614 (tp30) cc_final: 0.7058 (tt0) REVERT: G 41 ASN cc_start: 0.8759 (t0) cc_final: 0.8114 (t0) REVERT: G 75 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8295 (tm-30) REVERT: G 142 MET cc_start: 0.8101 (mtp) cc_final: 0.7649 (mtm) REVERT: H 17 GLU cc_start: 0.8146 (pp20) cc_final: 0.7909 (pp20) REVERT: H 41 ASN cc_start: 0.7984 (t0) cc_final: 0.7592 (t0) REVERT: H 185 TYR cc_start: 0.8713 (p90) cc_final: 0.8450 (p90) REVERT: I 84 GLU cc_start: 0.7972 (tp30) cc_final: 0.7428 (mm-30) REVERT: I 262 TYR cc_start: 0.6341 (m-10) cc_final: 0.5876 (m-10) REVERT: I 523 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6856 (mm-30) REVERT: I 563 THR cc_start: 0.9347 (m) cc_final: 0.8974 (p) REVERT: I 568 ASN cc_start: 0.8887 (p0) cc_final: 0.8552 (p0) REVERT: I 693 LEU cc_start: 0.8617 (tp) cc_final: 0.8351 (mp) REVERT: I 820 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7815 (tm-30) REVERT: I 882 ILE cc_start: 0.8601 (mp) cc_final: 0.8211 (tt) REVERT: I 1018 TYR cc_start: 0.7467 (t80) cc_final: 0.6387 (m-80) REVERT: I 1073 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7999 (pttp) REVERT: I 1290 MET cc_start: 0.8605 (mmt) cc_final: 0.8358 (mmt) REVERT: J 241 VAL cc_start: 0.9458 (t) cc_final: 0.9236 (m) REVERT: J 329 ASP cc_start: 0.8420 (m-30) cc_final: 0.7922 (m-30) REVERT: J 415 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.8980 (p) REVERT: J 462 ASP cc_start: 0.9154 (p0) cc_final: 0.8749 (p0) REVERT: J 466 MET cc_start: 0.8239 (ptm) cc_final: 0.7963 (ptm) REVERT: J 473 THR cc_start: 0.8717 (p) cc_final: 0.8503 (p) REVERT: J 479 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7661 (tm-30) REVERT: J 534 GLU cc_start: 0.8522 (tt0) cc_final: 0.8304 (tt0) REVERT: J 581 MET cc_start: 0.8263 (mtm) cc_final: 0.7819 (mtm) REVERT: J 697 MET cc_start: 0.8860 (ttp) cc_final: 0.8640 (ttp) REVERT: J 1121 LEU cc_start: 0.8684 (tp) cc_final: 0.8324 (mp) REVERT: J 1175 LEU cc_start: 0.8989 (tp) cc_final: 0.8785 (tt) REVERT: J 1189 MET cc_start: 0.8439 (mmm) cc_final: 0.8204 (mmm) REVERT: J 1317 GLU cc_start: 0.7846 (pm20) cc_final: 0.7354 (tp30) REVERT: K 11 GLU cc_start: 0.7734 (pm20) cc_final: 0.7262 (pm20) REVERT: K 28 ARG cc_start: 0.7628 (mmt90) cc_final: 0.7409 (mmt90) REVERT: K 72 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8329 (tp40) REVERT: K 75 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7970 (tm-30) REVERT: K 76 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7451 (mt-10) outliers start: 82 outliers final: 55 residues processed: 422 average time/residue: 0.4287 time to fit residues: 298.6994 Evaluate side-chains 376 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 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 H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR 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 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 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 1073 LYS 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 166 LEU Chi-restraints excluded: chain J residue 201 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 356 THR 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 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 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 3 optimal weight: 10.0000 chunk 279 optimal weight: 0.0000 chunk 126 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 201 optimal weight: 0.0570 chunk 263 optimal weight: 0.5980 chunk 206 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.116898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086565 restraints weight = 63998.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089001 restraints weight = 33263.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090601 restraints weight = 21952.208| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3412 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= 0.116 Angle : 0.589 9.308 37416 Z= 0.302 Chirality : 0.041 0.166 4309 Planarity : 0.004 0.054 4556 Dihedral : 15.659 163.476 4677 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.00 % Allowed : 19.73 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3152 helix: 0.46 (0.16), residues: 1114 sheet: -1.98 (0.27), residues: 356 loop : -1.41 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP J 115 HIS 0.004 0.001 HIS J 113 PHE 0.014 0.001 PHE J1325 TYR 0.029 0.001 TYR J 140 ARG 0.008 0.000 ARG I1033 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 1024) hydrogen bonds : angle 4.62932 ( 2838) covalent geometry : bond 0.00267 (27386) covalent geometry : angle 0.58864 (37416) *********************** 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 439 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 358 time to evaluate : 2.723 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: 0.7696 (tp30) cc_final: 0.7132 (tt0) REVERT: G 41 ASN cc_start: 0.8732 (t0) cc_final: 0.8119 (t0) REVERT: G 75 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8315 (tm-30) REVERT: G 142 MET cc_start: 0.8228 (mtp) cc_final: 0.7792 (mtm) REVERT: G 186 ASN cc_start: 0.8388 (m-40) cc_final: 0.7984 (m-40) REVERT: H 17 GLU cc_start: 0.8381 (pp20) cc_final: 0.8097 (pp20) REVERT: H 41 ASN cc_start: 0.8111 (t0) cc_final: 0.7723 (t0) REVERT: H 51 MET cc_start: 0.8585 (mpp) cc_final: 0.8222 (mpp) REVERT: H 177 TYR cc_start: 0.7724 (m-10) cc_final: 0.6822 (m-10) REVERT: H 185 TYR cc_start: 0.8685 (p90) cc_final: 0.8447 (p90) REVERT: I 14 ASP cc_start: 0.7827 (t0) cc_final: 0.7536 (t0) REVERT: I 84 GLU cc_start: 0.8218 (tp30) cc_final: 0.7544 (mm-30) REVERT: I 262 TYR cc_start: 0.6201 (m-10) cc_final: 0.5858 (m-10) REVERT: I 315 MET cc_start: 0.7891 (mmm) cc_final: 0.7360 (mmp) REVERT: I 563 THR cc_start: 0.9377 (m) cc_final: 0.8958 (p) REVERT: I 568 ASN cc_start: 0.8959 (p0) cc_final: 0.8713 (p0) REVERT: I 693 LEU cc_start: 0.8600 (tp) cc_final: 0.8365 (mp) REVERT: I 816 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8601 (mt) REVERT: I 820 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8010 (tm-30) REVERT: I 882 ILE cc_start: 0.8603 (mp) cc_final: 0.8201 (tt) REVERT: I 1018 TYR cc_start: 0.7539 (t80) cc_final: 0.6412 (m-80) REVERT: I 1180 MET cc_start: 0.8969 (tpp) cc_final: 0.8268 (tpp) REVERT: I 1274 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7415 (mm-30) REVERT: I 1290 MET cc_start: 0.8777 (mmt) cc_final: 0.8464 (mmt) REVERT: J 241 VAL cc_start: 0.9438 (t) cc_final: 0.9234 (m) REVERT: J 329 ASP cc_start: 0.8543 (m-30) cc_final: 0.7956 (m-30) REVERT: J 466 MET cc_start: 0.8339 (ptm) cc_final: 0.8014 (ptm) REVERT: J 479 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7759 (tm-30) REVERT: J 534 GLU cc_start: 0.8609 (tt0) cc_final: 0.8406 (tt0) REVERT: J 581 MET cc_start: 0.8264 (mtm) cc_final: 0.7832 (mtm) REVERT: J 1121 LEU cc_start: 0.8722 (tp) cc_final: 0.8346 (mp) REVERT: J 1175 LEU cc_start: 0.8989 (tp) cc_final: 0.8748 (tt) REVERT: J 1189 MET cc_start: 0.8485 (mmm) cc_final: 0.8250 (mmm) REVERT: J 1317 GLU cc_start: 0.7910 (pm20) cc_final: 0.7322 (tp30) outliers start: 81 outliers final: 46 residues processed: 421 average time/residue: 0.3455 time to fit residues: 241.4966 Evaluate side-chains 368 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU 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 217 ILE 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 458 GLU 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 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 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 166 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 202 optimal weight: 0.1980 chunk 148 optimal weight: 0.0170 chunk 283 optimal weight: 5.9990 overall best weight: 1.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN I 808 ASN I 965 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 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 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.115601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085612 restraints weight = 63978.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088281 restraints weight = 34729.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089047 restraints weight = 20732.310| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27386 Z= 0.137 Angle : 0.602 8.788 37416 Z= 0.308 Chirality : 0.042 0.200 4309 Planarity : 0.004 0.055 4556 Dihedral : 15.613 163.104 4677 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.11 % Allowed : 20.03 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3152 helix: 0.43 (0.16), residues: 1110 sheet: -1.91 (0.27), residues: 366 loop : -1.38 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 115 HIS 0.006 0.001 HIS J 113 PHE 0.014 0.001 PHE G 35 TYR 0.024 0.001 TYR J 140 ARG 0.010 0.000 ARG J 731 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1024) hydrogen bonds : angle 4.61637 ( 2838) covalent geometry : bond 0.00317 (27386) covalent geometry : angle 0.60210 (37416) *********************** 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 427 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 343 time to evaluate : 2.816 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: 0.7730 (tp30) cc_final: 0.7203 (tt0) REVERT: G 41 ASN cc_start: 0.8795 (t0) cc_final: 0.8129 (t0) REVERT: G 75 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 142 MET cc_start: 0.8194 (mtp) cc_final: 0.7753 (mtm) REVERT: G 186 ASN cc_start: 0.8408 (m-40) cc_final: 0.8010 (m-40) REVERT: H 17 GLU cc_start: 0.8490 (pp20) cc_final: 0.8163 (pp20) REVERT: H 147 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7803 (pp30) REVERT: H 185 TYR cc_start: 0.8717 (p90) cc_final: 0.8472 (p90) REVERT: I 84 GLU cc_start: 0.8113 (tp30) cc_final: 0.7557 (mm-30) REVERT: I 262 TYR cc_start: 0.6164 (m-10) cc_final: 0.5853 (m-10) REVERT: I 315 MET cc_start: 0.7908 (mmm) cc_final: 0.7392 (mmp) REVERT: I 464 PHE cc_start: 0.9143 (t80) cc_final: 0.8936 (t80) REVERT: I 563 THR cc_start: 0.9385 (m) cc_final: 0.8985 (p) REVERT: I 693 LEU cc_start: 0.8664 (tp) cc_final: 0.8404 (mp) REVERT: I 768 MET cc_start: 0.8063 (mmm) cc_final: 0.7795 (mmt) REVERT: I 788 SER cc_start: 0.8978 (m) cc_final: 0.8422 (p) REVERT: I 816 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8821 (mt) REVERT: I 820 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7863 (tm-30) REVERT: I 882 ILE cc_start: 0.8638 (mp) cc_final: 0.8220 (tt) REVERT: I 1018 TYR cc_start: 0.7625 (t80) cc_final: 0.6310 (m-80) REVERT: I 1180 MET cc_start: 0.8893 (tpp) cc_final: 0.8513 (tpp) REVERT: J 241 VAL cc_start: 0.9379 (t) cc_final: 0.9175 (m) REVERT: J 329 ASP cc_start: 0.8493 (m-30) cc_final: 0.8008 (m-30) REVERT: J 466 MET cc_start: 0.8425 (ptm) cc_final: 0.8061 (ptm) REVERT: J 473 THR cc_start: 0.8781 (p) cc_final: 0.8559 (p) REVERT: J 479 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7818 (tm-30) REVERT: J 534 GLU cc_start: 0.8569 (tt0) cc_final: 0.8261 (tt0) REVERT: J 697 MET cc_start: 0.8889 (ttp) cc_final: 0.8657 (ttp) REVERT: J 1098 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.6063 (pm20) REVERT: J 1121 LEU cc_start: 0.8688 (tp) cc_final: 0.8328 (mp) REVERT: J 1175 LEU cc_start: 0.8931 (tp) cc_final: 0.8703 (tt) REVERT: J 1189 MET cc_start: 0.8611 (mmm) cc_final: 0.8372 (mmm) REVERT: J 1306 LEU cc_start: 0.8954 (tp) cc_final: 0.8699 (tt) REVERT: J 1317 GLU cc_start: 0.7798 (pm20) cc_final: 0.7309 (tp30) REVERT: J 1366 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7790 (m-70) REVERT: K 11 GLU cc_start: 0.7679 (pm20) cc_final: 0.7025 (pm20) REVERT: K 12 LYS cc_start: 0.7346 (ptpt) cc_final: 0.7061 (ptpt) outliers start: 84 outliers final: 54 residues processed: 408 average time/residue: 0.3522 time to fit residues: 238.7583 Evaluate side-chains 369 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 3.146 ------------------------------------------------------------------------------- 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 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 147 GLN 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 369 MET 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 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.57 > 50: distance: 31 - 48: 22.223 distance: 35 - 57: 19.824 distance: 42 - 48: 22.278 distance: 48 - 49: 7.649 distance: 49 - 50: 17.496 distance: 49 - 52: 24.908 distance: 50 - 51: 17.875 distance: 50 - 57: 9.468 distance: 52 - 53: 26.045 distance: 53 - 54: 33.780 distance: 54 - 55: 9.317 distance: 54 - 56: 15.520 distance: 57 - 58: 7.535 distance: 58 - 59: 22.507 distance: 58 - 61: 7.448 distance: 59 - 60: 17.421 distance: 59 - 64: 9.909 distance: 61 - 62: 43.342 distance: 61 - 63: 29.006 distance: 64 - 65: 40.560 distance: 65 - 66: 6.744 distance: 66 - 67: 25.653 distance: 66 - 68: 57.609 distance: 68 - 69: 48.048 distance: 69 - 70: 38.948 distance: 70 - 71: 17.576 distance: 70 - 72: 47.878 distance: 72 - 73: 12.463 distance: 73 - 74: 7.471 distance: 73 - 76: 20.969 distance: 74 - 75: 7.781 distance: 74 - 81: 58.804 distance: 76 - 77: 10.597 distance: 77 - 78: 13.873 distance: 79 - 80: 39.565 distance: 81 - 82: 34.978 distance: 82 - 83: 12.068 distance: 82 - 85: 42.838 distance: 83 - 84: 23.517 distance: 83 - 89: 18.601 distance: 86 - 88: 37.624 distance: 89 - 90: 24.010 distance: 89 - 95: 20.404 distance: 90 - 91: 14.323 distance: 90 - 93: 14.403 distance: 91 - 92: 12.088 distance: 91 - 96: 5.474 distance: 93 - 94: 25.519 distance: 94 - 95: 27.402 distance: 96 - 97: 12.486 distance: 97 - 98: 25.009 distance: 97 - 100: 21.058 distance: 98 - 99: 5.616 distance: 98 - 104: 10.216 distance: 100 - 101: 13.654 distance: 101 - 102: 23.559 distance: 101 - 103: 11.473 distance: 104 - 105: 14.906 distance: 105 - 106: 24.752 distance: 105 - 108: 28.605 distance: 106 - 107: 15.642 distance: 106 - 111: 19.646 distance: 108 - 109: 16.702 distance: 108 - 110: 15.465 distance: 111 - 112: 8.397 distance: 111 - 117: 17.161 distance: 112 - 113: 27.630 distance: 112 - 115: 18.716 distance: 113 - 114: 13.723 distance: 113 - 118: 28.812 distance: 115 - 116: 16.585 distance: 116 - 117: 17.110