Starting phenix.real_space_refine on Wed Nov 19 19:04:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6asx_7002/11_2025/6asx_7002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6asx_7002/11_2025/6asx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6asx_7002/11_2025/6asx_7002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6asx_7002/11_2025/6asx_7002.map" model { file = "/net/cci-nas-00/data/ceres_data/6asx_7002/11_2025/6asx_7002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6asx_7002/11_2025/6asx_7002_neut.cif" } 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-2.0-5881/lib/python3.9/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: 6.50, per 1000 atoms: 0.25 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: 2.46 Conformation dependent library (CDL) restraints added in 1.3 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: 3.59 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: 7.08 Time building geometry restraints manager: 3.24 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=" N TRP J1193 " pdb=" CA TRP J1193 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.90e-02 2.77e+03 7.28e+00 bond pdb=" C VAL I1103 " pdb=" N PRO I1104 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.23e-02 6.61e+03 5.74e+00 bond pdb=" C LYS J1192 " pdb=" N TRP J1193 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.40e-02 5.10e+03 5.60e+00 bond pdb=" CB VAL J 801 " pdb=" CG2 VAL J 801 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.82e+00 bond pdb=" CB VAL J1255 " pdb=" CG1 VAL J1255 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 ... (remaining 26891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 36505 5.25 - 10.50: 128 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=" C LEU J1344 " pdb=" N ARG J1345 " pdb=" CA ARG J1345 " ideal model delta sigma weight residual 123.93 131.20 -7.27 1.54e+00 4.22e-01 2.23e+01 angle pdb=" C ASP J 18 " pdb=" N ALA J 19 " pdb=" CA ALA J 19 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+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 - 0.389: 4201 0.389 - 0.777: 1 0.777 - 1.166: 0 1.166 - 1.554: 0 1.554 - 1.943: 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 2.35 0.40 1.94 2.00e-01 2.50e+01 9.44e+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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 33.750 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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= 0.365 Angle : 1.058 29.408 36644 Z= 0.555 Chirality : 0.068 1.943 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 covalent geometry : bond 0.00845 (26896) covalent geometry : angle 1.03924 (36638) hydrogen bonds : bond 0.10828 ( 1051) hydrogen bonds : angle 5.96068 ( 2902) metal coordination : bond 0.13756 ( 7) metal coordination : angle 15.48272 ( 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 : 1.056 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: G 25 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8647 (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: 0.8101 (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: 0.7482 (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: 0.8103 (tpp) REVERT: J 264 ASP cc_start: 0.8487 (m-30) cc_final: 0.8226 (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: 0.7001 (mm-30) REVERT: J 1155 ILE cc_start: 0.9196 (pt) cc_final: 0.8730 (mt) REVERT: J 1165 PHE cc_start: 0.8321 (m-80) cc_final: 0.7656 (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: 0.2190 time to fit residues: 217.2480 Evaluate side-chains 298 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: H 194 GLN I 69 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS I 952 GLN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN I1220 GLN 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 J1367 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099022 restraints weight = 47967.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101399 restraints weight = 26073.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103500 restraints weight = 16572.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103374 restraints weight = 13591.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103436 restraints weight = 12889.150| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26903 Z= 0.159 Angle : 0.691 25.881 36644 Z= 0.356 Chirality : 0.053 1.928 4203 Planarity : 0.005 0.059 4541 Dihedral : 15.864 179.200 4379 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.40 % Allowed : 9.98 % Favored : 87.62 % 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: -2.78 (0.13), residues: 3159 helix: -0.66 (0.15), residues: 1097 sheet: -1.77 (0.25), residues: 372 loop : -2.78 (0.13), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 359 TYR 0.022 0.001 TYR J1186 PHE 0.018 0.001 PHE I 337 TRP 0.011 0.002 TRP I 997 HIS 0.005 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00358 (26896) covalent geometry : angle 0.69030 (36638) hydrogen bonds : bond 0.05144 ( 1051) hydrogen bonds : angle 4.88116 ( 2902) metal coordination : bond 0.00711 ( 7) metal coordination : angle 2.69843 ( 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 420 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 355 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8662 (ttpp) REVERT: H 16 ILE cc_start: 0.8848 (mt) cc_final: 0.8474 (tt) REVERT: H 58 GLU cc_start: 0.7773 (pt0) cc_final: 0.7333 (mt-10) REVERT: H 199 ASP cc_start: 0.7893 (m-30) cc_final: 0.7612 (m-30) REVERT: I 44 GLU cc_start: 0.7646 (pt0) cc_final: 0.7326 (tt0) REVERT: I 133 ASN cc_start: 0.8409 (m-40) cc_final: 0.8119 (m-40) REVERT: I 275 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7600 (mmp80) REVERT: I 322 LEU cc_start: 0.7456 (mt) cc_final: 0.7154 (tp) REVERT: I 424 ASP cc_start: 0.7835 (m-30) cc_final: 0.7626 (m-30) REVERT: I 434 ASP cc_start: 0.8081 (m-30) cc_final: 0.7822 (m-30) REVERT: I 1273 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: I 1290 MET cc_start: 0.8431 (tpp) cc_final: 0.8024 (tpp) REVERT: J 49 PHE cc_start: 0.7225 (m-10) cc_final: 0.6964 (m-10) REVERT: J 248 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8609 (t0) REVERT: J 264 ASP cc_start: 0.8462 (m-30) cc_final: 0.8098 (m-30) REVERT: J 295 GLU cc_start: 0.8198 (tp30) cc_final: 0.7510 (tp30) REVERT: J 372 MET cc_start: 0.8932 (mtp) cc_final: 0.8671 (ttm) REVERT: J 532 GLU cc_start: 0.7841 (pt0) cc_final: 0.7419 (tt0) REVERT: J 700 ASN cc_start: 0.8546 (t0) cc_final: 0.8341 (t0) REVERT: J 772 TYR cc_start: 0.8869 (t80) cc_final: 0.8441 (t80) REVERT: J 1025 MET cc_start: 0.7182 (mtp) cc_final: 0.6776 (mmt) REVERT: J 1155 ILE cc_start: 0.9125 (pt) cc_final: 0.8719 (mt) REVERT: J 1165 PHE cc_start: 0.8183 (m-80) cc_final: 0.7578 (m-10) REVERT: J 1168 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6313 (tm-30) REVERT: J 1189 MET cc_start: 0.7670 (ttm) cc_final: 0.7185 (tpp) REVERT: K 55 GLU cc_start: 0.7724 (tt0) cc_final: 0.7019 (tt0) REVERT: K 58 LEU cc_start: 0.8324 (pp) cc_final: 0.8105 (pp) outliers start: 65 outliers final: 33 residues processed: 399 average time/residue: 0.1795 time to fit residues: 114.5690 Evaluate side-chains 311 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 54 CYS 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 410 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 712 SER Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 111 THR 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 826 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1344 LEU 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: 3.9990 chunk 289 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** 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** K 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095243 restraints weight = 48222.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097513 restraints weight = 26411.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098230 restraints weight = 17459.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098730 restraints weight = 16146.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098668 restraints weight = 14104.097| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26903 Z= 0.238 Angle : 0.723 25.642 36644 Z= 0.370 Chirality : 0.054 1.929 4203 Planarity : 0.005 0.049 4541 Dihedral : 15.777 179.162 4377 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.44 % Allowed : 12.46 % Favored : 84.10 % 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: -2.32 (0.14), residues: 3159 helix: 0.03 (0.16), residues: 1091 sheet: -1.57 (0.25), residues: 377 loop : -2.72 (0.13), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 45 TYR 0.019 0.002 TYR G 177 PHE 0.014 0.002 PHE I 828 TRP 0.012 0.002 TRP I 183 HIS 0.006 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00557 (26896) covalent geometry : angle 0.72211 (36638) hydrogen bonds : bond 0.05462 ( 1051) hydrogen bonds : angle 4.78786 ( 2902) metal coordination : bond 0.01050 ( 7) metal coordination : angle 3.17663 ( 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: 93 poor density : 284 time to evaluate : 0.896 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: 0.8535 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: G 153 VAL cc_start: 0.9195 (t) cc_final: 0.8921 (m) REVERT: G 200 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8624 (ttpp) REVERT: H 58 GLU cc_start: 0.7860 (pt0) cc_final: 0.7322 (mt-10) REVERT: I 44 GLU cc_start: 0.7799 (pt0) cc_final: 0.7440 (tt0) REVERT: I 133 ASN cc_start: 0.8324 (m-40) cc_final: 0.8105 (m-40) REVERT: I 275 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7590 (mmp80) REVERT: I 434 ASP cc_start: 0.8044 (m-30) cc_final: 0.7792 (m-30) REVERT: I 472 GLU cc_start: 0.8454 (pt0) cc_final: 0.7651 (tt0) REVERT: I 800 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7450 (mtp) REVERT: I 1085 MET cc_start: 0.8955 (mmt) cc_final: 0.8415 (mmt) REVERT: I 1290 MET cc_start: 0.8455 (tpp) cc_final: 0.8020 (tpp) REVERT: J 151 MET cc_start: 0.6995 (pmm) cc_final: 0.6765 (pmm) REVERT: J 248 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8539 (t0) REVERT: J 252 LEU cc_start: 0.7932 (pp) cc_final: 0.7704 (pp) REVERT: J 295 GLU cc_start: 0.8237 (tp30) cc_final: 0.7531 (tp30) REVERT: J 372 MET cc_start: 0.8971 (mtp) cc_final: 0.8626 (ttm) REVERT: J 532 GLU cc_start: 0.7900 (pt0) cc_final: 0.7593 (tt0) REVERT: J 581 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8560 (ttm) REVERT: J 882 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8312 (m) REVERT: J 1155 ILE cc_start: 0.8993 (pt) cc_final: 0.8749 (mt) REVERT: J 1165 PHE cc_start: 0.8179 (m-80) cc_final: 0.7615 (m-80) REVERT: J 1189 MET cc_start: 0.7624 (ttm) cc_final: 0.7135 (tpp) REVERT: K 55 GLU cc_start: 0.7798 (tt0) cc_final: 0.7439 (tt0) REVERT: K 58 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8221 (pp) outliers start: 93 outliers final: 59 residues processed: 353 average time/residue: 0.1678 time to fit residues: 99.0277 Evaluate side-chains 325 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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 196 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 400 VAL 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 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 616 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 717 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 1036 ILE Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL 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 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 154 LEU 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 581 MET Chi-restraints excluded: chain J residue 826 ILE 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 1183 SER Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1361 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 255 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 277 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN I 150 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3703 r_free = 0.3703 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099380 restraints weight = 47784.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101040 restraints weight = 25958.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102150 restraints weight = 18312.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102627 restraints weight = 15476.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102625 restraints weight = 13752.151| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26903 Z= 0.127 Angle : 0.619 25.731 36644 Z= 0.315 Chirality : 0.052 1.942 4203 Planarity : 0.004 0.049 4541 Dihedral : 15.551 179.926 4375 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.81 % Allowed : 13.49 % Favored : 83.70 % 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: -1.81 (0.14), residues: 3159 helix: 0.55 (0.16), residues: 1083 sheet: -1.31 (0.26), residues: 369 loop : -2.46 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 359 TYR 0.014 0.001 TYR G 177 PHE 0.011 0.001 PHE J1319 TRP 0.011 0.001 TRP J 580 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00282 (26896) covalent geometry : angle 0.61812 (36638) hydrogen bonds : bond 0.04488 ( 1051) hydrogen bonds : angle 4.43894 ( 2902) metal coordination : bond 0.00443 ( 7) metal coordination : angle 1.87892 ( 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 395 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 319 time to evaluate : 1.032 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: 0.8489 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: G 153 VAL cc_start: 0.9149 (t) cc_final: 0.8883 (m) REVERT: G 200 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8621 (ttpp) REVERT: H 58 GLU cc_start: 0.7771 (pt0) cc_final: 0.7260 (mt-10) REVERT: H 130 ILE cc_start: 0.9097 (mt) cc_final: 0.8870 (mt) REVERT: I 44 GLU cc_start: 0.7736 (pt0) cc_final: 0.7333 (tt0) REVERT: I 133 ASN cc_start: 0.8234 (m-40) cc_final: 0.7968 (t0) REVERT: I 275 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7606 (mmp80) REVERT: I 383 SER cc_start: 0.8885 (m) cc_final: 0.8612 (p) REVERT: I 434 ASP cc_start: 0.7953 (m-30) cc_final: 0.7705 (m-30) REVERT: I 472 GLU cc_start: 0.8339 (pt0) cc_final: 0.7531 (tt0) REVERT: I 524 ILE cc_start: 0.9176 (tp) cc_final: 0.8975 (tp) REVERT: I 765 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8602 (mt) REVERT: I 978 VAL cc_start: 0.7901 (p) cc_final: 0.7607 (m) REVERT: I 1290 MET cc_start: 0.8465 (tpp) cc_final: 0.8132 (tpp) REVERT: J 151 MET cc_start: 0.6970 (pmm) cc_final: 0.6605 (pmm) REVERT: J 295 GLU cc_start: 0.8166 (tp30) cc_final: 0.7435 (tp30) REVERT: J 532 GLU cc_start: 0.7754 (pt0) cc_final: 0.7493 (tt0) REVERT: J 882 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8203 (m) REVERT: J 1025 MET cc_start: 0.7087 (mtp) cc_final: 0.6713 (mmt) REVERT: J 1148 ARG cc_start: 0.8274 (mpt-90) cc_final: 0.7776 (mpt-90) REVERT: J 1165 PHE cc_start: 0.8153 (m-80) cc_final: 0.7624 (m-80) REVERT: J 1189 MET cc_start: 0.7542 (ttm) cc_final: 0.7050 (tpp) REVERT: K 41 GLU cc_start: 0.8577 (pm20) cc_final: 0.8152 (pt0) REVERT: K 58 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8195 (pp) outliers start: 76 outliers final: 43 residues processed: 376 average time/residue: 0.1644 time to fit residues: 102.6288 Evaluate side-chains 324 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 H residue 9 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 104 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 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 819 SER 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 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 111 THR 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 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 826 ILE 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 1143 ASP 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 K residue 36 ASP Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 62 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 282 optimal weight: 20.0000 chunk 313 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.130159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097346 restraints weight = 47981.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100071 restraints weight = 26545.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100583 restraints weight = 16619.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101153 restraints weight = 15849.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101181 restraints weight = 14147.231| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26903 Z= 0.159 Angle : 0.634 25.729 36644 Z= 0.321 Chirality : 0.052 1.938 4203 Planarity : 0.004 0.046 4541 Dihedral : 15.500 179.642 4375 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.40 % Allowed : 14.05 % Favored : 82.55 % 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: -1.57 (0.15), residues: 3159 helix: 0.75 (0.16), residues: 1083 sheet: -1.07 (0.26), residues: 368 loop : -2.35 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 271 TYR 0.014 0.001 TYR G 177 PHE 0.010 0.001 PHE J1319 TRP 0.010 0.001 TRP J 580 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00365 (26896) covalent geometry : angle 0.63327 (36638) hydrogen bonds : bond 0.04691 ( 1051) hydrogen bonds : angle 4.37603 ( 2902) metal coordination : bond 0.00688 ( 7) metal coordination : angle 2.19951 ( 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 382 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 290 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: G 123 ILE cc_start: 0.9207 (mm) cc_final: 0.8942 (mm) REVERT: G 153 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8944 (m) REVERT: G 200 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8592 (ttpp) REVERT: H 58 GLU cc_start: 0.7850 (pt0) cc_final: 0.7287 (mt-10) REVERT: I 44 GLU cc_start: 0.7819 (pt0) cc_final: 0.7430 (tt0) REVERT: I 275 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7628 (mmp80) REVERT: I 424 ASP cc_start: 0.7966 (m-30) cc_final: 0.7721 (m-30) REVERT: I 434 ASP cc_start: 0.8005 (m-30) cc_final: 0.7744 (m-30) REVERT: I 472 GLU cc_start: 0.8400 (pt0) cc_final: 0.7556 (tt0) REVERT: I 978 VAL cc_start: 0.7965 (p) cc_final: 0.7711 (m) REVERT: I 1290 MET cc_start: 0.8438 (tpp) cc_final: 0.8079 (tpp) REVERT: J 151 MET cc_start: 0.7201 (pmm) cc_final: 0.6776 (pmm) REVERT: J 295 GLU cc_start: 0.8278 (tp30) cc_final: 0.7920 (tp30) REVERT: J 314 ARG cc_start: 0.6945 (ttp-170) cc_final: 0.6692 (ttp-170) REVERT: J 326 SER cc_start: 0.9200 (p) cc_final: 0.8790 (t) REVERT: J 714 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8254 (mm-30) REVERT: J 882 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8239 (m) REVERT: J 1025 MET cc_start: 0.7139 (mtp) cc_final: 0.6755 (mmt) REVERT: J 1148 ARG cc_start: 0.8261 (mpt-90) cc_final: 0.7943 (mpt-90) REVERT: J 1165 PHE cc_start: 0.8132 (m-80) cc_final: 0.7616 (m-80) REVERT: J 1189 MET cc_start: 0.7710 (ttm) cc_final: 0.7192 (tpp) REVERT: J 1361 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6465 (m) REVERT: K 55 GLU cc_start: 0.7522 (tt0) cc_final: 0.7249 (tt0) REVERT: K 58 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8248 (pp) REVERT: K 74 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7488 (mm-30) outliers start: 92 outliers final: 64 residues processed: 360 average time/residue: 0.1638 time to fit residues: 98.6274 Evaluate side-chains 338 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 153 VAL 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 158 ASP Chi-restraints excluded: chain I residue 196 VAL 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 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 576 SER 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 882 ILE Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1103 VAL Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1225 VAL 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 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 154 LEU 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 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 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1143 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1183 SER Chi-restraints excluded: chain J residue 1267 VAL 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 46 THR Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 62 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 246 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN J 458 ASN J1249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099897 restraints weight = 47764.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101931 restraints weight = 25861.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102876 restraints weight = 17435.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103319 restraints weight = 15647.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103339 restraints weight = 13708.975| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26903 Z= 0.118 Angle : 0.600 25.818 36644 Z= 0.303 Chirality : 0.052 1.944 4203 Planarity : 0.004 0.047 4541 Dihedral : 15.367 179.596 4375 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.99 % Allowed : 14.82 % Favored : 82.18 % 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: -1.32 (0.15), residues: 3159 helix: 0.93 (0.16), residues: 1080 sheet: -0.71 (0.28), residues: 338 loop : -2.21 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J1262 TYR 0.013 0.001 TYR G 177 PHE 0.012 0.001 PHE I 828 TRP 0.010 0.001 TRP J1193 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00265 (26896) covalent geometry : angle 0.59987 (36638) hydrogen bonds : bond 0.04234 ( 1051) hydrogen bonds : angle 4.23122 ( 2902) metal coordination : bond 0.00401 ( 7) metal coordination : angle 1.64469 ( 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 382 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: G 123 ILE cc_start: 0.9128 (mm) cc_final: 0.8883 (mm) REVERT: G 153 VAL cc_start: 0.9192 (t) cc_final: 0.8928 (m) REVERT: G 200 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8598 (ttpp) REVERT: H 75 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6828 (tm-30) REVERT: I 44 GLU cc_start: 0.7795 (pt0) cc_final: 0.7362 (tt0) REVERT: I 121 GLU cc_start: 0.7995 (pp20) cc_final: 0.7546 (pp20) REVERT: I 275 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7658 (mmp80) REVERT: I 383 SER cc_start: 0.8826 (m) cc_final: 0.8573 (p) REVERT: I 424 ASP cc_start: 0.8001 (m-30) cc_final: 0.7764 (m-30) REVERT: I 434 ASP cc_start: 0.7877 (m-30) cc_final: 0.7637 (m-30) REVERT: I 472 GLU cc_start: 0.8334 (pt0) cc_final: 0.7558 (tt0) REVERT: I 765 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8514 (mt) REVERT: I 862 LEU cc_start: 0.8579 (mt) cc_final: 0.8317 (tp) REVERT: I 978 VAL cc_start: 0.7935 (p) cc_final: 0.7725 (m) REVERT: I 1230 MET cc_start: 0.8892 (ttm) cc_final: 0.8655 (ttt) REVERT: I 1290 MET cc_start: 0.8433 (tpp) cc_final: 0.8096 (tpp) REVERT: J 151 MET cc_start: 0.7280 (pmm) cc_final: 0.6909 (pmm) REVERT: J 314 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.6575 (ttp-170) REVERT: J 882 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8227 (m) REVERT: J 1148 ARG cc_start: 0.8218 (mpt-90) cc_final: 0.7683 (mtt-85) REVERT: J 1165 PHE cc_start: 0.8110 (m-80) cc_final: 0.7653 (m-80) REVERT: J 1189 MET cc_start: 0.7762 (ttm) cc_final: 0.7244 (tpp) REVERT: K 41 GLU cc_start: 0.8516 (pm20) cc_final: 0.8066 (pt0) REVERT: K 51 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7738 (mp) REVERT: K 55 GLU cc_start: 0.7488 (tt0) cc_final: 0.7132 (tt0) REVERT: K 58 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8226 (pp) REVERT: K 74 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7421 (mm-30) outliers start: 81 outliers final: 52 residues processed: 362 average time/residue: 0.1663 time to fit residues: 100.2431 Evaluate side-chains 334 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 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 558 VAL Chi-restraints excluded: chain I residue 576 SER 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 882 ILE Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1082 ILE 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 1327 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 416 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 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 826 ILE Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 974 VAL 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 1267 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 242 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1080 ASN J 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099830 restraints weight = 47474.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101825 restraints weight = 25813.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102700 restraints weight = 17507.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103225 restraints weight = 15750.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103140 restraints weight = 13717.671| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26903 Z= 0.125 Angle : 0.597 25.875 36644 Z= 0.300 Chirality : 0.052 1.944 4203 Planarity : 0.004 0.047 4541 Dihedral : 15.280 179.688 4375 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.88 % Allowed : 15.90 % Favored : 81.22 % 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: -1.16 (0.15), residues: 3159 helix: 1.04 (0.16), residues: 1079 sheet: -0.51 (0.28), residues: 337 loop : -2.13 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1067 TYR 0.012 0.001 TYR J 631 PHE 0.009 0.001 PHE I 828 TRP 0.010 0.001 TRP J 580 HIS 0.008 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00282 (26896) covalent geometry : angle 0.59629 (36638) hydrogen bonds : bond 0.04225 ( 1051) hydrogen bonds : angle 4.17989 ( 2902) metal coordination : bond 0.00437 ( 7) metal coordination : angle 1.75155 ( 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 378 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 300 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: G 123 ILE cc_start: 0.9145 (mm) cc_final: 0.8897 (mm) REVERT: G 153 VAL cc_start: 0.9202 (t) cc_final: 0.8940 (m) REVERT: G 200 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8557 (ttpp) REVERT: H 75 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6908 (tm-30) REVERT: H 130 ILE cc_start: 0.9119 (mt) cc_final: 0.8803 (mt) REVERT: I 44 GLU cc_start: 0.7901 (pt0) cc_final: 0.7497 (tt0) REVERT: I 121 GLU cc_start: 0.8029 (pp20) cc_final: 0.7570 (pp20) REVERT: I 275 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7656 (mmp80) REVERT: I 283 LYS cc_start: 0.7537 (mttt) cc_final: 0.7141 (mtmt) REVERT: I 383 SER cc_start: 0.8825 (m) cc_final: 0.8565 (p) REVERT: I 424 ASP cc_start: 0.7998 (m-30) cc_final: 0.7767 (m-30) REVERT: I 434 ASP cc_start: 0.7921 (m-30) cc_final: 0.7692 (m-30) REVERT: I 472 GLU cc_start: 0.8359 (pt0) cc_final: 0.7562 (tt0) REVERT: I 681 MET cc_start: 0.8528 (ttm) cc_final: 0.8326 (mtt) REVERT: I 862 LEU cc_start: 0.8551 (mt) cc_final: 0.8319 (tp) REVERT: I 1166 ASP cc_start: 0.7648 (t0) cc_final: 0.7380 (t0) REVERT: I 1290 MET cc_start: 0.8464 (tpp) cc_final: 0.8101 (tpp) REVERT: J 49 PHE cc_start: 0.7124 (m-10) cc_final: 0.6816 (m-10) REVERT: J 151 MET cc_start: 0.7210 (pmm) cc_final: 0.6867 (pmm) REVERT: J 252 LEU cc_start: 0.7752 (pp) cc_final: 0.7497 (mt) REVERT: J 314 ARG cc_start: 0.6908 (ttp-170) cc_final: 0.6681 (ttp-170) REVERT: J 326 SER cc_start: 0.9124 (p) cc_final: 0.8665 (t) REVERT: J 882 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8238 (m) REVERT: J 1148 ARG cc_start: 0.8209 (mpt-90) cc_final: 0.7713 (mtt-85) REVERT: J 1165 PHE cc_start: 0.8075 (m-80) cc_final: 0.7634 (m-80) REVERT: J 1189 MET cc_start: 0.7792 (ttm) cc_final: 0.7307 (tpp) REVERT: K 41 GLU cc_start: 0.8599 (pm20) cc_final: 0.8137 (pt0) REVERT: K 58 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8216 (pp) outliers start: 78 outliers final: 62 residues processed: 357 average time/residue: 0.1637 time to fit residues: 96.5479 Evaluate side-chains 339 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 107 ILE 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 H residue 98 VAL 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 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 558 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 615 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 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1207 SER 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 44 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 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 651 HIS Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 974 VAL 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 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: 5.9990 chunk 93 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 194 GLN J 458 ASN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095067 restraints weight = 48239.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096748 restraints weight = 26636.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097142 restraints weight = 18061.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097656 restraints weight = 18087.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097791 restraints weight = 15643.473| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26903 Z= 0.234 Angle : 0.701 25.853 36644 Z= 0.354 Chirality : 0.054 1.935 4203 Planarity : 0.004 0.048 4541 Dihedral : 15.426 179.298 4375 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.51 % Allowed : 16.08 % Favored : 80.41 % 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: -1.30 (0.15), residues: 3159 helix: 0.81 (0.16), residues: 1088 sheet: -0.54 (0.27), residues: 363 loop : -2.17 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 275 TYR 0.015 0.002 TYR G 177 PHE 0.018 0.002 PHE I 828 TRP 0.011 0.002 TRP J 409 HIS 0.005 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00546 (26896) covalent geometry : angle 0.70051 (36638) hydrogen bonds : bond 0.05323 ( 1051) hydrogen bonds : angle 4.47880 ( 2902) metal coordination : bond 0.01055 ( 7) metal coordination : angle 2.84700 ( 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 376 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 281 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8176 (m-10) REVERT: G 127 GLN cc_start: 0.8649 (mp10) cc_final: 0.8426 (mp10) REVERT: G 153 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9053 (m) REVERT: G 200 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8669 (ttpp) REVERT: H 130 ILE cc_start: 0.9262 (mt) cc_final: 0.8942 (mt) REVERT: I 121 GLU cc_start: 0.8137 (pp20) cc_final: 0.7674 (pp20) REVERT: I 224 PHE cc_start: 0.7907 (m-80) cc_final: 0.7625 (m-10) REVERT: I 275 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7623 (mmp80) REVERT: I 283 LYS cc_start: 0.7543 (mttt) cc_final: 0.7070 (tptp) REVERT: I 434 ASP cc_start: 0.7952 (m-30) cc_final: 0.7720 (m-30) REVERT: I 604 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: I 862 LEU cc_start: 0.8590 (mt) cc_final: 0.8372 (tp) REVERT: I 1085 MET cc_start: 0.9244 (mmp) cc_final: 0.8859 (mmt) REVERT: I 1290 MET cc_start: 0.8515 (tpp) cc_final: 0.8194 (tpp) REVERT: J 49 PHE cc_start: 0.6978 (m-10) cc_final: 0.6710 (m-10) REVERT: J 151 MET cc_start: 0.7323 (pmm) cc_final: 0.6985 (pmm) REVERT: J 298 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7697 (ttp) REVERT: J 314 ARG cc_start: 0.7141 (ttp-170) cc_final: 0.6664 (ttp-170) REVERT: J 431 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8936 (ptt-90) REVERT: J 882 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8541 (m) REVERT: J 1165 PHE cc_start: 0.8127 (m-80) cc_final: 0.7675 (m-80) REVERT: J 1189 MET cc_start: 0.7698 (ttm) cc_final: 0.7088 (tpp) REVERT: K 55 GLU cc_start: 0.7577 (tt0) cc_final: 0.7106 (tt0) REVERT: K 58 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8260 (pp) outliers start: 95 outliers final: 72 residues processed: 352 average time/residue: 0.1640 time to fit residues: 96.0219 Evaluate side-chains 339 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 107 ILE Chi-restraints excluded: chain G residue 153 VAL 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 16 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 353 VAL 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 472 GLU 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 558 VAL Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 674 ASP Chi-restraints excluded: chain I residue 690 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 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 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 1325 VAL 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 111 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 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 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 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 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 133 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 0.0070 chunk 10 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 343 HIS I 517 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.130088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097747 restraints weight = 48309.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099247 restraints weight = 27897.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100149 restraints weight = 18899.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101137 restraints weight = 16777.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101048 restraints weight = 14593.348| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26903 Z= 0.151 Angle : 0.637 25.928 36644 Z= 0.322 Chirality : 0.052 1.943 4203 Planarity : 0.004 0.048 4541 Dihedral : 15.313 179.659 4375 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.77 % Allowed : 17.19 % Favored : 80.04 % 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: -1.16 (0.15), residues: 3159 helix: 0.95 (0.16), residues: 1091 sheet: -0.49 (0.27), residues: 356 loop : -2.09 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 731 TYR 0.014 0.001 TYR G 177 PHE 0.011 0.001 PHE I 828 TRP 0.016 0.001 TRP J1193 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00350 (26896) covalent geometry : angle 0.63660 (36638) hydrogen bonds : bond 0.04686 ( 1051) hydrogen bonds : angle 4.33092 ( 2902) metal coordination : bond 0.00564 ( 7) metal coordination : angle 2.05613 ( 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 346 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8192 (m-10) REVERT: G 123 ILE cc_start: 0.9169 (mm) cc_final: 0.8919 (mm) REVERT: G 127 GLN cc_start: 0.8639 (mp10) cc_final: 0.8388 (mp10) REVERT: G 153 VAL cc_start: 0.9221 (t) cc_final: 0.8970 (m) REVERT: G 200 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8590 (ttpp) REVERT: I 121 GLU cc_start: 0.8124 (pp20) cc_final: 0.7657 (pp20) REVERT: I 275 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7638 (mmp80) REVERT: I 424 ASP cc_start: 0.7734 (m-30) cc_final: 0.7418 (m-30) REVERT: I 434 ASP cc_start: 0.7956 (m-30) cc_final: 0.7717 (m-30) REVERT: I 765 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8582 (mt) REVERT: I 1166 ASP cc_start: 0.7734 (t0) cc_final: 0.7489 (t0) REVERT: I 1290 MET cc_start: 0.8560 (tpp) cc_final: 0.8243 (tpp) REVERT: J 49 PHE cc_start: 0.6937 (m-10) cc_final: 0.6670 (m-10) REVERT: J 151 MET cc_start: 0.7349 (pmm) cc_final: 0.7015 (pmm) REVERT: J 314 ARG cc_start: 0.7078 (ttp-170) cc_final: 0.6580 (ttp-170) REVERT: J 326 SER cc_start: 0.9184 (p) cc_final: 0.8678 (t) REVERT: J 625 MET cc_start: 0.9276 (ttp) cc_final: 0.8975 (ttp) REVERT: J 882 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8382 (m) REVERT: J 1148 ARG cc_start: 0.8180 (mpt-90) cc_final: 0.7798 (mtt-85) REVERT: J 1165 PHE cc_start: 0.8160 (m-80) cc_final: 0.7723 (m-80) REVERT: J 1189 MET cc_start: 0.7432 (ttm) cc_final: 0.6818 (tpp) REVERT: K 41 GLU cc_start: 0.8587 (pm20) cc_final: 0.8205 (pt0) REVERT: K 55 GLU cc_start: 0.7489 (tt0) cc_final: 0.7110 (tt0) REVERT: K 58 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8275 (pp) REVERT: K 74 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7342 (mm-30) outliers start: 75 outliers final: 63 residues processed: 331 average time/residue: 0.1600 time to fit residues: 88.3290 Evaluate side-chains 329 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL 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 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 558 VAL Chi-restraints excluded: chain I residue 576 SER 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 674 ASP Chi-restraints excluded: chain I residue 690 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 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 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 111 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 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 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 887 SER Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL 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: 0.0270 chunk 160 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 0.0870 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 688 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN J1367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099098 restraints weight = 47603.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101435 restraints weight = 26274.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102243 restraints weight = 17010.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102847 restraints weight = 15548.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102789 restraints weight = 13918.506| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26903 Z= 0.124 Angle : 0.608 25.992 36644 Z= 0.306 Chirality : 0.052 1.944 4203 Planarity : 0.004 0.052 4541 Dihedral : 15.186 179.700 4375 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.62 % Allowed : 17.49 % Favored : 79.89 % 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: 1.12 (0.16), residues: 1093 sheet: -0.29 (0.28), residues: 341 loop : -2.00 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 731 TYR 0.021 0.001 TYR J 144 PHE 0.022 0.001 PHE I 337 TRP 0.017 0.001 TRP J1193 HIS 0.003 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00280 (26896) covalent geometry : angle 0.60720 (36638) hydrogen bonds : bond 0.04262 ( 1051) hydrogen bonds : angle 4.17154 ( 2902) metal coordination : bond 0.00405 ( 7) metal coordination : angle 1.78222 ( 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 367 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: G 123 ILE cc_start: 0.9101 (mm) cc_final: 0.8858 (mm) REVERT: G 153 VAL cc_start: 0.9190 (t) cc_final: 0.8946 (m) REVERT: G 200 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8614 (ttpp) REVERT: H 130 ILE cc_start: 0.9049 (mt) cc_final: 0.8770 (mt) REVERT: I 121 GLU cc_start: 0.8100 (pp20) cc_final: 0.7637 (pp20) REVERT: I 275 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7650 (mmp80) REVERT: I 283 LYS cc_start: 0.7488 (mttt) cc_final: 0.7137 (mtmt) REVERT: I 383 SER cc_start: 0.8845 (m) cc_final: 0.8594 (p) REVERT: I 424 ASP cc_start: 0.7594 (m-30) cc_final: 0.7180 (m-30) REVERT: I 434 ASP cc_start: 0.7864 (m-30) cc_final: 0.7619 (m-30) REVERT: I 1166 ASP cc_start: 0.7598 (t0) cc_final: 0.7359 (t0) REVERT: I 1230 MET cc_start: 0.8928 (ttm) cc_final: 0.8678 (ttt) REVERT: I 1244 HIS cc_start: 0.7535 (t70) cc_final: 0.7207 (t70) REVERT: I 1290 MET cc_start: 0.8584 (tpp) cc_final: 0.8253 (tpp) REVERT: J 151 MET cc_start: 0.7357 (pmm) cc_final: 0.7130 (pmm) REVERT: J 314 ARG cc_start: 0.6987 (ttp-170) cc_final: 0.6720 (ttp-170) REVERT: J 326 SER cc_start: 0.9148 (p) cc_final: 0.8640 (t) REVERT: J 431 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8937 (ptt-90) REVERT: J 625 MET cc_start: 0.9226 (ttp) cc_final: 0.8908 (ttp) REVERT: J 882 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8323 (m) REVERT: J 1025 MET cc_start: 0.6925 (mtp) cc_final: 0.6581 (mpp) REVERT: J 1148 ARG cc_start: 0.8088 (mpt-90) cc_final: 0.7768 (mtt-85) REVERT: J 1165 PHE cc_start: 0.8063 (m-80) cc_final: 0.7705 (m-10) REVERT: J 1174 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6855 (ttm170) REVERT: J 1189 MET cc_start: 0.7716 (ttm) cc_final: 0.7297 (tpp) REVERT: K 41 GLU cc_start: 0.8607 (pm20) cc_final: 0.8236 (pt0) REVERT: K 58 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8198 (pp) REVERT: K 74 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7309 (mm-30) outliers start: 71 outliers final: 59 residues processed: 351 average time/residue: 0.1646 time to fit residues: 95.5974 Evaluate side-chains 344 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL 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 576 SER 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 674 ASP Chi-restraints excluded: chain I residue 690 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 992 LEU Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 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 283 LEU Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 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 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 974 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 1353 VAL 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: 20.0000 chunk 265 optimal weight: 0.0970 chunk 182 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 278 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 257 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 230 optimal weight: 0.0670 chunk 259 optimal weight: 0.9980 chunk 313 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 314 ASN I 343 HIS I 517 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102276 restraints weight = 47758.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104879 restraints weight = 26311.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105703 restraints weight = 16819.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106309 restraints weight = 14923.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106366 restraints weight = 13758.838| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4013 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= 0.110 Angle : 0.601 26.012 36644 Z= 0.302 Chirality : 0.051 1.948 4203 Planarity : 0.004 0.051 4541 Dihedral : 15.091 179.736 4375 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.48 % Allowed : 18.11 % Favored : 79.41 % 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: -0.82 (0.15), residues: 3159 helix: 1.19 (0.16), residues: 1095 sheet: -0.07 (0.28), residues: 339 loop : -1.91 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 731 TYR 0.021 0.001 TYR J 165 PHE 0.024 0.001 PHE I 337 TRP 0.023 0.001 TRP J1193 HIS 0.011 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00239 (26896) covalent geometry : angle 0.60080 (36638) hydrogen bonds : bond 0.03919 ( 1051) hydrogen bonds : angle 4.09499 ( 2902) metal coordination : bond 0.00356 ( 7) metal coordination : angle 1.39971 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4094.54 seconds wall clock time: 71 minutes 41.20 seconds (4301.20 seconds total)