Starting phenix.real_space_refine on Mon May 26 05:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pen_17632/05_2025/8pen_17632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pen_17632/05_2025/8pen_17632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pen_17632/05_2025/8pen_17632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pen_17632/05_2025/8pen_17632.map" model { file = "/net/cci-nas-00/data/ceres_data/8pen_17632/05_2025/8pen_17632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pen_17632/05_2025/8pen_17632.cif" } resolution = 3.1 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= 0.008 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 87 5.49 5 Mg 1 5.21 5 S 111 5.16 5 C 17106 2.51 5 N 4916 2.21 5 O 5511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27734 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Chain: "J" Number of atoms: 10440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10440 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11683 SG CYS J 70 24.339 70.116 82.825 1.00158.85 S ATOM 11697 SG CYS J 72 23.467 66.390 82.627 1.00157.54 S ATOM 11805 SG CYS J 85 21.833 68.586 85.226 1.00162.84 S ATOM 11829 SG CYS J 88 25.555 67.757 85.507 1.00159.71 S ATOM 17517 SG CYS J 814 57.178 127.202 91.358 1.00127.02 S ATOM 18082 SG CYS J 888 58.687 123.881 90.311 1.00123.55 S ATOM 18133 SG CYS J 895 57.708 126.423 87.633 1.00123.37 S ATOM 18154 SG CYS J 898 60.659 127.089 89.908 1.00122.70 S Time building chain proxies: 17.05, per 1000 atoms: 0.61 Number of scatterers: 27734 At special positions: 0 Unit cell: (139.776, 169.728, 157.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 111 16.00 P 87 15.00 Mg 1 11.99 O 5511 8.00 N 4916 7.00 C 17106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.67 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 51 sheets defined 39.0% alpha, 18.5% beta 39 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 11.16 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.581A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 99 Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.569A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.676A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.909A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.927A 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 247 removed outlier: 3.758A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 4.032A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.863A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 410 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.512A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.708A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.800A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 4.024A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.761A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.780A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.006A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.588A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.571A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 removed outlier: 3.704A pdb=" N ARG I 996 " --> pdb=" O PRO I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.107A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 3.996A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.617A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.523A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.098A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE I1164 " --> pdb=" O LEU I1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1160 through 1164' Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.647A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1293 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.751A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.519A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.781A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.549A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.598A 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: 3.925A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.203A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.047A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.085A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 4.023A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 874 Processing helix chain 'J' and resid 896 through 900 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: 3.724A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.308A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.792A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.607A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.350A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.638A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 4.186A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.279A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.576A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 162 removed outlier: 3.795A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.122A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.582A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.599A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.795A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 37 removed outlier: 3.821A pdb=" N THR P 44 " --> pdb=" O LYS P 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.501A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.063A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.853A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AA9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB1, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AB2, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.147A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.790A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 529 through 531 Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.573A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 716 through 717 removed outlier: 7.043A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 748 through 752 removed outlier: 7.050A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.475A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.230A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.736A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC6, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.810A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC8, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC9, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.747A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 159 through 160 removed outlier: 7.217A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.155A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD4, first strand: chain 'J' and resid 705 through 709 removed outlier: 3.746A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD6, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'J' and resid 825 through 827 removed outlier: 3.657A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.075A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.494A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.718A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AE3, first strand: chain 'J' and resid 1024 through 1029 removed outlier: 6.242A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP J1119 " --> pdb=" O THR J1029 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 4.844A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.552A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.505A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.615A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.007A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.575A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF2, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.897A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF4, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.720A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 97 through 105 removed outlier: 8.000A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.579A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1118 hydrogen bonds defined for protein. 3170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 13.82 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5794 1.33 - 1.45: 6318 1.45 - 1.57: 15865 1.57 - 1.70: 172 1.70 - 1.82: 192 Bond restraints: 28341 Sorted by residual: bond pdb=" CB ARG H 12 " pdb=" CG ARG H 12 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CB GLN K 70 " pdb=" CG GLN K 70 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB GLU J1317 " pdb=" CG GLU J1317 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB GLN P 15 " pdb=" CG GLN P 15 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CA MET J1025 " pdb=" CB MET J1025 " ideal model delta sigma weight residual 1.534 1.556 -0.022 1.57e-02 4.06e+03 1.96e+00 ... (remaining 28336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 38508 3.19 - 6.38: 136 6.38 - 9.58: 26 9.58 - 12.77: 4 12.77 - 15.96: 1 Bond angle restraints: 38675 Sorted by residual: angle pdb=" C GLU K 74 " pdb=" N GLN K 75 " pdb=" CA GLN K 75 " ideal model delta sigma weight residual 121.66 112.88 8.78 1.76e+00 3.23e-01 2.49e+01 angle pdb=" CA LEU I 237 " pdb=" CB LEU I 237 " pdb=" CG LEU I 237 " ideal model delta sigma weight residual 116.30 132.26 -15.96 3.50e+00 8.16e-02 2.08e+01 angle pdb=" CA GLN K 70 " pdb=" CB GLN K 70 " pdb=" CG GLN K 70 " ideal model delta sigma weight residual 114.10 122.12 -8.02 2.00e+00 2.50e-01 1.61e+01 angle pdb=" CB MET P 32 " pdb=" CG MET P 32 " pdb=" SD MET P 32 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CA GLU P 48 " pdb=" CB GLU P 48 " pdb=" CG GLU P 48 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 ... (remaining 38670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 16286 35.75 - 71.50: 904 71.50 - 107.25: 42 107.25 - 142.99: 2 142.99 - 178.74: 2 Dihedral angle restraints: 17236 sinusoidal: 7723 harmonic: 9513 Sorted by residual: dihedral pdb=" C4' DC B 28 " pdb=" C3' DC B 28 " pdb=" O3' DC B 28 " pdb=" P DC B 29 " ideal model delta sinusoidal sigma weight residual 220.00 41.26 178.74 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 71.71 148.29 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" C4' DC A 6 " pdb=" C3' DC A 6 " pdb=" O3' DC A 6 " pdb=" P DC A 7 " ideal model delta sinusoidal sigma weight residual -140.00 -4.73 -135.27 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 17233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4071 0.076 - 0.151: 346 0.151 - 0.227: 1 0.227 - 0.303: 0 0.303 - 0.379: 1 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CB ILE J 500 " pdb=" CA ILE J 500 " pdb=" CG1 ILE J 500 " pdb=" CG2 ILE J 500 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA ILE H 99 " pdb=" N ILE H 99 " pdb=" C ILE H 99 " pdb=" CB ILE H 99 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA GLN K 75 " pdb=" N GLN K 75 " pdb=" C GLN K 75 " pdb=" CB GLN K 75 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 4416 not shown) Planarity restraints: 4753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 67 " -0.155 9.50e-02 1.11e+02 7.02e-02 3.94e+00 pdb=" NE ARG K 67 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG K 67 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG K 67 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG K 67 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 8 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" CG ASP K 8 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP K 8 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP K 8 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 71 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" CD GLU K 71 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU K 71 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU K 71 " -0.011 2.00e-02 2.50e+03 ... (remaining 4750 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 316 2.60 - 3.18: 23215 3.18 - 3.75: 45458 3.75 - 4.33: 59329 4.33 - 4.90: 98060 Nonbonded interactions: 226378 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.030 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.104 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.122 2.170 ... (remaining 226373 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 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 79.050 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.130 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.002 0.046 28349 Z= 0.110 Angle : 0.559 15.961 38687 Z= 0.290 Chirality : 0.040 0.379 4419 Planarity : 0.004 0.070 4753 Dihedral : 19.244 178.743 11114 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 28.76 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.05 (0.15), residues: 3292 helix: 2.05 (0.16), residues: 1170 sheet: 0.38 (0.23), residues: 501 loop : -0.16 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 183 HIS 0.002 0.000 HIS J 430 PHE 0.008 0.001 PHE I 405 TYR 0.028 0.001 TYR H 185 ARG 0.017 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.13060 ( 1213) hydrogen bonds : angle 4.97674 ( 3368) metal coordination : bond 0.00264 ( 8) metal coordination : angle 0.96461 ( 12) covalent geometry : bond 0.00246 (28341) covalent geometry : angle 0.55859 (38675) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 546 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8965 (mp0) REVERT: J 497 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8439 (mm-30) REVERT: J 513 MET cc_start: 0.8829 (mtp) cc_final: 0.8600 (mtp) REVERT: J 1100 PHE cc_start: 0.8512 (t80) cc_final: 0.7712 (t80) REVERT: J 1193 TRP cc_start: 0.8822 (p90) cc_final: 0.8502 (p90) outliers start: 41 outliers final: 38 residues processed: 247 average time/residue: 0.3966 time to fit residues: 162.0332 Evaluate side-chains 237 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.8980 chunk 255 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 172 optimal weight: 0.0170 chunk 136 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 HIS I 518 ASN I1236 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049896 restraints weight = 93652.423| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.20 r_work: 0.2766 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28349 Z= 0.240 Angle : 0.584 13.888 38687 Z= 0.305 Chirality : 0.042 0.324 4419 Planarity : 0.004 0.043 4753 Dihedral : 15.921 174.530 4690 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 3.15 % Allowed : 25.43 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.96 (0.15), residues: 3292 helix: 2.02 (0.15), residues: 1167 sheet: 0.25 (0.23), residues: 516 loop : -0.22 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 183 HIS 0.007 0.001 HIS P 65 PHE 0.012 0.001 PHE J 437 TYR 0.018 0.001 TYR J 631 ARG 0.011 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 1213) hydrogen bonds : angle 4.26322 ( 3368) metal coordination : bond 0.03474 ( 8) metal coordination : angle 4.25328 ( 12) covalent geometry : bond 0.00542 (28341) covalent geometry : angle 0.57955 (38675) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 209 time to evaluate : 3.089 Fit side-chains REVERT: P 60 ASP cc_start: 0.8411 (t0) cc_final: 0.8200 (t0) REVERT: I 370 MET cc_start: 0.9199 (mmm) cc_final: 0.8948 (tpt) REVERT: I 696 ASP cc_start: 0.8489 (t0) cc_final: 0.8272 (t0) REVERT: J 136 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8649 (tp30) REVERT: J 599 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8674 (tppt) REVERT: J 1100 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7728 (t80) REVERT: J 1101 LEU cc_start: 0.8810 (mm) cc_final: 0.8465 (mp) REVERT: J 1189 MET cc_start: 0.8278 (tpt) cc_final: 0.8005 (tpt) REVERT: K 8 ASP cc_start: 0.8183 (p0) cc_final: 0.7833 (p0) REVERT: K 67 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7967 (ttm110) REVERT: H 205 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8419 (ttm) outliers start: 88 outliers final: 49 residues processed: 277 average time/residue: 0.3594 time to fit residues: 165.6745 Evaluate side-chains 241 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1254 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 141 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 100 optimal weight: 0.0370 chunk 177 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 279 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 128 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.072025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051508 restraints weight = 114481.894| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.58 r_work: 0.2800 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28349 Z= 0.102 Angle : 0.499 13.805 38687 Z= 0.262 Chirality : 0.040 0.318 4419 Planarity : 0.003 0.042 4753 Dihedral : 15.786 176.526 4659 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 2.76 % Allowed : 25.22 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.08 (0.15), residues: 3292 helix: 2.15 (0.15), residues: 1167 sheet: 0.31 (0.23), residues: 523 loop : -0.19 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 183 HIS 0.003 0.000 HIS P 77 PHE 0.012 0.001 PHE I 405 TYR 0.012 0.001 TYR J 631 ARG 0.007 0.000 ARG J 250 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1213) hydrogen bonds : angle 4.00676 ( 3368) metal coordination : bond 0.00637 ( 8) metal coordination : angle 3.04992 ( 12) covalent geometry : bond 0.00222 (28341) covalent geometry : angle 0.49610 (38675) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8408 (t0) cc_final: 0.8190 (t0) REVERT: I 165 HIS cc_start: 0.7987 (t-90) cc_final: 0.7714 (t70) REVERT: I 370 MET cc_start: 0.9275 (mmm) cc_final: 0.9007 (tpt) REVERT: I 696 ASP cc_start: 0.8569 (t0) cc_final: 0.8326 (t0) REVERT: J 503 SER cc_start: 0.8609 (m) cc_final: 0.8314 (t) REVERT: J 1095 MET cc_start: 0.6723 (tmt) cc_final: 0.6522 (tmt) REVERT: J 1100 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7690 (t80) REVERT: J 1189 MET cc_start: 0.8318 (tpt) cc_final: 0.8064 (tpt) REVERT: K 8 ASP cc_start: 0.8187 (p0) cc_final: 0.7824 (p0) REVERT: K 30 MET cc_start: 0.9145 (mtt) cc_final: 0.8836 (mtt) REVERT: K 67 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7999 (ttm110) REVERT: G 51 MET cc_start: 0.9126 (tpt) cc_final: 0.8829 (tpt) REVERT: G 101 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8919 (p) REVERT: H 205 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8410 (ttm) outliers start: 77 outliers final: 50 residues processed: 271 average time/residue: 0.3597 time to fit residues: 161.0847 Evaluate side-chains 255 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1254 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 210 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 284 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN J 266 ASN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN K 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050198 restraints weight = 96348.206| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.21 r_work: 0.2782 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28349 Z= 0.151 Angle : 0.508 12.551 38687 Z= 0.266 Chirality : 0.040 0.333 4419 Planarity : 0.003 0.041 4753 Dihedral : 15.766 175.086 4654 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 3.12 % Allowed : 25.19 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.06 (0.15), residues: 3292 helix: 2.15 (0.15), residues: 1169 sheet: 0.32 (0.23), residues: 515 loop : -0.21 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 183 HIS 0.004 0.001 HIS P 65 PHE 0.011 0.001 PHE I 405 TYR 0.013 0.001 TYR J 631 ARG 0.005 0.000 ARG I1106 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1213) hydrogen bonds : angle 3.95425 ( 3368) metal coordination : bond 0.00933 ( 8) metal coordination : angle 3.02717 ( 12) covalent geometry : bond 0.00346 (28341) covalent geometry : angle 0.50556 (38675) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 211 time to evaluate : 3.237 Fit side-chains REVERT: P 42 LYS cc_start: 0.8370 (pptt) cc_final: 0.7746 (pptt) REVERT: P 60 ASP cc_start: 0.8441 (t0) cc_final: 0.8192 (t0) REVERT: I 370 MET cc_start: 0.9273 (mmm) cc_final: 0.8957 (tpt) REVERT: I 696 ASP cc_start: 0.8500 (t0) cc_final: 0.8243 (t0) REVERT: I 968 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8398 (pp20) REVERT: I 1085 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: J 136 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8672 (tp30) REVERT: J 1100 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7727 (t80) REVERT: K 8 ASP cc_start: 0.8124 (p0) cc_final: 0.7731 (p0) REVERT: K 30 MET cc_start: 0.9171 (mtt) cc_final: 0.8927 (mtt) REVERT: K 69 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7582 (ttm110) REVERT: G 101 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8966 (p) REVERT: H 205 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8330 (ttm) outliers start: 87 outliers final: 63 residues processed: 281 average time/residue: 0.3707 time to fit residues: 172.0445 Evaluate side-chains 269 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 201 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1254 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 205 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 258 optimal weight: 0.0030 chunk 99 optimal weight: 0.0010 chunk 91 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN J 341 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.071283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051302 restraints weight = 111197.791| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.49 r_work: 0.2796 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28349 Z= 0.100 Angle : 0.498 13.203 38687 Z= 0.259 Chirality : 0.040 0.342 4419 Planarity : 0.003 0.039 4753 Dihedral : 15.726 176.477 4653 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 2.98 % Allowed : 25.61 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.10 (0.15), residues: 3292 helix: 2.24 (0.15), residues: 1157 sheet: 0.31 (0.23), residues: 523 loop : -0.20 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 183 HIS 0.004 0.001 HIS I 165 PHE 0.013 0.001 PHE I 405 TYR 0.008 0.001 TYR I 123 ARG 0.005 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 1213) hydrogen bonds : angle 3.84388 ( 3368) metal coordination : bond 0.00503 ( 8) metal coordination : angle 2.48504 ( 12) covalent geometry : bond 0.00222 (28341) covalent geometry : angle 0.49664 (38675) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 220 time to evaluate : 2.968 Fit side-chains revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8414 (pptt) cc_final: 0.7785 (pptt) REVERT: P 60 ASP cc_start: 0.8455 (t0) cc_final: 0.8199 (t0) REVERT: I 320 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8996 (p0) REVERT: I 370 MET cc_start: 0.9290 (mmm) cc_final: 0.8962 (tpt) REVERT: I 696 ASP cc_start: 0.8530 (t0) cc_final: 0.8270 (t0) REVERT: I 968 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8365 (pp20) REVERT: I 1107 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8782 (tpp) REVERT: J 136 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8697 (tp30) REVERT: J 503 SER cc_start: 0.8604 (m) cc_final: 0.8316 (t) REVERT: J 1100 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7781 (t80) REVERT: J 1189 MET cc_start: 0.8383 (tpt) cc_final: 0.8149 (tpt) REVERT: K 30 MET cc_start: 0.9183 (mtt) cc_final: 0.8916 (mtt) REVERT: K 69 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7573 (ttm110) REVERT: K 74 GLU cc_start: 0.9146 (pp20) cc_final: 0.8906 (pp20) REVERT: K 76 GLU cc_start: 0.8941 (pp20) cc_final: 0.8563 (mm-30) REVERT: G 101 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8886 (p) outliers start: 83 outliers final: 54 residues processed: 290 average time/residue: 0.3588 time to fit residues: 170.3295 Evaluate side-chains 266 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 327 optimal weight: 0.9980 chunk 330 optimal weight: 8.9990 chunk 94 optimal weight: 0.0270 chunk 151 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 494 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.070764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050425 restraints weight = 94695.858| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.22 r_work: 0.2783 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28349 Z= 0.156 Angle : 0.523 13.001 38687 Z= 0.272 Chirality : 0.040 0.356 4419 Planarity : 0.003 0.041 4753 Dihedral : 15.742 174.863 4652 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 3.19 % Allowed : 25.33 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.09 (0.15), residues: 3292 helix: 2.24 (0.15), residues: 1157 sheet: 0.31 (0.23), residues: 536 loop : -0.23 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 183 HIS 0.004 0.001 HIS H 23 PHE 0.010 0.001 PHE I 405 TYR 0.015 0.001 TYR I 47 ARG 0.006 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 1213) hydrogen bonds : angle 3.87315 ( 3368) metal coordination : bond 0.00878 ( 8) metal coordination : angle 2.78212 ( 12) covalent geometry : bond 0.00356 (28341) covalent geometry : angle 0.52058 (38675) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 198 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8447 (t0) cc_final: 0.8145 (t0) REVERT: I 37 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8953 (ttpp) REVERT: I 268 ARG cc_start: 0.7852 (tmm-80) cc_final: 0.7587 (ttp80) REVERT: I 320 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.9003 (p0) REVERT: I 370 MET cc_start: 0.9267 (mmm) cc_final: 0.8903 (tpt) REVERT: I 494 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8458 (p0) REVERT: I 696 ASP cc_start: 0.8513 (t0) cc_final: 0.8241 (t0) REVERT: I 968 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8373 (pp20) REVERT: I 1085 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9063 (mmm) REVERT: J 1100 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7819 (t80) REVERT: K 8 ASP cc_start: 0.8445 (p0) cc_final: 0.8108 (p0) REVERT: K 30 MET cc_start: 0.9196 (mtt) cc_final: 0.8956 (mtt) REVERT: K 69 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7607 (ttm110) REVERT: G 101 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8974 (p) REVERT: H 205 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8395 (ttm) outliers start: 89 outliers final: 66 residues processed: 271 average time/residue: 0.3790 time to fit residues: 169.4279 Evaluate side-chains 266 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 192 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 231 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 494 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050439 restraints weight = 87802.036| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.08 r_work: 0.2785 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28349 Z= 0.149 Angle : 0.519 13.152 38687 Z= 0.271 Chirality : 0.040 0.361 4419 Planarity : 0.003 0.040 4753 Dihedral : 15.741 175.061 4652 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 2.94 % Allowed : 25.54 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.07 (0.15), residues: 3292 helix: 2.22 (0.15), residues: 1164 sheet: 0.30 (0.23), residues: 529 loop : -0.26 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 183 HIS 0.003 0.001 HIS P 65 PHE 0.010 0.001 PHE I 405 TYR 0.015 0.001 TYR I 47 ARG 0.007 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 1213) hydrogen bonds : angle 3.87255 ( 3368) metal coordination : bond 0.00853 ( 8) metal coordination : angle 2.84438 ( 12) covalent geometry : bond 0.00342 (28341) covalent geometry : angle 0.51687 (38675) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 198 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8447 (t0) cc_final: 0.8137 (t0) REVERT: I 320 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.9001 (p0) REVERT: I 370 MET cc_start: 0.9253 (mmm) cc_final: 0.8883 (tpt) REVERT: I 494 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8440 (p0) REVERT: I 696 ASP cc_start: 0.8521 (t0) cc_final: 0.8224 (t0) REVERT: I 968 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8371 (pp20) REVERT: I 1085 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9041 (mmm) REVERT: J 503 SER cc_start: 0.8693 (m) cc_final: 0.8416 (t) REVERT: J 1100 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7804 (t80) REVERT: K 8 ASP cc_start: 0.8327 (p0) cc_final: 0.8078 (p0) REVERT: K 30 MET cc_start: 0.9207 (mtt) cc_final: 0.8976 (mtt) REVERT: K 69 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7687 (ttm110) REVERT: K 73 GLN cc_start: 0.8272 (pp30) cc_final: 0.7867 (pp30) REVERT: K 76 GLU cc_start: 0.9101 (pt0) cc_final: 0.8373 (mm-30) REVERT: G 51 MET cc_start: 0.9190 (tpt) cc_final: 0.8841 (tpt) REVERT: G 101 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8963 (p) REVERT: H 205 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8378 (ttm) outliers start: 82 outliers final: 66 residues processed: 264 average time/residue: 0.3698 time to fit residues: 160.3978 Evaluate side-chains 264 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 137 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 494 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049490 restraints weight = 93743.251| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.18 r_work: 0.2756 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28349 Z= 0.179 Angle : 0.544 13.127 38687 Z= 0.283 Chirality : 0.041 0.380 4419 Planarity : 0.003 0.040 4753 Dihedral : 15.776 174.281 4651 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 3.19 % Allowed : 25.43 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.00 (0.15), residues: 3292 helix: 2.17 (0.15), residues: 1166 sheet: 0.23 (0.23), residues: 532 loop : -0.28 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 183 HIS 0.004 0.001 HIS P 65 PHE 0.010 0.001 PHE I 385 TYR 0.023 0.001 TYR I 47 ARG 0.007 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1213) hydrogen bonds : angle 3.92950 ( 3368) metal coordination : bond 0.01035 ( 8) metal coordination : angle 3.07903 ( 12) covalent geometry : bond 0.00410 (28341) covalent geometry : angle 0.54143 (38675) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 194 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8475 (t0) cc_final: 0.8171 (t0) REVERT: I 37 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8975 (ttpp) REVERT: I 268 ARG cc_start: 0.7886 (tmm-80) cc_final: 0.7650 (ttp80) REVERT: I 320 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.9024 (p0) REVERT: I 370 MET cc_start: 0.9261 (mmm) cc_final: 0.8849 (tpt) REVERT: I 494 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8716 (p0) REVERT: I 696 ASP cc_start: 0.8556 (t0) cc_final: 0.8255 (t0) REVERT: I 800 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8486 (mtp) REVERT: I 968 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8382 (pp20) REVERT: I 1085 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9053 (mmm) REVERT: J 1100 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7753 (t80) REVERT: K 30 MET cc_start: 0.9226 (mtt) cc_final: 0.8998 (mtt) REVERT: G 101 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8986 (p) outliers start: 89 outliers final: 67 residues processed: 267 average time/residue: 0.3871 time to fit residues: 168.3138 Evaluate side-chains 266 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 191 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 957 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 286 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 299 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 130 optimal weight: 0.0870 chunk 317 optimal weight: 9.9990 chunk 254 optimal weight: 0.0060 chunk 183 optimal weight: 0.4980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN K 75 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.071599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051510 restraints weight = 87648.407| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.09 r_work: 0.2816 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28349 Z= 0.105 Angle : 0.521 13.554 38687 Z= 0.271 Chirality : 0.040 0.376 4419 Planarity : 0.003 0.038 4753 Dihedral : 15.717 177.176 4650 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 2.44 % Allowed : 26.18 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.05 (0.15), residues: 3292 helix: 2.22 (0.15), residues: 1165 sheet: 0.30 (0.23), residues: 510 loop : -0.27 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 183 HIS 0.003 0.000 HIS J 430 PHE 0.014 0.001 PHE I 405 TYR 0.018 0.001 TYR I 47 ARG 0.013 0.000 ARG H 12 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 1213) hydrogen bonds : angle 3.80767 ( 3368) metal coordination : bond 0.00444 ( 8) metal coordination : angle 2.37195 ( 12) covalent geometry : bond 0.00237 (28341) covalent geometry : angle 0.51928 (38675) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 ASP cc_start: 0.8459 (t0) cc_final: 0.8167 (t0) REVERT: I 37 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9000 (ttpp) REVERT: I 268 ARG cc_start: 0.7877 (tmm-80) cc_final: 0.7664 (ttp80) REVERT: I 320 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8991 (p0) REVERT: I 370 MET cc_start: 0.9269 (mmm) cc_final: 0.8906 (tpt) REVERT: I 696 ASP cc_start: 0.8564 (t0) cc_final: 0.8276 (t0) REVERT: I 968 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8342 (pp20) REVERT: I 1085 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8926 (mtp) REVERT: I 1279 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8832 (mt-10) REVERT: J 259 ARG cc_start: 0.7551 (ptm160) cc_final: 0.7223 (ptm160) REVERT: J 503 SER cc_start: 0.8646 (m) cc_final: 0.8380 (t) REVERT: J 1100 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7766 (t80) REVERT: K 30 MET cc_start: 0.9198 (mtt) cc_final: 0.8988 (mtt) REVERT: K 76 GLU cc_start: 0.9082 (pt0) cc_final: 0.8384 (mm-30) REVERT: G 101 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8922 (p) REVERT: H 12 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7788 (mmm160) outliers start: 68 outliers final: 57 residues processed: 261 average time/residue: 0.3969 time to fit residues: 168.0018 Evaluate side-chains 261 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 131 optimal weight: 3.9990 chunk 299 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 323 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 chunk 211 optimal weight: 0.0970 chunk 266 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.071151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051332 restraints weight = 96383.420| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.20 r_work: 0.2806 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28349 Z= 0.110 Angle : 0.522 13.487 38687 Z= 0.270 Chirality : 0.040 0.376 4419 Planarity : 0.003 0.039 4753 Dihedral : 15.699 176.583 4650 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 26.21 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.07 (0.15), residues: 3292 helix: 2.24 (0.15), residues: 1166 sheet: 0.27 (0.23), residues: 504 loop : -0.26 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 183 HIS 0.003 0.000 HIS P 77 PHE 0.015 0.001 PHE I 389 TYR 0.017 0.001 TYR I 47 ARG 0.009 0.000 ARG J 312 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 1213) hydrogen bonds : angle 3.78446 ( 3368) metal coordination : bond 0.00515 ( 8) metal coordination : angle 2.28111 ( 12) covalent geometry : bond 0.00252 (28341) covalent geometry : angle 0.52022 (38675) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 42 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8298 (pptt) REVERT: P 60 ASP cc_start: 0.8490 (t0) cc_final: 0.8199 (t0) REVERT: I 37 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9022 (ttpp) REVERT: I 268 ARG cc_start: 0.7869 (tmm-80) cc_final: 0.7661 (ttp80) REVERT: I 320 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8994 (p0) REVERT: I 370 MET cc_start: 0.9281 (mmm) cc_final: 0.8932 (tpt) REVERT: I 386 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: I 696 ASP cc_start: 0.8564 (t0) cc_final: 0.8290 (t0) REVERT: I 968 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8335 (pp20) REVERT: I 1085 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9031 (mmm) REVERT: J 259 ARG cc_start: 0.7564 (ptm160) cc_final: 0.7343 (ptm160) REVERT: J 503 SER cc_start: 0.8692 (m) cc_final: 0.8420 (t) REVERT: J 1100 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7728 (t80) REVERT: K 30 MET cc_start: 0.9180 (mtt) cc_final: 0.8972 (mtt) REVERT: G 101 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8940 (p) outliers start: 65 outliers final: 54 residues processed: 256 average time/residue: 0.3898 time to fit residues: 162.4791 Evaluate side-chains 260 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 28 CYS Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 770 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 704 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 235 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 274 optimal weight: 0.4980 chunk 268 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.070577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050064 restraints weight = 99743.121| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.32 r_work: 0.2766 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28349 Z= 0.149 Angle : 0.539 13.335 38687 Z= 0.280 Chirality : 0.041 0.380 4419 Planarity : 0.003 0.040 4753 Dihedral : 15.728 175.514 4650 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 2.55 % Allowed : 26.07 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 1.05 (0.15), residues: 3292 helix: 2.24 (0.15), residues: 1166 sheet: 0.21 (0.23), residues: 516 loop : -0.27 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 183 HIS 0.004 0.001 HIS P 65 PHE 0.011 0.001 PHE I 389 TYR 0.017 0.001 TYR I 47 ARG 0.009 0.000 ARG J 312 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 1213) hydrogen bonds : angle 3.84269 ( 3368) metal coordination : bond 0.00831 ( 8) metal coordination : angle 2.64048 ( 12) covalent geometry : bond 0.00343 (28341) covalent geometry : angle 0.53743 (38675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14843.73 seconds wall clock time: 257 minutes 23.25 seconds (15443.25 seconds total)