Starting phenix.real_space_refine on Mon Sep 14 00:02:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6asx_7002/09_2026/6asx_7002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6asx_7002/09_2026/6asx_7002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6asx_7002/09_2026/6asx_7002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6asx_7002/09_2026/6asx_7002_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6asx_7002/09_2026/6asx_7002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6asx_7002/09_2026/6asx_7002.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 71 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16287 2.51 5 N 4662 2.21 5 O 5230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26359 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "B" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 608 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'RNA': 21} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain breaks: 1 Chain: "G" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "H" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1695 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "I" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10397 Classifications: {'peptide': 1318} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10409 Classifications: {'peptide': 1338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15741 SG CYS J 70 54.394 120.299 62.304 1.00105.33 S ATOM 15755 SG CYS J 72 55.449 123.815 62.338 1.00114.14 S ATOM 15863 SG CYS J 85 53.475 122.801 59.474 1.00104.26 S ATOM 21575 SG CYS J 814 52.888 53.167 47.956 1.00 65.49 S ATOM 22140 SG CYS J 888 55.790 56.400 49.230 1.00 60.63 S ATOM 22191 SG CYS J 895 52.909 55.310 51.417 1.00 58.58 S ATOM 22212 SG CYS J 898 55.479 53.007 50.555 1.00 58.95 S Time building chain proxies: 5.06, per 1000 atoms: 0.19 Number of scatterers: 26359 At special positions: 0 Unit cell: (153.47, 138.02, 151.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 71 15.00 Mg 1 11.99 O 5230 8.00 N 4662 7.00 C 16287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " Number of angles added : 6 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 51 sheets defined 36.5% alpha, 15.9% beta 32 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.751A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 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 212 through 228 Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.628A pdb=" N VAL G 232 " --> pdb=" O GLU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'H' and resid 36 through 41 Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.698A pdb=" N LEU H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 159 removed outlier: 3.818A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 removed outlier: 3.760A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR H 222 " --> pdb=" O ARG H 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 Processing helix chain 'I' and resid 48 through 57 removed outlier: 4.121A 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 Processing helix chain 'I' and resid 216 through 224 removed outlier: 3.708A pdb=" N ILE I 220 " --> pdb=" O THR I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 removed outlier: 4.053A pdb=" N ASP I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.968A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.504A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) 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 386 Processing helix chain 'I' and resid 398 through 408 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.911A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.867A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 4.048A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 612 removed outlier: 3.591A pdb=" N GLU I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 607 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 819 through 825 removed outlier: 4.240A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 860 through 865 removed outlier: 4.027A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 943 through 981 removed outlier: 3.724A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 989 Processing helix chain 'I' and resid 993 through 997 removed outlier: 3.566A pdb=" N TRP I 997 " --> pdb=" O ARG I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.633A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.745A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.870A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.584A pdb=" N ILE I1195 " --> pdb=" O LYS I1191 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.733A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.563A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 through 117 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 180 through 191 removed outlier: 3.751A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.583A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 228 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 removed outlier: 4.141A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.713A pdb=" N ASP J 308 " --> pdb=" O ASP J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 removed outlier: 3.527A pdb=" N LEU J 387 " --> pdb=" O GLY J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 406 through 417 removed outlier: 4.109A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) 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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 removed outlier: 3.515A pdb=" N GLN J 477 " --> pdb=" O THR J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 removed outlier: 3.509A pdb=" N ALA J 533 " --> pdb=" O GLY J 529 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 581 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 598 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.659A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 4.126A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 669 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.607A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.722A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.657A pdb=" N TYR J 772 " --> pdb=" O ASN J 768 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.871A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.862A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1072 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.498A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1287 Processing helix chain 'J' and resid 1290 through 1295 removed outlier: 3.734A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1290 through 1295' Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 4.050A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1352 Processing helix chain 'J' and resid 1359 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.947A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 84 removed outlier: 3.609A pdb=" N GLU K 74 " --> pdb=" O GLN K 70 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.526A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 101 removed outlier: 3.761A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.742A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.778A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL H 14 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.778A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL H 14 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 52 through 56 Processing sheet with id=AB1, first strand: chain 'H' and resid 52 through 56 removed outlier: 3.894A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.707A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.914A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.215A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.717A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 228 through 231 Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.966A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.979A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.954A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 599 through 603 removed outlier: 5.337A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC8, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.657A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.922A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD2, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.485A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD4, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.829A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.787A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD9, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.556A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1335 through 1337 Processing sheet with id=AE2, first strand: chain 'J' and resid 36 through 37 removed outlier: 6.489A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE4, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AE5, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE6, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'J' and resid 825 through 826 removed outlier: 4.182A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.081A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.765A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU J 982 " --> pdb=" O TYR J 995 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF4, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.711A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.628A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 2.87 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: 7533 1.33 - 1.45: 4293 1.45 - 1.57: 14747 1.57 - 1.69: 139 1.69 - 1.81: 184 Bond restraints: 26896 Sorted by residual: bond pdb=" C3' DG B 17 " pdb=" O3' DG B 17 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" N7 DA B 21 " pdb=" C5 DA B 21 " ideal model delta sigma weight residual 1.388 1.367 0.021 6.00e-03 2.78e+04 1.18e+01 bond pdb=" C3' DC B 25 " pdb=" C2' DC B 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C1' DC B 18 " pdb=" N1 DC B 18 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.84e+00 bond pdb=" C3' DT A 4 " pdb=" C2' DT A 4 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 ... (remaining 26891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 36503 5.25 - 10.50: 130 10.50 - 15.75: 2 15.75 - 21.00: 1 21.00 - 26.25: 2 Bond angle restraints: 36638 Sorted by residual: angle pdb=" C LYS J1192 " pdb=" N TRP J1193 " pdb=" CA TRP J1193 " ideal model delta sigma weight residual 121.70 140.23 -18.53 1.80e+00 3.09e-01 1.06e+02 angle pdb=" O3' DT B 2 " pdb=" P DC B 3 " pdb=" OP1 DC B 3 " ideal model delta sigma weight residual 108.00 81.75 26.25 3.00e+00 1.11e-01 7.66e+01 angle pdb=" O3' DT B 2 " pdb=" P DC B 3 " pdb=" OP2 DC B 3 " ideal model delta sigma weight residual 108.00 83.91 24.09 3.00e+00 1.11e-01 6.45e+01 angle pdb=" C1' C R 28 " pdb=" N1 C R 28 " pdb=" C2 C R 28 " ideal model delta sigma weight residual 118.80 127.37 -8.57 1.10e+00 8.26e-01 6.07e+01 angle pdb=" N1 C R 2 " pdb=" C6 C R 2 " pdb=" C5 C R 2 " ideal model delta sigma weight residual 121.00 124.59 -3.59 5.00e-01 4.00e+00 5.14e+01 ... (remaining 36633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 16089 35.85 - 71.71: 343 71.71 - 107.56: 15 107.56 - 143.41: 2 143.41 - 179.26: 3 Dihedral angle restraints: 16452 sinusoidal: 7330 harmonic: 9122 Sorted by residual: dihedral pdb=" CA GLN J1326 " pdb=" C GLN J1326 " pdb=" N GLU J1327 " pdb=" CA GLU J1327 " ideal model delta harmonic sigma weight residual 180.00 -137.48 -42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA LYS J1192 " pdb=" C LYS J1192 " pdb=" N TRP J1193 " pdb=" CA TRP J1193 " ideal model delta harmonic sigma weight residual 0.00 41.05 -41.05 0 5.00e+00 4.00e-02 6.74e+01 dihedral pdb=" CA ILE J 416 " pdb=" C ILE J 416 " pdb=" N ARG J 417 " pdb=" CA ARG J 417 " ideal model delta harmonic sigma weight residual 180.00 -143.25 -36.75 0 5.00e+00 4.00e-02 5.40e+01 ... (remaining 16449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.387: 4201 0.387 - 0.773: 1 0.773 - 1.159: 0 1.159 - 1.546: 0 1.546 - 1.932: 1 Chirality restraints: 4203 Sorted by residual: chirality pdb=" P DC B 3 " pdb=" OP1 DC B 3 " pdb=" OP2 DC B 3 " pdb=" O5' DC B 3 " both_signs ideal model delta sigma weight residual True 2.34 0.40 1.93 2.00e-01 2.50e+01 9.34e+01 chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" C3' G R 20 " pdb=" C4' G R 20 " pdb=" O3' G R 20 " pdb=" C2' G R 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4200 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J1344 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C LEU J1344 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU J1344 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG J1345 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO I 520 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 29 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO G 30 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 30 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 30 " 0.034 5.00e-02 4.00e+02 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 249 2.63 - 3.20: 21855 3.20 - 3.77: 38239 3.77 - 4.33: 51487 4.33 - 4.90: 84710 Nonbonded interactions: 196540 Sorted by model distance: nonbonded pdb=" O2 DC A 28 " pdb=" N2 DG B 5 " model vdw 2.065 2.496 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG R1501 " model vdw 2.145 2.170 nonbonded pdb=" O5' U R 22 " pdb=" NZ LYS J 325 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU I1222 " pdb=" OH TYR J 512 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR J1186 " pdb=" OE1 GLU J1188 " model vdw 2.286 3.040 ... (remaining 196535 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 7 through 158 or resid 168 through 232)) selection = (chain 'H' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.009 0.202 26903 Z= 0.405 Angle : 1.073 29.408 36644 Z= 0.618 Chirality : 0.069 1.932 4203 Planarity : 0.008 0.079 4541 Dihedral : 13.674 179.264 10584 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.65 % Favored : 90.28 % Rotamer: Outliers : 0.26 % Allowed : 2.85 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.12), residues: 3159 helix: -2.52 (0.12), residues: 1094 sheet: -2.22 (0.24), residues: 360 loop : -3.12 (0.12), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I1223 TYR 0.039 0.003 TYR G 177 PHE 0.036 0.003 PHE J 620 TRP 0.032 0.004 TRP I 183 HIS 0.010 0.002 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.40 (26896) covalent geometry : angle 1.05461 / 0.62 (36638) hydrogen bonds : bond 0.10828 / 12.00 ( 1051) hydrogen bonds : angle 5.96068 / 6.84 ( 2902) metal coordination : bond 0.13756 / 14.93 ( 7) metal coordination : angle 15.48272 / 22.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 656 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8648 (mtpp) REVERT: G 54 CYS cc_start: 0.7981 (m) cc_final: 0.7656 (t) REVERT: G 153 VAL cc_start: 0.9120 (t) cc_final: 0.8874 (m) REVERT: G 200 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8226 (tttt) REVERT: H 16 ILE cc_start: 0.8831 (mt) cc_final: 0.8515 (tt) REVERT: H 76 GLU cc_start: 0.7502 (mp0) cc_final: 0.6736 (mp0) REVERT: H 199 ASP cc_start: 0.8004 (m-30) cc_final: 0.7756 (m-30) REVERT: I 44 GLU cc_start: 0.7656 (pt0) cc_final: 0.7329 (tt0) REVERT: I 133 ASN cc_start: 0.8340 (m-40) cc_final: 0.8102 (m-40) REVERT: I 224 PHE cc_start: 0.8186 (m-80) cc_final: 0.7929 (m-10) REVERT: I 275 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7483 (mmt-90) REVERT: I 424 ASP cc_start: 0.7963 (m-30) cc_final: 0.7522 (m-30) REVERT: I 434 ASP cc_start: 0.8034 (m-30) cc_final: 0.7750 (m-30) REVERT: I 1151 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8589 (tp) REVERT: I 1290 MET cc_start: 0.8373 (tpp) cc_final: 0.8105 (tpp) REVERT: J 264 ASP cc_start: 0.8487 (m-30) cc_final: 0.8225 (m-30) REVERT: J 295 GLU cc_start: 0.8250 (tp30) cc_final: 0.7793 (tp30) REVERT: J 308 ASP cc_start: 0.8178 (t0) cc_final: 0.7480 (t0) REVERT: J 754 ILE cc_start: 0.9123 (tt) cc_final: 0.8891 (mt) REVERT: J 890 THR cc_start: 0.8255 (m) cc_final: 0.7990 (m) REVERT: J 947 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7002 (mm-30) REVERT: J 1155 ILE cc_start: 0.9196 (pt) cc_final: 0.8731 (mt) REVERT: J 1165 PHE cc_start: 0.8321 (m-80) cc_final: 0.7655 (m-10) REVERT: J 1189 MET cc_start: 0.7716 (ttm) cc_final: 0.6881 (tpp) REVERT: J 1268 ASN cc_start: 0.8628 (t160) cc_final: 0.8422 (t0) REVERT: K 8 ASP cc_start: 0.8324 (m-30) cc_final: 0.7978 (m-30) REVERT: K 58 LEU cc_start: 0.8429 (pp) cc_final: 0.8139 (pp) outliers start: 7 outliers final: 2 residues processed: 662 average time/residue: 0.1869 time to fit residues: 186.9731 Evaluate side-chains 299 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN I 69 GLN I 150 HIS I 580 GLN I 604 HIS I 952 GLN I1080 ASN I1209 GLN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 HIS I1268 GLN I1313 HIS I1324 ASN J 232 ASN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN J 777 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1268 ASN J1326 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099761 restraints weight = 47985.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102812 restraints weight = 25627.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103647 restraints weight = 16204.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104104 restraints weight = 13966.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104124 restraints weight = 13059.724| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26903 Z= 0.167 Angle : 0.724 25.075 36644 Z= 0.377 Chirality : 0.055 1.905 4203 Planarity : 0.006 0.060 4541 Dihedral : 16.043 178.509 4379 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.03 % Allowed : 10.20 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.13), residues: 3159 helix: -0.85 (0.15), residues: 1105 sheet: -1.79 (0.25), residues: 371 loop : -2.86 (0.13), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 359 TYR 0.021 0.001 TYR J1186 PHE 0.016 0.002 PHE I 337 TRP 0.012 0.002 TRP J 409 HIS 0.008 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (26896) covalent geometry : angle 0.72271 / 0.38 (36638) hydrogen bonds : bond 0.05676 / 6.24 ( 1051) hydrogen bonds : angle 5.05592 / 5.93 ( 2902) metal coordination : bond 0.00837 / 0.84 ( 7) metal coordination : angle 2.77856 / 3.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 344 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8496 (tttt) REVERT: H 16 ILE cc_start: 0.8863 (mt) cc_final: 0.8480 (tt) REVERT: H 58 GLU cc_start: 0.7752 (pt0) cc_final: 0.7313 (mt-10) REVERT: H 199 ASP cc_start: 0.7908 (m-30) cc_final: 0.7634 (m-30) REVERT: I 44 GLU cc_start: 0.7611 (pt0) cc_final: 0.7360 (tt0) REVERT: I 133 ASN cc_start: 0.8374 (m-40) cc_final: 0.8155 (m-40) REVERT: I 275 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7531 (mmt-90) REVERT: I 322 LEU cc_start: 0.7514 (mt) cc_final: 0.7175 (tp) REVERT: I 434 ASP cc_start: 0.8075 (m-30) cc_final: 0.7799 (m-30) REVERT: I 1073 LYS cc_start: 0.8386 (mttm) cc_final: 0.7954 (mttm) REVERT: I 1290 MET cc_start: 0.8462 (tpp) cc_final: 0.8192 (tpp) REVERT: J 248 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8624 (t0) REVERT: J 264 ASP cc_start: 0.8480 (m-30) cc_final: 0.8124 (m-30) REVERT: J 295 GLU cc_start: 0.8274 (tp30) cc_final: 0.7606 (tp30) REVERT: J 372 MET cc_start: 0.8999 (mtp) cc_final: 0.8693 (ttm) REVERT: J 532 GLU cc_start: 0.7835 (pt0) cc_final: 0.7435 (tt0) REVERT: J 754 ILE cc_start: 0.9147 (tt) cc_final: 0.8921 (mt) REVERT: J 772 TYR cc_start: 0.8941 (t80) cc_final: 0.8460 (t80) REVERT: J 1025 MET cc_start: 0.7213 (mtp) cc_final: 0.6800 (mmt) REVERT: J 1155 ILE cc_start: 0.9132 (pt) cc_final: 0.8702 (mt) REVERT: J 1165 PHE cc_start: 0.8199 (m-80) cc_final: 0.7570 (m-10) REVERT: J 1168 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6343 (tm-30) REVERT: J 1189 MET cc_start: 0.7625 (ttm) cc_final: 0.6818 (tpp) REVERT: K 58 LEU cc_start: 0.8332 (pp) cc_final: 0.8093 (pp) outliers start: 55 outliers final: 30 residues processed: 379 average time/residue: 0.1613 time to fit residues: 97.6267 Evaluate side-chains 301 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 191 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 271 optimal weight: 0.1980 chunk 138 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097899 restraints weight = 48102.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099612 restraints weight = 27033.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100667 restraints weight = 18153.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101125 restraints weight = 16061.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101142 restraints weight = 14358.495| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26903 Z= 0.176 Angle : 0.685 24.909 36644 Z= 0.354 Chirality : 0.054 1.901 4203 Planarity : 0.005 0.053 4541 Dihedral : 15.913 178.156 4377 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.77 % Allowed : 11.98 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 3159 helix: -0.05 (0.16), residues: 1086 sheet: -1.49 (0.26), residues: 369 loop : -2.70 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1067 TYR 0.019 0.001 TYR G 177 PHE 0.013 0.001 PHE I 337 TRP 0.010 0.001 TRP J 409 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (26896) covalent geometry : angle 0.68444 / 0.35 (36638) hydrogen bonds : bond 0.05259 / 5.81 ( 1051) hydrogen bonds : angle 4.83076 / 5.70 ( 2902) metal coordination : bond 0.00733 / 0.73 ( 7) metal coordination : angle 1.96173 / 3.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8596 (ttpp) REVERT: H 16 ILE cc_start: 0.8861 (mt) cc_final: 0.8509 (tt) REVERT: H 58 GLU cc_start: 0.7781 (pt0) cc_final: 0.7317 (mt-10) REVERT: H 75 GLN cc_start: 0.7145 (tt0) cc_final: 0.6842 (tm-30) REVERT: I 44 GLU cc_start: 0.7700 (pt0) cc_final: 0.7388 (tt0) REVERT: I 133 ASN cc_start: 0.8360 (m-40) cc_final: 0.8090 (m-40) REVERT: I 275 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7607 (mmp80) REVERT: I 322 LEU cc_start: 0.7424 (mt) cc_final: 0.7141 (tp) REVERT: I 383 SER cc_start: 0.8947 (m) cc_final: 0.8630 (p) REVERT: I 434 ASP cc_start: 0.8032 (m-30) cc_final: 0.7797 (m-30) REVERT: I 800 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7489 (mtp) REVERT: I 1290 MET cc_start: 0.8406 (tpp) cc_final: 0.8032 (tpp) REVERT: J 248 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8617 (t0) REVERT: J 295 GLU cc_start: 0.8250 (tp30) cc_final: 0.7542 (tp30) REVERT: J 330 MET cc_start: 0.7601 (mtp) cc_final: 0.7385 (mtp) REVERT: J 372 MET cc_start: 0.9004 (mtp) cc_final: 0.8719 (ttm) REVERT: J 532 GLU cc_start: 0.7878 (pt0) cc_final: 0.7536 (tt0) REVERT: J 624 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9095 (tt) REVERT: J 645 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9001 (m) REVERT: J 754 ILE cc_start: 0.9202 (tt) cc_final: 0.8989 (mt) REVERT: J 882 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8230 (m) REVERT: J 1155 ILE cc_start: 0.9089 (pt) cc_final: 0.8713 (mt) REVERT: J 1165 PHE cc_start: 0.8149 (m-80) cc_final: 0.7535 (m-80) REVERT: J 1168 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6473 (tm-30) REVERT: J 1189 MET cc_start: 0.7702 (ttm) cc_final: 0.7116 (tpp) REVERT: K 51 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8164 (mp) REVERT: K 58 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8164 (pp) outliers start: 75 outliers final: 46 residues processed: 355 average time/residue: 0.1507 time to fit residues: 89.2321 Evaluate side-chains 320 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 255 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100688 restraints weight = 47872.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102253 restraints weight = 26548.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103514 restraints weight = 18374.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103944 restraints weight = 15566.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103942 restraints weight = 13874.893| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26903 Z= 0.120 Angle : 0.624 24.724 36644 Z= 0.321 Chirality : 0.053 1.912 4203 Planarity : 0.004 0.052 4541 Dihedral : 15.752 177.544 4377 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.74 % Allowed : 13.27 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.14), residues: 3159 helix: 0.36 (0.16), residues: 1093 sheet: -1.23 (0.26), residues: 368 loop : -2.52 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J1148 TYR 0.015 0.001 TYR G 177 PHE 0.011 0.001 PHE I 337 TRP 0.009 0.001 TRP J 580 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (26896) covalent geometry : angle 0.62363 / 0.32 (36638) hydrogen bonds : bond 0.04588 / 5.09 ( 1051) hydrogen bonds : angle 4.54271 / 5.36 ( 2902) metal coordination : bond 0.00355 / 0.36 ( 7) metal coordination : angle 0.98636 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 316 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: G 200 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8601 (ttpp) REVERT: H 16 ILE cc_start: 0.8835 (mt) cc_final: 0.8466 (tt) REVERT: H 58 GLU cc_start: 0.7772 (pt0) cc_final: 0.7252 (mt-10) REVERT: H 75 GLN cc_start: 0.7351 (tt0) cc_final: 0.6987 (tm-30) REVERT: H 130 ILE cc_start: 0.9070 (mt) cc_final: 0.8840 (mt) REVERT: I 44 GLU cc_start: 0.7664 (pt0) cc_final: 0.7314 (tt0) REVERT: I 133 ASN cc_start: 0.8337 (m-40) cc_final: 0.7935 (t0) REVERT: I 275 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7616 (mmp80) REVERT: I 383 SER cc_start: 0.8881 (m) cc_final: 0.8587 (p) REVERT: I 434 ASP cc_start: 0.7937 (m-30) cc_final: 0.7737 (m-30) REVERT: I 472 GLU cc_start: 0.8257 (pt0) cc_final: 0.7520 (tt0) REVERT: I 654 ASP cc_start: 0.8196 (t0) cc_final: 0.7892 (t0) REVERT: I 800 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7379 (mtp) REVERT: I 978 VAL cc_start: 0.7861 (p) cc_final: 0.7610 (m) REVERT: I 1161 LEU cc_start: 0.8133 (tp) cc_final: 0.7921 (tp) REVERT: I 1290 MET cc_start: 0.8348 (tpp) cc_final: 0.7947 (tpp) REVERT: I 1327 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8858 (mt) REVERT: J 248 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8646 (t0) REVERT: J 295 GLU cc_start: 0.8192 (tp30) cc_final: 0.7470 (tp30) REVERT: J 532 GLU cc_start: 0.7794 (pt0) cc_final: 0.7493 (tt0) REVERT: J 624 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9004 (tt) REVERT: J 645 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8957 (m) REVERT: J 698 MET cc_start: 0.8816 (tpt) cc_final: 0.8564 (tpp) REVERT: J 882 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8089 (m) REVERT: J 1148 ARG cc_start: 0.8163 (mmt90) cc_final: 0.7937 (mpt-90) REVERT: J 1155 ILE cc_start: 0.9052 (pt) cc_final: 0.8742 (mt) REVERT: J 1165 PHE cc_start: 0.8144 (m-80) cc_final: 0.7548 (m-10) REVERT: J 1168 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6520 (tm-30) REVERT: J 1189 MET cc_start: 0.7587 (ttm) cc_final: 0.7124 (tpp) REVERT: K 41 GLU cc_start: 0.8557 (pm20) cc_final: 0.8114 (pt0) REVERT: K 55 GLU cc_start: 0.7547 (tt0) cc_final: 0.7340 (tt0) outliers start: 74 outliers final: 36 residues processed: 370 average time/residue: 0.1527 time to fit residues: 93.2041 Evaluate side-chains 313 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 62 optimal weight: 30.0000 chunk 228 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 313 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN J 320 ASN J 458 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099161 restraints weight = 47826.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100808 restraints weight = 26179.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102039 restraints weight = 17894.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102476 restraints weight = 15661.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102429 restraints weight = 13827.169| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26903 Z= 0.146 Angle : 0.633 24.735 36644 Z= 0.323 Chirality : 0.053 1.906 4203 Planarity : 0.004 0.049 4541 Dihedral : 15.708 176.854 4377 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.85 % Allowed : 13.68 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3159 helix: 0.59 (0.16), residues: 1083 sheet: -1.08 (0.26), residues: 382 loop : -2.41 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1036 TYR 0.015 0.001 TYR G 177 PHE 0.012 0.001 PHE J 49 TRP 0.009 0.001 TRP J 580 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (26896) covalent geometry : angle 0.63255 / 0.32 (36638) hydrogen bonds : bond 0.04663 / 5.18 ( 1051) hydrogen bonds : angle 4.45793 / 5.26 ( 2902) metal coordination : bond 0.00589 / 0.58 ( 7) metal coordination : angle 1.87310 / 2.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: G 123 ILE cc_start: 0.9189 (mm) cc_final: 0.8941 (mm) REVERT: G 200 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8617 (ttpp) REVERT: G 233 ASP cc_start: 0.5602 (t0) cc_final: 0.5384 (t0) REVERT: H 16 ILE cc_start: 0.8863 (mt) cc_final: 0.8478 (tt) REVERT: H 58 GLU cc_start: 0.7790 (pt0) cc_final: 0.7259 (mt-10) REVERT: H 75 GLN cc_start: 0.7395 (tt0) cc_final: 0.7011 (tm-30) REVERT: H 130 ILE cc_start: 0.9099 (mt) cc_final: 0.8873 (mt) REVERT: I 44 GLU cc_start: 0.7728 (pt0) cc_final: 0.7342 (tt0) REVERT: I 133 ASN cc_start: 0.8283 (m-40) cc_final: 0.7845 (t0) REVERT: I 224 PHE cc_start: 0.7907 (m-80) cc_final: 0.7573 (m-10) REVERT: I 275 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7618 (mmp80) REVERT: I 434 ASP cc_start: 0.7995 (m-30) cc_final: 0.7776 (m-30) REVERT: I 472 GLU cc_start: 0.8349 (pt0) cc_final: 0.7548 (tt0) REVERT: I 800 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7441 (mtp) REVERT: I 978 VAL cc_start: 0.7944 (p) cc_final: 0.7662 (m) REVERT: I 1290 MET cc_start: 0.8393 (tpp) cc_final: 0.8048 (tpp) REVERT: J 295 GLU cc_start: 0.8240 (tp30) cc_final: 0.7476 (tp30) REVERT: J 532 GLU cc_start: 0.7784 (pt0) cc_final: 0.7516 (tt0) REVERT: J 645 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8964 (m) REVERT: J 698 MET cc_start: 0.8851 (tpt) cc_final: 0.8595 (tpp) REVERT: J 882 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8203 (m) REVERT: J 1025 MET cc_start: 0.7118 (mtp) cc_final: 0.6735 (mmt) REVERT: J 1148 ARG cc_start: 0.8195 (mmt90) cc_final: 0.7817 (mpt-90) REVERT: J 1155 ILE cc_start: 0.8983 (pt) cc_final: 0.8717 (mt) REVERT: J 1165 PHE cc_start: 0.8134 (m-80) cc_final: 0.7566 (m-10) REVERT: J 1168 GLU cc_start: 0.6695 (tm-30) cc_final: 0.6478 (tm-30) REVERT: J 1189 MET cc_start: 0.7629 (ttm) cc_final: 0.7157 (tpp) REVERT: J 1361 THR cc_start: 0.6866 (OUTLIER) cc_final: 0.6497 (m) REVERT: K 55 GLU cc_start: 0.7588 (tt0) cc_final: 0.7387 (tt0) outliers start: 77 outliers final: 49 residues processed: 344 average time/residue: 0.1453 time to fit residues: 83.7519 Evaluate side-chains 333 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1183 SER Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 62 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 246 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN J 458 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 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 = 0.3691 r_free = 0.3691 target = 0.130315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098074 restraints weight = 48229.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099569 restraints weight = 28546.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100563 restraints weight = 18950.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101071 restraints weight = 16890.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101151 restraints weight = 14996.496| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26903 Z= 0.176 Angle : 0.649 24.682 36644 Z= 0.331 Chirality : 0.053 1.901 4203 Planarity : 0.004 0.046 4541 Dihedral : 15.680 177.274 4375 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.25 % Allowed : 14.27 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 3159 helix: 0.71 (0.16), residues: 1084 sheet: -1.00 (0.26), residues: 382 loop : -2.34 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1148 TYR 0.015 0.001 TYR G 177 PHE 0.014 0.001 PHE J 49 TRP 0.008 0.001 TRP J 409 HIS 0.005 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (26896) covalent geometry : angle 0.64842 / 0.33 (36638) hydrogen bonds : bond 0.04824 / 5.35 ( 1051) hydrogen bonds : angle 4.43757 / 5.27 ( 2902) metal coordination : bond 0.00792 / 0.78 ( 7) metal coordination : angle 2.16538 / 2.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 292 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: G 200 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8577 (ttpp) REVERT: G 233 ASP cc_start: 0.5689 (t0) cc_final: 0.5445 (t0) REVERT: H 58 GLU cc_start: 0.7845 (pt0) cc_final: 0.7294 (mt-10) REVERT: H 75 GLN cc_start: 0.7379 (tt0) cc_final: 0.6980 (tm-30) REVERT: H 130 ILE cc_start: 0.9110 (mt) cc_final: 0.8893 (mt) REVERT: I 44 GLU cc_start: 0.7864 (pt0) cc_final: 0.7407 (tt0) REVERT: I 224 PHE cc_start: 0.7922 (m-80) cc_final: 0.7630 (m-10) REVERT: I 275 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7608 (mmp80) REVERT: I 283 LYS cc_start: 0.7576 (mttt) cc_final: 0.7033 (tptp) REVERT: I 434 ASP cc_start: 0.8018 (m-30) cc_final: 0.7764 (m-30) REVERT: I 472 GLU cc_start: 0.8400 (pt0) cc_final: 0.7569 (tt0) REVERT: I 765 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8622 (mt) REVERT: I 800 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7388 (mtp) REVERT: I 978 VAL cc_start: 0.7955 (p) cc_final: 0.7692 (m) REVERT: I 1290 MET cc_start: 0.8434 (tpp) cc_final: 0.8081 (tpp) REVERT: J 248 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8688 (t0) REVERT: J 252 LEU cc_start: 0.7781 (pp) cc_final: 0.7544 (pp) REVERT: J 295 GLU cc_start: 0.8185 (tp30) cc_final: 0.7450 (tp30) REVERT: J 625 MET cc_start: 0.9204 (ttp) cc_final: 0.8948 (ttp) REVERT: J 645 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8987 (m) REVERT: J 698 MET cc_start: 0.8917 (tpt) cc_final: 0.8635 (tpp) REVERT: J 714 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8293 (mm-30) REVERT: J 882 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8282 (m) REVERT: J 1025 MET cc_start: 0.7136 (mtp) cc_final: 0.6763 (mmt) REVERT: J 1148 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7920 (mpt-90) REVERT: J 1155 ILE cc_start: 0.8969 (pt) cc_final: 0.8744 (mt) REVERT: J 1165 PHE cc_start: 0.8149 (m-80) cc_final: 0.7603 (m-80) REVERT: J 1168 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6496 (tm-30) REVERT: J 1189 MET cc_start: 0.7661 (ttm) cc_final: 0.7141 (tpp) REVERT: K 55 GLU cc_start: 0.7589 (tt0) cc_final: 0.7358 (tt0) outliers start: 88 outliers final: 63 residues processed: 356 average time/residue: 0.1425 time to fit residues: 84.6691 Evaluate side-chains 340 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1103 VAL Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1183 SER Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 242 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN I 133 ASN J 458 ASN ** J1249 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 = 0.3707 r_free = 0.3707 target = 0.131278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099757 restraints weight = 47579.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101357 restraints weight = 26443.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102503 restraints weight = 17948.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102978 restraints weight = 15843.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102921 restraints weight = 14001.815| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26903 Z= 0.121 Angle : 0.613 24.742 36644 Z= 0.312 Chirality : 0.052 1.909 4203 Planarity : 0.004 0.046 4541 Dihedral : 15.562 177.004 4375 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.77 % Allowed : 15.30 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 3159 helix: 0.92 (0.16), residues: 1084 sheet: -0.77 (0.27), residues: 369 loop : -2.26 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J1148 TYR 0.014 0.001 TYR G 177 PHE 0.022 0.001 PHE I 337 TRP 0.011 0.001 TRP J1193 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (26896) covalent geometry : angle 0.61249 / 0.31 (36638) hydrogen bonds : bond 0.04437 / 4.94 ( 1051) hydrogen bonds : angle 4.30306 / 5.08 ( 2902) metal coordination : bond 0.00450 / 0.45 ( 7) metal coordination : angle 1.41522 / 2.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 290 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: G 123 ILE cc_start: 0.9114 (mm) cc_final: 0.8868 (mm) REVERT: G 200 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8579 (ttpp) REVERT: H 58 GLU cc_start: 0.7741 (pt0) cc_final: 0.7198 (mt-10) REVERT: H 75 GLN cc_start: 0.7408 (tt0) cc_final: 0.7044 (tm-30) REVERT: H 130 ILE cc_start: 0.9099 (mt) cc_final: 0.8875 (mt) REVERT: I 44 GLU cc_start: 0.7804 (pt0) cc_final: 0.7361 (tt0) REVERT: I 224 PHE cc_start: 0.7856 (m-80) cc_final: 0.7534 (m-10) REVERT: I 275 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7621 (mmp80) REVERT: I 283 LYS cc_start: 0.7558 (mttt) cc_final: 0.7004 (tptp) REVERT: I 434 ASP cc_start: 0.7953 (m-30) cc_final: 0.7695 (m-30) REVERT: I 472 GLU cc_start: 0.8368 (pt0) cc_final: 0.7562 (tt0) REVERT: I 765 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8581 (mt) REVERT: I 978 VAL cc_start: 0.7994 (p) cc_final: 0.7788 (m) REVERT: I 1085 MET cc_start: 0.8782 (mmt) cc_final: 0.8561 (mmt) REVERT: I 1290 MET cc_start: 0.8409 (tpp) cc_final: 0.8072 (tpp) REVERT: J 248 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8702 (t0) REVERT: J 252 LEU cc_start: 0.7740 (pp) cc_final: 0.7495 (mt) REVERT: J 295 GLU cc_start: 0.8161 (tp30) cc_final: 0.7425 (tp30) REVERT: J 645 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8964 (m) REVERT: J 714 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8254 (mm-30) REVERT: J 882 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8269 (m) REVERT: J 1025 MET cc_start: 0.7085 (mtp) cc_final: 0.6730 (mmt) REVERT: J 1148 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7696 (mtt-85) REVERT: J 1165 PHE cc_start: 0.8121 (m-80) cc_final: 0.7586 (m-80) REVERT: J 1189 MET cc_start: 0.7638 (ttm) cc_final: 0.7184 (tpp) REVERT: J 1361 THR cc_start: 0.6712 (OUTLIER) cc_final: 0.6173 (m) REVERT: K 41 GLU cc_start: 0.8388 (pm20) cc_final: 0.8006 (tt0) REVERT: K 55 GLU cc_start: 0.7555 (tt0) cc_final: 0.7316 (tt0) REVERT: K 74 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7477 (mm-30) outliers start: 75 outliers final: 53 residues processed: 346 average time/residue: 0.1524 time to fit residues: 87.4165 Evaluate side-chains 335 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 10 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN J 458 ASN J1249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099984 restraints weight = 47884.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102459 restraints weight = 25967.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103854 restraints weight = 16462.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104258 restraints weight = 14125.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104149 restraints weight = 13086.621| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26903 Z= 0.116 Angle : 0.603 24.798 36644 Z= 0.308 Chirality : 0.052 1.911 4203 Planarity : 0.004 0.046 4541 Dihedral : 15.478 177.200 4375 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.29 % Allowed : 16.16 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 3159 helix: 1.02 (0.16), residues: 1081 sheet: -0.45 (0.28), residues: 343 loop : -2.17 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1067 TYR 0.013 0.001 TYR G 177 PHE 0.019 0.001 PHE I 337 TRP 0.010 0.001 TRP J 580 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (26896) covalent geometry : angle 0.60238 / 0.31 (36638) hydrogen bonds : bond 0.04272 / 4.78 ( 1051) hydrogen bonds : angle 4.21604 / 4.96 ( 2902) metal coordination : bond 0.00403 / 0.41 ( 7) metal coordination : angle 1.61990 / 2.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 291 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: G 123 ILE cc_start: 0.9117 (mm) cc_final: 0.8866 (mm) REVERT: G 200 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8565 (ttpp) REVERT: H 75 GLN cc_start: 0.7443 (tt0) cc_final: 0.7076 (tm-30) REVERT: H 130 ILE cc_start: 0.9084 (mt) cc_final: 0.8875 (mt) REVERT: I 44 GLU cc_start: 0.7809 (pt0) cc_final: 0.7343 (tt0) REVERT: I 224 PHE cc_start: 0.7899 (m-80) cc_final: 0.7575 (m-10) REVERT: I 275 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7643 (mmp80) REVERT: I 283 LYS cc_start: 0.7521 (mttt) cc_final: 0.6934 (tptp) REVERT: I 434 ASP cc_start: 0.7948 (m-30) cc_final: 0.7694 (m-30) REVERT: I 472 GLU cc_start: 0.8332 (pt0) cc_final: 0.7567 (tt0) REVERT: I 765 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8521 (mt) REVERT: I 1290 MET cc_start: 0.8413 (tpp) cc_final: 0.8063 (tpp) REVERT: J 248 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8706 (t0) REVERT: J 252 LEU cc_start: 0.7789 (pp) cc_final: 0.7465 (mt) REVERT: J 295 GLU cc_start: 0.8162 (tp30) cc_final: 0.7409 (tp30) REVERT: J 645 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8959 (m) REVERT: J 882 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8246 (m) REVERT: J 1025 MET cc_start: 0.7074 (mtp) cc_final: 0.6720 (mmt) REVERT: J 1148 ARG cc_start: 0.8090 (mmt90) cc_final: 0.7790 (mpt-90) REVERT: J 1165 PHE cc_start: 0.8127 (m-80) cc_final: 0.7605 (m-80) REVERT: J 1189 MET cc_start: 0.7645 (ttm) cc_final: 0.7214 (tpp) REVERT: K 41 GLU cc_start: 0.8359 (pm20) cc_final: 0.8040 (tt0) REVERT: K 55 GLU cc_start: 0.7503 (tt0) cc_final: 0.7287 (tt0) REVERT: K 74 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7440 (mm-30) outliers start: 62 outliers final: 46 residues processed: 339 average time/residue: 0.1497 time to fit residues: 84.4339 Evaluate side-chains 326 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 133 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 319 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.0000 chunk 10 optimal weight: 0.6980 chunk 202 optimal weight: 6.9990 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101849 restraints weight = 47988.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103490 restraints weight = 26301.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104730 restraints weight = 18080.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105139 restraints weight = 15497.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105068 restraints weight = 13736.162| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26903 Z= 0.108 Angle : 0.592 24.852 36644 Z= 0.302 Chirality : 0.052 1.913 4203 Planarity : 0.004 0.049 4541 Dihedral : 15.410 178.380 4375 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.44 % Allowed : 16.23 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3159 helix: 1.12 (0.16), residues: 1081 sheet: -0.36 (0.28), residues: 338 loop : -2.10 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1067 TYR 0.013 0.001 TYR G 177 PHE 0.020 0.001 PHE I 337 TRP 0.010 0.001 TRP J 580 HIS 0.003 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (26896) covalent geometry : angle 0.59212 / 0.30 (36638) hydrogen bonds : bond 0.04077 / 4.58 ( 1051) hydrogen bonds : angle 4.15981 / 4.87 ( 2902) metal coordination : bond 0.00310 / 0.32 ( 7) metal coordination : angle 1.41723 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 300 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8193 (m-10) REVERT: G 123 ILE cc_start: 0.9082 (mm) cc_final: 0.8834 (mm) REVERT: G 200 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8551 (ttpp) REVERT: H 75 GLN cc_start: 0.7419 (tt0) cc_final: 0.7076 (tm-30) REVERT: H 76 GLU cc_start: 0.6592 (mp0) cc_final: 0.6297 (mp0) REVERT: H 130 ILE cc_start: 0.9073 (mt) cc_final: 0.8868 (mt) REVERT: I 44 GLU cc_start: 0.7823 (pt0) cc_final: 0.7324 (tt0) REVERT: I 121 GLU cc_start: 0.7960 (pp20) cc_final: 0.7479 (pp20) REVERT: I 275 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7644 (mmp80) REVERT: I 283 LYS cc_start: 0.7541 (mttt) cc_final: 0.7130 (mtmt) REVERT: I 383 SER cc_start: 0.8780 (m) cc_final: 0.8528 (p) REVERT: I 434 ASP cc_start: 0.7865 (m-30) cc_final: 0.7610 (m-30) REVERT: I 472 GLU cc_start: 0.8299 (pt0) cc_final: 0.7553 (tt0) REVERT: I 765 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8545 (mt) REVERT: I 1244 HIS cc_start: 0.7588 (t70) cc_final: 0.7261 (t70) REVERT: I 1290 MET cc_start: 0.8409 (tpp) cc_final: 0.8021 (tpp) REVERT: J 248 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8667 (t0) REVERT: J 252 LEU cc_start: 0.7772 (pp) cc_final: 0.7446 (mt) REVERT: J 295 GLU cc_start: 0.8248 (tp30) cc_final: 0.7457 (tp30) REVERT: J 882 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8228 (m) REVERT: J 1148 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7757 (mpt-90) REVERT: J 1165 PHE cc_start: 0.8087 (m-80) cc_final: 0.7584 (m-10) REVERT: J 1189 MET cc_start: 0.7562 (ttm) cc_final: 0.7163 (tpp) REVERT: K 74 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7466 (mm-30) outliers start: 66 outliers final: 49 residues processed: 352 average time/residue: 0.1457 time to fit residues: 85.5535 Evaluate side-chains 333 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 212 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 194 GLN I 343 HIS ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099480 restraints weight = 47771.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101448 restraints weight = 26130.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102603 restraints weight = 17593.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102955 restraints weight = 15538.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102903 restraints weight = 13781.766| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26903 Z= 0.149 Angle : 0.631 24.832 36644 Z= 0.318 Chirality : 0.052 1.905 4203 Planarity : 0.004 0.046 4541 Dihedral : 15.430 178.134 4375 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.18 % Allowed : 17.08 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3159 helix: 1.16 (0.16), residues: 1082 sheet: -0.28 (0.28), residues: 345 loop : -2.07 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1067 TYR 0.022 0.001 TYR J 165 PHE 0.016 0.001 PHE J 49 TRP 0.009 0.001 TRP J 409 HIS 0.003 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (26896) covalent geometry : angle 0.63032 / 0.32 (36638) hydrogen bonds : bond 0.04365 / 4.86 ( 1051) hydrogen bonds : angle 4.19915 / 4.99 ( 2902) metal coordination : bond 0.00606 / 0.61 ( 7) metal coordination : angle 2.04352 / 2.71 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: G 123 ILE cc_start: 0.9147 (mm) cc_final: 0.8891 (mm) REVERT: G 200 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8590 (ttpp) REVERT: H 75 GLN cc_start: 0.7462 (tt0) cc_final: 0.7094 (tm-30) REVERT: H 130 ILE cc_start: 0.9100 (mt) cc_final: 0.8885 (mt) REVERT: I 44 GLU cc_start: 0.7837 (pt0) cc_final: 0.7366 (tt0) REVERT: I 121 GLU cc_start: 0.8018 (pp20) cc_final: 0.7544 (pp20) REVERT: I 224 PHE cc_start: 0.7916 (m-80) cc_final: 0.7614 (m-10) REVERT: I 275 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7640 (mmp80) REVERT: I 283 LYS cc_start: 0.7550 (mttt) cc_final: 0.7131 (mtmt) REVERT: I 434 ASP cc_start: 0.7924 (m-30) cc_final: 0.7665 (m-30) REVERT: I 472 GLU cc_start: 0.8347 (pt0) cc_final: 0.7592 (tt0) REVERT: I 1290 MET cc_start: 0.8459 (tpp) cc_final: 0.8082 (tpp) REVERT: J 248 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8703 (t0) REVERT: J 252 LEU cc_start: 0.7801 (pp) cc_final: 0.7451 (mt) REVERT: J 625 MET cc_start: 0.9207 (ttp) cc_final: 0.8952 (ttp) REVERT: J 698 MET cc_start: 0.8765 (tpt) cc_final: 0.8515 (tpp) REVERT: J 882 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8310 (m) REVERT: J 1148 ARG cc_start: 0.8099 (mmt90) cc_final: 0.7790 (mpt-90) REVERT: J 1165 PHE cc_start: 0.8062 (m-80) cc_final: 0.7554 (m-80) REVERT: J 1189 MET cc_start: 0.7502 (ttm) cc_final: 0.7083 (tpp) REVERT: K 41 GLU cc_start: 0.8374 (pm20) cc_final: 0.8011 (pt0) outliers start: 59 outliers final: 47 residues processed: 324 average time/residue: 0.1534 time to fit residues: 82.4167 Evaluate side-chains 324 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 30.0000 chunk 265 optimal weight: 0.3980 chunk 182 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 517 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101008 restraints weight = 47873.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103208 restraints weight = 26539.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104678 restraints weight = 17395.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104846 restraints weight = 15299.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104679 restraints weight = 13249.302| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26903 Z= 0.125 Angle : 0.614 24.860 36644 Z= 0.311 Chirality : 0.052 1.908 4203 Planarity : 0.004 0.047 4541 Dihedral : 15.403 178.613 4375 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.92 % Allowed : 17.52 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3159 helix: 1.16 (0.16), residues: 1081 sheet: -0.21 (0.28), residues: 340 loop : -2.03 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1194 TYR 0.028 0.001 TYR J 165 PHE 0.026 0.001 PHE I 337 TRP 0.010 0.001 TRP J 580 HIS 0.003 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (26896) covalent geometry : angle 0.61412 / 0.31 (36638) hydrogen bonds : bond 0.04258 / 4.76 ( 1051) hydrogen bonds : angle 4.15360 / 4.93 ( 2902) metal coordination : bond 0.00450 / 0.45 ( 7) metal coordination : angle 1.57635 / 2.28 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.04 seconds wall clock time: 64 minutes 3.09 seconds (3843.09 seconds total)