Starting phenix.real_space_refine on Sat Jun 6 09:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10mc_75281/06_2026/10mc_75281.cif Found real_map, /net/cci-nas-00/data/ceres_data/10mc_75281/06_2026/10mc_75281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10mc_75281/06_2026/10mc_75281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10mc_75281/06_2026/10mc_75281.map" model { file = "/net/cci-nas-00/data/ceres_data/10mc_75281/06_2026/10mc_75281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10mc_75281/06_2026/10mc_75281.cif" } resolution = 2.8 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= 0.001 sd= 0.007 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 62 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16167 2.51 5 N 4610 2.21 5 O 5819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26767 Number of models: 1 Model: "" Number of chains: 18 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: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 303 Classifications: {'water': 303} Link IDs: {None: 302} Chain: "J" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 239 Classifications: {'water': 239} Link IDs: {None: 238} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16109 SG CYS J 70 116.822 66.686 71.606 1.00235.78 S ATOM 16123 SG CYS J 72 117.379 63.319 69.667 1.00240.36 S ATOM 16231 SG CYS J 85 118.459 65.642 68.097 1.00237.18 S ATOM 16255 SG CYS J 88 115.614 66.303 67.826 1.00235.73 S ATOM 21943 SG CYS J 814 87.706 128.986 68.186 1.00181.78 S ATOM 22508 SG CYS J 888 86.118 125.466 68.351 1.00161.80 S ATOM 22559 SG CYS J 895 87.079 127.271 71.608 1.00166.66 S ATOM 22580 SG CYS J 898 84.892 127.807 70.613 1.00170.25 S Time building chain proxies: 6.10, per 1000 atoms: 0.23 Number of scatterers: 26767 At special positions: 0 Unit cell: (143.312, 168.324, 164.944, 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 62 15.00 Mg 1 11.99 O 5819 8.00 N 4610 7.00 C 16167 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " Number of angles added : 12 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 46 sheets defined 39.1% alpha, 17.5% beta 21 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.801A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.994A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.002A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.662A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.994A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.886A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.967A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.836A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.619A pdb=" N GLN I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 292 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 354 removed outlier: 3.808A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.169A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.846A pdb=" N ARG I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.593A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 3.716A pdb=" N GLY I 612 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN I 613 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 668 removed outlier: 3.994A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.521A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.758A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 942 through 945 Processing helix chain 'I' and resid 946 through 983 removed outlier: 3.891A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 Processing helix chain 'I' and resid 993 through 1000 Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.899A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.597A pdb=" N THR I1115 " --> pdb=" O GLN I1111 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA I1120 " --> pdb=" O HIS I1116 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.593A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.642A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 removed outlier: 3.612A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.816A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.041A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.730A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.610A pdb=" N SER J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.573A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.859A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.503A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.586A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.587A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.577A pdb=" N MET J 330 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 327 through 331' Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 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 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.725A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.546A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 634 removed outlier: 3.698A pdb=" N ALA J 633 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.650A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.781A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.112A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.570A pdb=" N TYR J 772 " --> pdb=" O ASN J 768 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.845A 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 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.623A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.927A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1037 through 1041 removed outlier: 3.760A pdb=" N ILE J1041 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.898A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.891A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.341A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.813A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.661A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.897A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1371 removed outlier: 3.619A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 20 removed outlier: 8.832A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 19 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.038A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.713A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.672A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 201 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 8.108A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 59 " --> pdb=" O LEU H 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.678A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.008A pdb=" N ILE I 59 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 68 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.348A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 4.974A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.918A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.649A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.810A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.682A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.177A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.090A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 840 removed outlier: 4.009A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.956A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.443A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.564A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.852A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.283A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD6, first strand: chain 'J' and resid 254 through 255 Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.689A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD9, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.423A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.173A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN J1019 " --> pdb=" O VAL J1002 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 991 through 997 removed outlier: 3.506A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 3.880A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE7, first strand: chain 'J' and resid 1059 through 1060 Processing sheet with id=AE8, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.515A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.863A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.114A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7964 1.33 - 1.45: 3484 1.45 - 1.57: 14856 1.57 - 1.69: 121 1.69 - 1.81: 184 Bond restraints: 26609 Sorted by residual: bond pdb=" N VAL I 887 " pdb=" CA VAL I 887 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.23e+00 bond pdb=" N SER I 917 " pdb=" CA SER I 917 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.81e+00 bond pdb=" N LYS I 886 " pdb=" CA LYS I 886 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.80e+00 bond pdb=" P DC B 25 " pdb=" OP2 DC B 25 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" N ILE J1134 " pdb=" CA ILE J1134 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.77e+00 ... (remaining 26604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 35916 2.19 - 4.39: 270 4.39 - 6.58: 20 6.58 - 8.77: 5 8.77 - 10.97: 1 Bond angle restraints: 36212 Sorted by residual: angle pdb=" CA THR J1135 " pdb=" C THR J1135 " pdb=" O THR J1135 " ideal model delta sigma weight residual 121.56 118.21 3.35 1.09e+00 8.42e-01 9.47e+00 angle pdb=" C THR I 888 " pdb=" CA THR I 888 " pdb=" CB THR I 888 " ideal model delta sigma weight residual 108.86 113.14 -4.28 1.44e+00 4.82e-01 8.83e+00 angle pdb=" O3' G R 10 " pdb=" C3' G R 10 " pdb=" C2' G R 10 " ideal model delta sigma weight residual 113.70 118.12 -4.42 1.50e+00 4.44e-01 8.67e+00 angle pdb=" CA THR I 888 " pdb=" C THR I 888 " pdb=" O THR I 888 " ideal model delta sigma weight residual 120.60 118.02 2.58 9.00e-01 1.23e+00 8.20e+00 angle pdb=" CA THR J1135 " pdb=" CB THR J1135 " pdb=" OG1 THR J1135 " ideal model delta sigma weight residual 109.60 105.49 4.11 1.50e+00 4.44e-01 7.49e+00 ... (remaining 36207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 15785 27.46 - 54.91: 452 54.91 - 82.37: 72 82.37 - 109.82: 4 109.82 - 137.28: 1 Dihedral angle restraints: 16314 sinusoidal: 7223 harmonic: 9091 Sorted by residual: dihedral pdb=" CD ARG J 933 " pdb=" NE ARG J 933 " pdb=" CZ ARG J 933 " pdb=" NH1 ARG J 933 " ideal model delta sinusoidal sigma weight residual 0.00 -81.92 81.92 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CA ARG J 425 " pdb=" C ARG J 425 " pdb=" N ALA J 426 " pdb=" CA ALA J 426 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG I1106 " pdb=" C ARG I1106 " pdb=" N MET I1107 " pdb=" CA MET I1107 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 16311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 4102 0.119 - 0.237: 44 0.237 - 0.355: 0 0.355 - 0.474: 0 0.474 - 0.592: 4 Chirality restraints: 4150 Sorted by residual: chirality pdb=" P DC B 25 " pdb=" OP1 DC B 25 " pdb=" OP2 DC B 25 " pdb=" O5' DC B 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" P DG B 27 " pdb=" OP1 DG B 27 " pdb=" OP2 DG B 27 " pdb=" O5' DG B 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" P DG B 28 " pdb=" OP1 DG B 28 " pdb=" OP2 DG B 28 " pdb=" O5' DG B 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 4147 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 933 " 1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG J 933 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 933 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 933 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG J 933 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO I 190 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 559 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO I 560 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 560 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 560 " -0.025 5.00e-02 4.00e+02 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 32 2.61 - 3.19: 22312 3.19 - 3.76: 38774 3.76 - 4.33: 53484 4.33 - 4.90: 91166 Nonbonded interactions: 205768 Sorted by model distance: nonbonded pdb=" O3' U R 19 " pdb="MG MG J1501 " model vdw 2.044 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.224 2.170 nonbonded pdb=" O4 DT B 13 " pdb=" O6 DG A 19 " model vdw 2.272 2.432 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.279 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.315 2.170 ... (remaining 205763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.170 Find NCS groups from input model: 0.210 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26617 Z= 0.155 Angle : 0.617 43.172 36224 Z= 0.287 Chirality : 0.044 0.592 4150 Planarity : 0.008 0.487 4517 Dihedral : 12.568 137.279 10466 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.15 % Allowed : 5.16 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3148 helix: 1.86 (0.16), residues: 1078 sheet: 0.77 (0.25), residues: 453 loop : -0.32 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I1246 TYR 0.011 0.001 TYR J 679 PHE 0.010 0.001 PHE J 437 TRP 0.007 0.001 TRP J 409 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (26609) covalent geometry : angle 0.50924 / 0.28 (36212) hydrogen bonds : bond 0.14197 / 8.30 ( 1108) hydrogen bonds : angle 5.43322 / 3.45 ( 3058) metal coordination : bond 0.06741 / 3.35 ( 8) metal coordination : angle 19.11447 / 12.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 459 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7844 (mttm) cc_final: 0.7623 (mttm) REVERT: G 67 GLU cc_start: 0.8290 (pt0) cc_final: 0.7939 (pm20) REVERT: G 72 GLU cc_start: 0.8115 (tt0) cc_final: 0.7851 (tm-30) REVERT: G 96 ASP cc_start: 0.6866 (p0) cc_final: 0.6593 (p0) REVERT: G 99 ILE cc_start: 0.7917 (mt) cc_final: 0.7648 (mp) REVERT: G 122 GLU cc_start: 0.6982 (tt0) cc_final: 0.6363 (tm-30) REVERT: G 127 GLN cc_start: 0.7603 (mp10) cc_final: 0.7300 (mp10) REVERT: H 15 ASP cc_start: 0.6838 (m-30) cc_final: 0.6403 (t0) REVERT: H 38 THR cc_start: 0.6083 (OUTLIER) cc_final: 0.5042 (m) REVERT: H 50 SER cc_start: 0.8533 (t) cc_final: 0.8316 (t) REVERT: H 51 MET cc_start: 0.7125 (tpt) cc_final: 0.6769 (mmt) REVERT: H 66 HIS cc_start: 0.7946 (t-90) cc_final: 0.7368 (t70) REVERT: H 77 ASP cc_start: 0.7860 (t0) cc_final: 0.7169 (t0) REVERT: H 80 GLU cc_start: 0.7504 (tt0) cc_final: 0.7150 (mt-10) REVERT: H 96 ASP cc_start: 0.7623 (m-30) cc_final: 0.6715 (p0) REVERT: H 120 ASP cc_start: 0.4642 (p0) cc_final: 0.4183 (p0) REVERT: H 135 ASP cc_start: 0.7921 (t0) cc_final: 0.7479 (t0) REVERT: H 150 ARG cc_start: 0.5986 (mpt180) cc_final: 0.5703 (mtm110) REVERT: H 176 CYS cc_start: 0.8947 (m) cc_final: 0.7425 (t) REVERT: H 188 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6279 (mt-10) REVERT: H 197 ASP cc_start: 0.7467 (p0) cc_final: 0.6845 (t0) REVERT: H 200 LYS cc_start: 0.6637 (tttt) cc_final: 0.6327 (tttp) REVERT: H 204 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7025 (mp0) REVERT: I 20 GLN cc_start: 0.8102 (mt0) cc_final: 0.7842 (pt0) REVERT: I 36 GLN cc_start: 0.6904 (tp40) cc_final: 0.6696 (tp40) REVERT: I 46 GLN cc_start: 0.6599 (pt0) cc_final: 0.5360 (tp-100) REVERT: I 117 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6769 (mm) REVERT: I 160 ASP cc_start: 0.5959 (m-30) cc_final: 0.5373 (p0) REVERT: I 201 ARG cc_start: 0.5805 (mtt-85) cc_final: 0.4946 (mtt180) REVERT: I 202 ARG cc_start: 0.6975 (ptm-80) cc_final: 0.6627 (ptt-90) REVERT: I 407 ARG cc_start: 0.8042 (ttt-90) cc_final: 0.7822 (tmm-80) REVERT: I 446 ASP cc_start: 0.7719 (m-30) cc_final: 0.7387 (m-30) REVERT: I 546 GLU cc_start: 0.8541 (mp0) cc_final: 0.7745 (tt0) REVERT: I 602 GLU cc_start: 0.7570 (pt0) cc_final: 0.7173 (pt0) REVERT: I 628 HIS cc_start: 0.8283 (m90) cc_final: 0.8078 (m90) REVERT: I 647 ARG cc_start: 0.7904 (ttt180) cc_final: 0.7363 (ttm110) REVERT: I 681 MET cc_start: 0.6178 (mtt) cc_final: 0.5891 (mtp) REVERT: I 696 ASP cc_start: 0.8132 (t0) cc_final: 0.7864 (t0) REVERT: I 720 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.8065 (mtp180) REVERT: I 741 MET cc_start: 0.6204 (mtm) cc_final: 0.5789 (mtp) REVERT: I 775 GLU cc_start: 0.7051 (tt0) cc_final: 0.6810 (tm-30) REVERT: I 834 GLN cc_start: 0.8044 (pt0) cc_final: 0.7535 (pt0) REVERT: I 1064 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6503 (p0) REVERT: I 1119 MET cc_start: 0.6739 (ttt) cc_final: 0.6259 (tpt) REVERT: I 1134 GLN cc_start: 0.7445 (pt0) cc_final: 0.7043 (pt0) REVERT: I 1135 GLN cc_start: 0.7644 (mt0) cc_final: 0.7222 (mm-40) REVERT: I 1154 ASP cc_start: 0.8014 (m-30) cc_final: 0.7417 (t0) REVERT: I 1168 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6721 (mt-10) REVERT: I 1292 THR cc_start: 0.8621 (m) cc_final: 0.8359 (p) REVERT: I 1315 MET cc_start: 0.8005 (ptm) cc_final: 0.7683 (ptm) REVERT: J 21 LYS cc_start: 0.7510 (tttm) cc_final: 0.6630 (ptmm) REVERT: J 94 GLN cc_start: 0.7063 (mt0) cc_final: 0.6511 (mp10) REVERT: J 135 ILE cc_start: 0.7018 (mt) cc_final: 0.6769 (mt) REVERT: J 192 MET cc_start: 0.6795 (ttm) cc_final: 0.6359 (ttp) REVERT: J 198 CYS cc_start: 0.8490 (t) cc_final: 0.8073 (t) REVERT: J 217 LEU cc_start: 0.8902 (mt) cc_final: 0.8374 (pp) REVERT: J 227 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.5882 (t80) REVERT: J 329 ASP cc_start: 0.7409 (m-30) cc_final: 0.7108 (m-30) REVERT: J 348 ASP cc_start: 0.7311 (m-30) cc_final: 0.6499 (t0) REVERT: J 375 GLU cc_start: 0.7716 (tp30) cc_final: 0.7259 (tp30) REVERT: J 402 GLU cc_start: 0.9006 (tt0) cc_final: 0.8623 (tm-30) REVERT: J 404 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7216 (mp0) REVERT: J 645 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7668 (p) REVERT: J 649 LYS cc_start: 0.6313 (OUTLIER) cc_final: 0.6088 (mmmt) REVERT: J 811 GLU cc_start: 0.7425 (tt0) cc_final: 0.7102 (mt-10) REVERT: J 862 THR cc_start: 0.8026 (m) cc_final: 0.7796 (p) REVERT: J 1156 LEU cc_start: 0.9011 (mp) cc_final: 0.8798 (mm) REVERT: J 1194 ARG cc_start: 0.9160 (mmm-85) cc_final: 0.8828 (mmt180) REVERT: J 1236 GLU cc_start: 0.7700 (tp30) cc_final: 0.7258 (mm-30) REVERT: J 1275 LEU cc_start: 0.8961 (tp) cc_final: 0.8440 (tt) REVERT: J 1282 TYR cc_start: 0.6365 (t80) cc_final: 0.6002 (t80) REVERT: J 1334 GLU cc_start: 0.6730 (tp30) cc_final: 0.6213 (mt-10) outliers start: 85 outliers final: 31 residues processed: 536 average time/residue: 0.6786 time to fit residues: 418.2470 Evaluate side-chains 333 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 50.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 186 ASN I 618 GLN I1134 GLN J 817 HIS J1227 HIS J1366 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.197219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122586 restraints weight = 35096.042| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.33 r_work: 0.3423 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26617 Z= 0.161 Angle : 0.584 14.531 36224 Z= 0.296 Chirality : 0.043 0.228 4150 Planarity : 0.005 0.054 4517 Dihedral : 13.480 132.912 4333 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.56 % Allowed : 13.02 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3148 helix: 1.87 (0.16), residues: 1093 sheet: 0.54 (0.24), residues: 456 loop : -0.40 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG I 841 TYR 0.011 0.001 TYR J 679 PHE 0.016 0.001 PHE J 892 TRP 0.015 0.001 TRP J1020 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (26609) covalent geometry : angle 0.57321 / 0.30 (36212) hydrogen bonds : bond 0.05136 / 3.13 ( 1108) hydrogen bonds : angle 4.37209 / 2.79 ( 3058) metal coordination : bond 0.00777 / 0.39 ( 8) metal coordination : angle 6.18068 / 4.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 304 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8551 (mmm-85) REVERT: G 67 GLU cc_start: 0.8269 (pt0) cc_final: 0.7925 (pm20) REVERT: G 72 GLU cc_start: 0.8149 (tt0) cc_final: 0.7858 (tm-30) REVERT: G 96 ASP cc_start: 0.7020 (p0) cc_final: 0.6758 (p0) REVERT: G 99 ILE cc_start: 0.7898 (mt) cc_final: 0.7632 (mp) REVERT: G 122 GLU cc_start: 0.6931 (tt0) cc_final: 0.6333 (tm-30) REVERT: G 127 GLN cc_start: 0.7670 (mp10) cc_final: 0.7359 (mp10) REVERT: H 38 THR cc_start: 0.5990 (OUTLIER) cc_final: 0.5662 (p) REVERT: H 50 SER cc_start: 0.8610 (t) cc_final: 0.8345 (t) REVERT: H 51 MET cc_start: 0.7302 (tpt) cc_final: 0.7008 (mmm) REVERT: H 66 HIS cc_start: 0.7752 (t-90) cc_final: 0.7332 (t70) REVERT: H 80 GLU cc_start: 0.7477 (tt0) cc_final: 0.7225 (mt-10) REVERT: H 150 ARG cc_start: 0.5943 (mpt180) cc_final: 0.5643 (mtm110) REVERT: H 176 CYS cc_start: 0.8670 (m) cc_final: 0.7574 (t) REVERT: H 188 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6259 (mt-10) REVERT: H 197 ASP cc_start: 0.7384 (p0) cc_final: 0.6820 (t0) REVERT: H 200 LYS cc_start: 0.6616 (tttt) cc_final: 0.6321 (tttp) REVERT: H 204 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7087 (mp0) REVERT: I 20 GLN cc_start: 0.8099 (mt0) cc_final: 0.7779 (pt0) REVERT: I 46 GLN cc_start: 0.6575 (pt0) cc_final: 0.5233 (tp-100) REVERT: I 77 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7919 (mm-30) REVERT: I 117 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6798 (mm) REVERT: I 142 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: I 160 ASP cc_start: 0.5351 (m-30) cc_final: 0.4639 (p0) REVERT: I 201 ARG cc_start: 0.5983 (mtt-85) cc_final: 0.5383 (mtt-85) REVERT: I 202 ARG cc_start: 0.6980 (ptm-80) cc_final: 0.6520 (ptt-90) REVERT: I 407 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7839 (tmm-80) REVERT: I 446 ASP cc_start: 0.7927 (m-30) cc_final: 0.7486 (m-30) REVERT: I 488 MET cc_start: 0.8627 (tpt) cc_final: 0.8220 (tmt) REVERT: I 539 THR cc_start: 0.6727 (OUTLIER) cc_final: 0.6096 (p) REVERT: I 546 GLU cc_start: 0.8519 (mp0) cc_final: 0.7748 (tt0) REVERT: I 565 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7052 (mp0) REVERT: I 602 GLU cc_start: 0.7011 (pt0) cc_final: 0.6653 (pt0) REVERT: I 653 MET cc_start: 0.8224 (ttt) cc_final: 0.7879 (tpt) REVERT: I 681 MET cc_start: 0.6059 (mtt) cc_final: 0.5736 (mtp) REVERT: I 696 ASP cc_start: 0.8133 (t0) cc_final: 0.7890 (t0) REVERT: I 775 GLU cc_start: 0.7049 (tt0) cc_final: 0.6845 (tt0) REVERT: I 834 GLN cc_start: 0.8021 (pt0) cc_final: 0.7526 (pt0) REVERT: I 882 ILE cc_start: 0.8257 (mp) cc_final: 0.7840 (tt) REVERT: I 1064 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6494 (p0) REVERT: I 1119 MET cc_start: 0.6986 (ttt) cc_final: 0.6540 (tpt) REVERT: I 1136 GLN cc_start: 0.7596 (mt0) cc_final: 0.7109 (mt0) REVERT: I 1154 ASP cc_start: 0.8027 (m-30) cc_final: 0.7419 (t0) REVERT: I 1168 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6706 (mt-10) REVERT: I 1292 THR cc_start: 0.8509 (m) cc_final: 0.8172 (p) REVERT: I 1315 MET cc_start: 0.7836 (ptm) cc_final: 0.7541 (ptm) REVERT: I 1316 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: I 1319 MET cc_start: 0.7999 (ttm) cc_final: 0.7767 (ttp) REVERT: J 21 LYS cc_start: 0.7309 (tttm) cc_final: 0.6473 (ptmm) REVERT: J 122 SER cc_start: 0.7141 (t) cc_final: 0.6913 (p) REVERT: J 137 ARG cc_start: 0.8569 (mtm180) cc_final: 0.8250 (mtm110) REVERT: J 197 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: J 227 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5989 (t80) REVERT: J 320 ASN cc_start: 0.7291 (p0) cc_final: 0.6743 (p0) REVERT: J 322 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7499 (mpp80) REVERT: J 329 ASP cc_start: 0.7423 (m-30) cc_final: 0.7085 (m-30) REVERT: J 348 ASP cc_start: 0.7529 (m-30) cc_final: 0.6647 (t0) REVERT: J 363 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6780 (tt) REVERT: J 375 GLU cc_start: 0.7683 (tp30) cc_final: 0.7385 (tp30) REVERT: J 402 GLU cc_start: 0.8973 (tt0) cc_final: 0.8690 (tm-30) REVERT: J 404 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7519 (mp0) REVERT: J 645 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7558 (p) REVERT: J 712 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8272 (mm-40) REVERT: J 811 GLU cc_start: 0.7263 (tt0) cc_final: 0.6979 (mt-10) REVERT: J 862 THR cc_start: 0.8011 (m) cc_final: 0.7752 (p) REVERT: J 1156 LEU cc_start: 0.9151 (mp) cc_final: 0.8926 (mm) REVERT: J 1243 LEU cc_start: 0.8087 (tt) cc_final: 0.7833 (mp) REVERT: J 1275 LEU cc_start: 0.8915 (tp) cc_final: 0.8389 (tt) REVERT: J 1334 GLU cc_start: 0.6706 (tp30) cc_final: 0.6175 (mt-10) outliers start: 96 outliers final: 51 residues processed: 379 average time/residue: 0.6675 time to fit residues: 293.3026 Evaluate side-chains 334 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 273 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 715 THR Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1316 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 1134 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 292 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.193584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117863 restraints weight = 35258.549| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.52 r_work: 0.3351 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 26617 Z= 0.292 Angle : 0.691 13.845 36224 Z= 0.355 Chirality : 0.047 0.228 4150 Planarity : 0.005 0.055 4517 Dihedral : 13.593 127.378 4325 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.34 % Allowed : 12.76 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.31 (0.15), residues: 3148 helix: 1.46 (0.16), residues: 1092 sheet: 0.36 (0.24), residues: 456 loop : -0.72 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 53 TYR 0.023 0.002 TYR J1282 PHE 0.017 0.002 PHE I 405 TRP 0.020 0.002 TRP J1020 HIS 0.009 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.29 (26609) covalent geometry : angle 0.68508 / 0.35 (36212) hydrogen bonds : bond 0.06718 / 4.08 ( 1108) hydrogen bonds : angle 4.53512 / 2.92 ( 3058) metal coordination : bond 0.01041 / 0.52 ( 8) metal coordination : angle 4.99805 / 3.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 284 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8287 (pt0) cc_final: 0.7872 (pm20) REVERT: G 72 GLU cc_start: 0.8281 (tt0) cc_final: 0.7927 (tm-30) REVERT: G 96 ASP cc_start: 0.7175 (p0) cc_final: 0.6947 (p0) REVERT: G 122 GLU cc_start: 0.6908 (tt0) cc_final: 0.6242 (tm-30) REVERT: G 127 GLN cc_start: 0.7770 (mp10) cc_final: 0.7397 (mp10) REVERT: G 158 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6852 (ptt180) REVERT: G 229 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7263 (tp30) REVERT: H 38 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.6059 (t) REVERT: H 50 SER cc_start: 0.8827 (t) cc_final: 0.8626 (t) REVERT: H 66 HIS cc_start: 0.7606 (t-90) cc_final: 0.7141 (t70) REVERT: H 80 GLU cc_start: 0.7646 (tt0) cc_final: 0.7366 (mt-10) REVERT: H 150 ARG cc_start: 0.6108 (mpt180) cc_final: 0.5728 (mtm110) REVERT: H 176 CYS cc_start: 0.8730 (m) cc_final: 0.7569 (t) REVERT: H 188 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6225 (mt-10) REVERT: H 197 ASP cc_start: 0.7496 (p0) cc_final: 0.6895 (t0) REVERT: H 200 LYS cc_start: 0.6730 (tttt) cc_final: 0.6423 (tttp) REVERT: H 204 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7118 (mp0) REVERT: I 77 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8022 (mm-30) REVERT: I 117 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6790 (mm) REVERT: I 132 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7967 (t0) REVERT: I 160 ASP cc_start: 0.5702 (m-30) cc_final: 0.5031 (p0) REVERT: I 200 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: I 201 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.5658 (mtt180) REVERT: I 407 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7837 (tmm-80) REVERT: I 446 ASP cc_start: 0.8085 (m-30) cc_final: 0.7614 (m-30) REVERT: I 539 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6160 (p) REVERT: I 546 GLU cc_start: 0.8550 (mp0) cc_final: 0.7849 (tt0) REVERT: I 602 GLU cc_start: 0.7132 (pt0) cc_final: 0.6775 (pt0) REVERT: I 628 HIS cc_start: 0.8260 (m90) cc_final: 0.7801 (m90) REVERT: I 681 MET cc_start: 0.6216 (mtt) cc_final: 0.5948 (mtp) REVERT: I 694 ARG cc_start: 0.6810 (mtm180) cc_final: 0.6440 (mtm180) REVERT: I 696 ASP cc_start: 0.8200 (t0) cc_final: 0.7924 (t0) REVERT: I 882 ILE cc_start: 0.8172 (mp) cc_final: 0.7771 (tt) REVERT: I 1064 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6270 (p0) REVERT: I 1119 MET cc_start: 0.7282 (ttt) cc_final: 0.6780 (tpt) REVERT: I 1136 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: I 1154 ASP cc_start: 0.8021 (m-30) cc_final: 0.7414 (t0) REVERT: I 1168 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6719 (mt-10) REVERT: I 1230 MET cc_start: 0.8929 (ttp) cc_final: 0.8607 (ttp) REVERT: J 21 LYS cc_start: 0.7334 (tttm) cc_final: 0.6466 (ptmm) REVERT: J 94 GLN cc_start: 0.7318 (mt0) cc_final: 0.6925 (mp10) REVERT: J 197 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: J 217 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8768 (pp) REVERT: J 329 ASP cc_start: 0.7495 (m-30) cc_final: 0.7203 (m-30) REVERT: J 363 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6988 (tt) REVERT: J 402 GLU cc_start: 0.8966 (tt0) cc_final: 0.8695 (tm-30) REVERT: J 404 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7489 (mp0) REVERT: J 709 ARG cc_start: 0.8183 (tmm-80) cc_final: 0.7923 (tmm-80) REVERT: J 712 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8249 (mm-40) REVERT: J 802 ASP cc_start: 0.6051 (t70) cc_final: 0.5323 (m-30) REVERT: J 811 GLU cc_start: 0.7464 (tt0) cc_final: 0.7128 (mt-10) REVERT: J 821 MET cc_start: 0.8609 (mmm) cc_final: 0.8371 (mmm) REVERT: J 860 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7541 (tpt-90) REVERT: J 862 THR cc_start: 0.8167 (m) cc_final: 0.7872 (p) REVERT: J 1074 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7634 (pp) REVERT: J 1156 LEU cc_start: 0.9133 (mp) cc_final: 0.8915 (mm) REVERT: J 1194 ARG cc_start: 0.9102 (mmt180) cc_final: 0.8762 (mmt180) REVERT: J 1222 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7451 (mpp80) REVERT: J 1243 LEU cc_start: 0.8085 (tt) cc_final: 0.7817 (mp) REVERT: J 1275 LEU cc_start: 0.8874 (tp) cc_final: 0.8360 (tt) REVERT: J 1334 GLU cc_start: 0.6826 (tp30) cc_final: 0.6289 (mt-10) outliers start: 144 outliers final: 70 residues processed: 396 average time/residue: 0.6324 time to fit residues: 291.3740 Evaluate side-chains 348 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 265 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 715 THR Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1370 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.197011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123061 restraints weight = 34903.405| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.25 r_work: 0.3434 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26617 Z= 0.124 Angle : 0.543 10.021 36224 Z= 0.279 Chirality : 0.041 0.227 4150 Planarity : 0.004 0.056 4517 Dihedral : 13.331 127.069 4319 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.78 % Allowed : 15.36 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3148 helix: 1.76 (0.16), residues: 1098 sheet: 0.40 (0.24), residues: 456 loop : -0.64 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 88 TYR 0.021 0.001 TYR J1282 PHE 0.010 0.001 PHE I 828 TRP 0.019 0.001 TRP J1020 HIS 0.003 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (26609) covalent geometry : angle 0.53855 / 0.28 (36212) hydrogen bonds : bond 0.04573 / 2.85 ( 1108) hydrogen bonds : angle 4.21171 / 2.69 ( 3058) metal coordination : bond 0.00469 / 0.23 ( 8) metal coordination : angle 3.76151 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 274 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8223 (pt0) cc_final: 0.7825 (pm20) REVERT: G 72 GLU cc_start: 0.8198 (tt0) cc_final: 0.7846 (tm-30) REVERT: G 96 ASP cc_start: 0.7118 (p0) cc_final: 0.6915 (p0) REVERT: G 99 ILE cc_start: 0.7779 (mt) cc_final: 0.7504 (mp) REVERT: G 122 GLU cc_start: 0.6889 (tt0) cc_final: 0.6242 (tm-30) REVERT: G 127 GLN cc_start: 0.7748 (mp10) cc_final: 0.7375 (mp10) REVERT: H 38 THR cc_start: 0.5924 (OUTLIER) cc_final: 0.5607 (p) REVERT: H 50 SER cc_start: 0.8675 (t) cc_final: 0.8435 (t) REVERT: H 66 HIS cc_start: 0.7585 (t-90) cc_final: 0.7099 (t70) REVERT: H 80 GLU cc_start: 0.7625 (tt0) cc_final: 0.7410 (mt-10) REVERT: H 114 ASP cc_start: 0.7326 (t0) cc_final: 0.6954 (t70) REVERT: H 150 ARG cc_start: 0.5984 (mpt180) cc_final: 0.5639 (mtm110) REVERT: H 176 CYS cc_start: 0.8670 (m) cc_final: 0.7521 (t) REVERT: H 188 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6210 (mt-10) REVERT: H 197 ASP cc_start: 0.7411 (p0) cc_final: 0.6855 (t0) REVERT: H 200 LYS cc_start: 0.6702 (tttt) cc_final: 0.6406 (tttp) REVERT: H 204 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7113 (mp0) REVERT: I 77 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8001 (mm-30) REVERT: I 117 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6851 (mm) REVERT: I 142 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: I 200 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7456 (mmm-85) REVERT: I 201 ARG cc_start: 0.6141 (mtt-85) cc_final: 0.5863 (mtt-85) REVERT: I 202 ARG cc_start: 0.7022 (ptm-80) cc_final: 0.6620 (ptt-90) REVERT: I 407 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7802 (tmm-80) REVERT: I 446 ASP cc_start: 0.7926 (m-30) cc_final: 0.7441 (m-30) REVERT: I 488 MET cc_start: 0.8657 (tpt) cc_final: 0.8453 (tpt) REVERT: I 539 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.5945 (p) REVERT: I 546 GLU cc_start: 0.8563 (mp0) cc_final: 0.7823 (tt0) REVERT: I 602 GLU cc_start: 0.6937 (pt0) cc_final: 0.6635 (pt0) REVERT: I 644 LEU cc_start: 0.8034 (mt) cc_final: 0.7786 (mt) REVERT: I 653 MET cc_start: 0.8130 (ttt) cc_final: 0.7890 (tpt) REVERT: I 696 ASP cc_start: 0.8109 (t0) cc_final: 0.7773 (t0) REVERT: I 835 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: I 882 ILE cc_start: 0.7973 (mp) cc_final: 0.7694 (tt) REVERT: I 1064 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6336 (p0) REVERT: I 1119 MET cc_start: 0.6980 (ttt) cc_final: 0.6409 (tpt) REVERT: I 1154 ASP cc_start: 0.8027 (m-30) cc_final: 0.7436 (t0) REVERT: I 1168 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6708 (mt-10) REVERT: I 1230 MET cc_start: 0.8891 (ttp) cc_final: 0.8621 (ttp) REVERT: I 1265 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: I 1310 ASP cc_start: 0.7330 (m-30) cc_final: 0.7107 (m-30) REVERT: J 21 LYS cc_start: 0.7198 (tttm) cc_final: 0.6375 (ptmm) REVERT: J 197 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: J 217 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8822 (pp) REVERT: J 227 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.6068 (t80) REVERT: J 329 ASP cc_start: 0.7516 (m-30) cc_final: 0.7195 (m-30) REVERT: J 348 ASP cc_start: 0.7542 (m-30) cc_final: 0.6670 (t0) REVERT: J 363 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6791 (tt) REVERT: J 402 GLU cc_start: 0.8953 (tt0) cc_final: 0.8688 (tm-30) REVERT: J 404 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7422 (mp0) REVERT: J 413 ASP cc_start: 0.8087 (t70) cc_final: 0.7795 (t0) REVERT: J 606 ASN cc_start: 0.6312 (t0) cc_final: 0.5948 (m110) REVERT: J 709 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7819 (tmm-80) REVERT: J 712 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8269 (mm-40) REVERT: J 811 GLU cc_start: 0.7360 (tt0) cc_final: 0.7019 (mt-10) REVERT: J 860 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7704 (tpt-90) REVERT: J 862 THR cc_start: 0.8188 (m) cc_final: 0.7841 (p) REVERT: J 913 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6336 (mm-30) REVERT: J 932 MET cc_start: 0.8294 (ttm) cc_final: 0.7566 (mtp) REVERT: J 1243 LEU cc_start: 0.8006 (tt) cc_final: 0.7748 (mp) REVERT: J 1275 LEU cc_start: 0.8850 (tp) cc_final: 0.8328 (tt) REVERT: J 1334 GLU cc_start: 0.6640 (tp30) cc_final: 0.6138 (mt-10) outliers start: 102 outliers final: 54 residues processed: 353 average time/residue: 0.6378 time to fit residues: 262.1901 Evaluate side-chains 331 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 264 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Chi-restraints excluded: chain J residue 1370 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 208 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 289 optimal weight: 40.0000 chunk 186 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 193 ASN I 518 ASN ** I1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.192762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116124 restraints weight = 34885.412| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.25 r_work: 0.3343 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 26617 Z= 0.312 Angle : 0.699 14.368 36224 Z= 0.358 Chirality : 0.047 0.223 4150 Planarity : 0.006 0.060 4517 Dihedral : 13.545 123.372 4319 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.49 % Allowed : 15.84 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.10 (0.15), residues: 3148 helix: 1.32 (0.16), residues: 1100 sheet: 0.25 (0.24), residues: 458 loop : -0.88 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 53 TYR 0.021 0.002 TYR J1282 PHE 0.019 0.002 PHE I 405 TRP 0.021 0.002 TRP J1020 HIS 0.009 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.31 (26609) covalent geometry : angle 0.69550 / 0.36 (36212) hydrogen bonds : bond 0.06880 / 4.18 ( 1108) hydrogen bonds : angle 4.50331 / 2.90 ( 3058) metal coordination : bond 0.01005 / 0.50 ( 8) metal coordination : angle 3.95543 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 263 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8261 (pt0) cc_final: 0.7845 (pm20) REVERT: G 72 GLU cc_start: 0.8312 (tt0) cc_final: 0.7933 (tm-30) REVERT: G 122 GLU cc_start: 0.6919 (tt0) cc_final: 0.6222 (tm-30) REVERT: G 127 GLN cc_start: 0.7815 (mp10) cc_final: 0.7459 (mp10) REVERT: H 38 THR cc_start: 0.6303 (OUTLIER) cc_final: 0.6102 (t) REVERT: H 50 SER cc_start: 0.8887 (t) cc_final: 0.8658 (t) REVERT: H 66 HIS cc_start: 0.7587 (t-90) cc_final: 0.7108 (t70) REVERT: H 80 GLU cc_start: 0.7645 (tt0) cc_final: 0.7384 (mt-10) REVERT: H 114 ASP cc_start: 0.7631 (t0) cc_final: 0.6895 (m-30) REVERT: H 150 ARG cc_start: 0.6037 (mpt180) cc_final: 0.5682 (mtm110) REVERT: H 176 CYS cc_start: 0.8750 (m) cc_final: 0.7608 (t) REVERT: H 188 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6263 (mt-10) REVERT: H 197 ASP cc_start: 0.7501 (p0) cc_final: 0.6868 (t0) REVERT: H 200 LYS cc_start: 0.6748 (tttt) cc_final: 0.6439 (tttp) REVERT: H 204 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7160 (mp0) REVERT: I 14 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7371 (t70) REVERT: I 77 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7995 (mm-30) REVERT: I 117 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6858 (mm) REVERT: I 132 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7973 (t0) REVERT: I 160 ASP cc_start: 0.5827 (m-30) cc_final: 0.5210 (p0) REVERT: I 200 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7529 (mmm-85) REVERT: I 201 ARG cc_start: 0.6048 (mtt-85) cc_final: 0.5680 (mtt180) REVERT: I 202 ARG cc_start: 0.6961 (ptm-80) cc_final: 0.6526 (ptt-90) REVERT: I 407 ARG cc_start: 0.8117 (ttt-90) cc_final: 0.7842 (tmm-80) REVERT: I 446 ASP cc_start: 0.8066 (m-30) cc_final: 0.7439 (m-30) REVERT: I 470 ARG cc_start: 0.6937 (tpp80) cc_final: 0.6724 (tpp80) REVERT: I 488 MET cc_start: 0.8705 (tpt) cc_final: 0.8496 (tpt) REVERT: I 539 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6167 (p) REVERT: I 546 GLU cc_start: 0.8601 (mp0) cc_final: 0.7972 (tt0) REVERT: I 602 GLU cc_start: 0.7113 (pt0) cc_final: 0.6749 (pt0) REVERT: I 644 LEU cc_start: 0.8117 (mt) cc_final: 0.7848 (mt) REVERT: I 647 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7434 (ttm110) REVERT: I 694 ARG cc_start: 0.6785 (mtm180) cc_final: 0.6444 (mtm180) REVERT: I 696 ASP cc_start: 0.8191 (t0) cc_final: 0.7894 (t0) REVERT: I 882 ILE cc_start: 0.8139 (mp) cc_final: 0.7758 (tt) REVERT: I 1064 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6228 (OUTLIER) REVERT: I 1119 MET cc_start: 0.7323 (ttt) cc_final: 0.6826 (tpt) REVERT: I 1154 ASP cc_start: 0.8025 (m-30) cc_final: 0.7453 (t0) REVERT: I 1168 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6733 (mt-10) REVERT: I 1230 MET cc_start: 0.8998 (ttp) cc_final: 0.8673 (ttp) REVERT: I 1265 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: J 21 LYS cc_start: 0.7317 (tttm) cc_final: 0.6473 (ptmm) REVERT: J 94 GLN cc_start: 0.7397 (mt0) cc_final: 0.6968 (mp10) REVERT: J 180 MET cc_start: 0.7561 (ttm) cc_final: 0.7012 (tpt) REVERT: J 197 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8512 (tt0) REVERT: J 217 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8866 (pp) REVERT: J 329 ASP cc_start: 0.7580 (m-30) cc_final: 0.7321 (m-30) REVERT: J 363 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7027 (tt) REVERT: J 402 GLU cc_start: 0.8943 (tt0) cc_final: 0.8653 (tm-30) REVERT: J 404 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7388 (mp0) REVERT: J 413 ASP cc_start: 0.8120 (t70) cc_final: 0.7822 (t0) REVERT: J 423 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7672 (mp) REVERT: J 709 ARG cc_start: 0.8185 (tmm-80) cc_final: 0.7976 (tmm-80) REVERT: J 712 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8451 (mm-40) REVERT: J 802 ASP cc_start: 0.5985 (t70) cc_final: 0.5328 (m-30) REVERT: J 811 GLU cc_start: 0.7519 (tt0) cc_final: 0.7189 (mt-10) REVERT: J 860 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7542 (tpt-90) REVERT: J 862 THR cc_start: 0.8300 (m) cc_final: 0.7866 (p) REVERT: J 1194 ARG cc_start: 0.9144 (mmt180) cc_final: 0.8896 (mmt180) REVERT: J 1243 LEU cc_start: 0.8113 (tt) cc_final: 0.7856 (mp) REVERT: J 1275 LEU cc_start: 0.8844 (tp) cc_final: 0.8355 (tt) outliers start: 121 outliers final: 78 residues processed: 361 average time/residue: 0.6258 time to fit residues: 262.9526 Evaluate side-chains 341 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 253 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 715 THR Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Chi-restraints excluded: chain J residue 1248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.196972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123741 restraints weight = 34833.426| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.20 r_work: 0.3428 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 26617 Z= 0.125 Angle : 0.552 11.383 36224 Z= 0.282 Chirality : 0.042 0.223 4150 Planarity : 0.004 0.059 4517 Dihedral : 13.362 124.562 4317 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.75 % Allowed : 16.92 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3148 helix: 1.60 (0.16), residues: 1103 sheet: 0.31 (0.24), residues: 462 loop : -0.78 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 88 TYR 0.019 0.001 TYR J1282 PHE 0.011 0.001 PHE I 828 TRP 0.024 0.001 TRP J1020 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (26609) covalent geometry : angle 0.54953 / 0.28 (36212) hydrogen bonds : bond 0.04608 / 2.88 ( 1108) hydrogen bonds : angle 4.20840 / 2.69 ( 3058) metal coordination : bond 0.00401 / 0.20 ( 8) metal coordination : angle 3.16192 / 2.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 266 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8188 (pt0) cc_final: 0.7824 (pm20) REVERT: G 72 GLU cc_start: 0.8227 (tt0) cc_final: 0.7816 (tm-30) REVERT: G 99 ILE cc_start: 0.7874 (mt) cc_final: 0.7591 (mp) REVERT: G 122 GLU cc_start: 0.6937 (tt0) cc_final: 0.6230 (tm-30) REVERT: G 127 GLN cc_start: 0.7797 (mp10) cc_final: 0.7433 (mp10) REVERT: H 38 THR cc_start: 0.5924 (OUTLIER) cc_final: 0.5615 (p) REVERT: H 50 SER cc_start: 0.8723 (t) cc_final: 0.8444 (t) REVERT: H 66 HIS cc_start: 0.7625 (t-90) cc_final: 0.7131 (t70) REVERT: H 114 ASP cc_start: 0.7467 (t0) cc_final: 0.6898 (m-30) REVERT: H 150 ARG cc_start: 0.5934 (mpt180) cc_final: 0.5588 (mtm110) REVERT: H 176 CYS cc_start: 0.8697 (m) cc_final: 0.7585 (t) REVERT: H 197 ASP cc_start: 0.7413 (p0) cc_final: 0.6828 (t0) REVERT: H 200 LYS cc_start: 0.6742 (tttt) cc_final: 0.6531 (tttp) REVERT: H 204 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7116 (mp0) REVERT: I 70 TYR cc_start: 0.6271 (t80) cc_final: 0.5957 (t80) REVERT: I 77 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8038 (mm-30) REVERT: I 132 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8045 (t0) REVERT: I 160 ASP cc_start: 0.5788 (m-30) cc_final: 0.5198 (p0) REVERT: I 200 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7561 (mmm-85) REVERT: I 201 ARG cc_start: 0.6261 (mtt-85) cc_final: 0.5950 (mtp180) REVERT: I 202 ARG cc_start: 0.7117 (ptm-80) cc_final: 0.6774 (ptt-90) REVERT: I 407 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7793 (tmm-80) REVERT: I 446 ASP cc_start: 0.7942 (m-30) cc_final: 0.7437 (m-30) REVERT: I 470 ARG cc_start: 0.6828 (tpp80) cc_final: 0.6608 (tpp80) REVERT: I 488 MET cc_start: 0.8686 (tpt) cc_final: 0.8481 (tpt) REVERT: I 539 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.5900 (p) REVERT: I 546 GLU cc_start: 0.8551 (mp0) cc_final: 0.7804 (tt0) REVERT: I 602 GLU cc_start: 0.6926 (pt0) cc_final: 0.6584 (pt0) REVERT: I 632 ASP cc_start: 0.8075 (p0) cc_final: 0.7579 (m-30) REVERT: I 633 LEU cc_start: 0.7935 (mt) cc_final: 0.7548 (mp) REVERT: I 644 LEU cc_start: 0.8152 (mt) cc_final: 0.7842 (mt) REVERT: I 645 PHE cc_start: 0.7554 (m-80) cc_final: 0.7269 (m-80) REVERT: I 653 MET cc_start: 0.8158 (ttt) cc_final: 0.7905 (tpt) REVERT: I 696 ASP cc_start: 0.8129 (t0) cc_final: 0.7708 (t0) REVERT: I 882 ILE cc_start: 0.7939 (mp) cc_final: 0.7671 (tt) REVERT: I 1064 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6300 (p0) REVERT: I 1119 MET cc_start: 0.7034 (ttt) cc_final: 0.6464 (tpt) REVERT: I 1136 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7296 (mt0) REVERT: I 1154 ASP cc_start: 0.8001 (m-30) cc_final: 0.7448 (t0) REVERT: I 1168 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6747 (mt-10) REVERT: I 1230 MET cc_start: 0.8928 (ttp) cc_final: 0.8626 (ttp) REVERT: I 1265 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7847 (m-10) REVERT: I 1310 ASP cc_start: 0.7406 (m-30) cc_final: 0.7201 (m-30) REVERT: J 21 LYS cc_start: 0.7226 (tttm) cc_final: 0.6379 (ptmm) REVERT: J 60 ARG cc_start: 0.8703 (ttm170) cc_final: 0.7967 (ttm-80) REVERT: J 94 GLN cc_start: 0.7422 (mt0) cc_final: 0.7016 (mp10) REVERT: J 180 MET cc_start: 0.7604 (ttm) cc_final: 0.7270 (tpt) REVERT: J 197 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8502 (tt0) REVERT: J 217 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8840 (pp) REVERT: J 227 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.6028 (t80) REVERT: J 329 ASP cc_start: 0.7590 (m-30) cc_final: 0.7292 (m-30) REVERT: J 348 ASP cc_start: 0.7555 (m-30) cc_final: 0.6734 (t0) REVERT: J 363 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6820 (tt) REVERT: J 402 GLU cc_start: 0.8934 (tt0) cc_final: 0.8573 (tm-30) REVERT: J 404 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7345 (mp0) REVERT: J 413 ASP cc_start: 0.8088 (t70) cc_final: 0.7780 (t0) REVERT: J 709 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7926 (tmm-80) REVERT: J 712 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8387 (mm-40) REVERT: J 811 GLU cc_start: 0.7440 (tt0) cc_final: 0.7107 (mt-10) REVERT: J 860 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7568 (tpt-90) REVERT: J 862 THR cc_start: 0.8260 (m) cc_final: 0.7873 (p) REVERT: J 913 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: J 932 MET cc_start: 0.8422 (ttm) cc_final: 0.7714 (mtp) REVERT: J 1189 MET cc_start: 0.9313 (tpp) cc_final: 0.9102 (tpp) REVERT: J 1194 ARG cc_start: 0.9117 (mmt180) cc_final: 0.8911 (mmt180) REVERT: J 1243 LEU cc_start: 0.8086 (tt) cc_final: 0.7846 (mp) REVERT: J 1275 LEU cc_start: 0.8848 (tp) cc_final: 0.8334 (tt) REVERT: J 1334 GLU cc_start: 0.6646 (tp30) cc_final: 0.6154 (mt-10) outliers start: 101 outliers final: 62 residues processed: 345 average time/residue: 0.6241 time to fit residues: 250.8871 Evaluate side-chains 332 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Chi-restraints excluded: chain J residue 1248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 13 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 286 optimal weight: 50.0000 chunk 183 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 193 ASN ** I1134 GLN ** 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 = 0.4411 r_free = 0.4411 target = 0.196764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122584 restraints weight = 34608.629| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.26 r_work: 0.3406 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26617 Z= 0.142 Angle : 0.561 11.643 36224 Z= 0.286 Chirality : 0.042 0.223 4150 Planarity : 0.004 0.050 4517 Dihedral : 13.298 124.309 4314 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.41 % Allowed : 17.70 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 3148 helix: 1.73 (0.16), residues: 1096 sheet: 0.41 (0.24), residues: 454 loop : -0.73 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 133 TYR 0.018 0.001 TYR J1282 PHE 0.013 0.001 PHE I 57 TRP 0.024 0.001 TRP J1020 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (26609) covalent geometry : angle 0.55845 / 0.29 (36212) hydrogen bonds : bond 0.04757 / 2.95 ( 1108) hydrogen bonds : angle 4.15725 / 2.66 ( 3058) metal coordination : bond 0.00465 / 0.23 ( 8) metal coordination : angle 2.93599 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 260 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8202 (pt0) cc_final: 0.7844 (pm20) REVERT: G 72 GLU cc_start: 0.8249 (tt0) cc_final: 0.7853 (tm-30) REVERT: G 99 ILE cc_start: 0.7897 (mt) cc_final: 0.7623 (mp) REVERT: G 122 GLU cc_start: 0.6959 (tt0) cc_final: 0.6296 (tm-30) REVERT: G 127 GLN cc_start: 0.7799 (mp10) cc_final: 0.7434 (mp10) REVERT: H 38 THR cc_start: 0.6141 (OUTLIER) cc_final: 0.5814 (p) REVERT: H 50 SER cc_start: 0.8736 (t) cc_final: 0.8486 (t) REVERT: H 66 HIS cc_start: 0.7600 (t-90) cc_final: 0.7113 (t70) REVERT: H 80 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7779 (mt-10) REVERT: H 114 ASP cc_start: 0.7632 (t0) cc_final: 0.6954 (m-30) REVERT: H 150 ARG cc_start: 0.6011 (mpt180) cc_final: 0.5636 (mtm110) REVERT: H 176 CYS cc_start: 0.8706 (m) cc_final: 0.7626 (t) REVERT: H 197 ASP cc_start: 0.7439 (p0) cc_final: 0.6842 (t0) REVERT: H 200 LYS cc_start: 0.6801 (tttt) cc_final: 0.6581 (tttp) REVERT: H 204 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7193 (mp0) REVERT: I 46 GLN cc_start: 0.6733 (pt0) cc_final: 0.6523 (pm20) REVERT: I 70 TYR cc_start: 0.6241 (t80) cc_final: 0.5953 (t80) REVERT: I 77 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8093 (mm-30) REVERT: I 132 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7996 (t0) REVERT: I 160 ASP cc_start: 0.5830 (m-30) cc_final: 0.5239 (p0) REVERT: I 200 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: I 201 ARG cc_start: 0.6258 (mtt-85) cc_final: 0.5857 (mtt180) REVERT: I 202 ARG cc_start: 0.6964 (ptm-80) cc_final: 0.6610 (ptt-90) REVERT: I 407 ARG cc_start: 0.8128 (ttt-90) cc_final: 0.7815 (tmm-80) REVERT: I 446 ASP cc_start: 0.7988 (m-30) cc_final: 0.7444 (m-30) REVERT: I 488 MET cc_start: 0.8714 (tpt) cc_final: 0.8514 (tpt) REVERT: I 546 GLU cc_start: 0.8539 (mp0) cc_final: 0.7798 (tt0) REVERT: I 602 GLU cc_start: 0.6893 (pt0) cc_final: 0.6616 (pt0) REVERT: I 632 ASP cc_start: 0.8041 (p0) cc_final: 0.7557 (m-30) REVERT: I 633 LEU cc_start: 0.7955 (mt) cc_final: 0.7594 (mp) REVERT: I 644 LEU cc_start: 0.8111 (mt) cc_final: 0.7817 (mt) REVERT: I 645 PHE cc_start: 0.7614 (m-80) cc_final: 0.7277 (m-80) REVERT: I 653 MET cc_start: 0.8254 (ttt) cc_final: 0.8036 (tpt) REVERT: I 694 ARG cc_start: 0.6606 (mtm180) cc_final: 0.6254 (mtm180) REVERT: I 696 ASP cc_start: 0.8131 (t0) cc_final: 0.7804 (t0) REVERT: I 882 ILE cc_start: 0.7930 (mp) cc_final: 0.7679 (tt) REVERT: I 1064 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6288 (p0) REVERT: I 1119 MET cc_start: 0.7222 (ttt) cc_final: 0.6655 (tpt) REVERT: I 1136 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: I 1154 ASP cc_start: 0.7992 (m-30) cc_final: 0.7458 (t0) REVERT: I 1168 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6764 (mt-10) REVERT: I 1230 MET cc_start: 0.8984 (ttp) cc_final: 0.8704 (ttp) REVERT: I 1265 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7821 (m-10) REVERT: I 1310 ASP cc_start: 0.7473 (m-30) cc_final: 0.7266 (m-30) REVERT: J 60 ARG cc_start: 0.8695 (ttm170) cc_final: 0.7985 (ttm-80) REVERT: J 94 GLN cc_start: 0.7410 (mt0) cc_final: 0.7025 (mp10) REVERT: J 197 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8477 (tt0) REVERT: J 217 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8829 (pp) REVERT: J 227 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5926 (t80) REVERT: J 329 ASP cc_start: 0.7613 (m-30) cc_final: 0.7296 (m-30) REVERT: J 348 ASP cc_start: 0.7660 (m-30) cc_final: 0.6760 (t0) REVERT: J 363 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6868 (tt) REVERT: J 413 ASP cc_start: 0.8112 (t70) cc_final: 0.7812 (t0) REVERT: J 709 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7899 (tmm-80) REVERT: J 712 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8441 (mm-40) REVERT: J 811 GLU cc_start: 0.7476 (tt0) cc_final: 0.7143 (mt-10) REVERT: J 822 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: J 860 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7591 (tpt-90) REVERT: J 862 THR cc_start: 0.8256 (m) cc_final: 0.7883 (p) REVERT: J 913 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: J 932 MET cc_start: 0.8423 (ttm) cc_final: 0.7676 (mtp) REVERT: J 1156 LEU cc_start: 0.9266 (mt) cc_final: 0.8983 (tp) REVERT: J 1243 LEU cc_start: 0.8120 (tt) cc_final: 0.7882 (mp) REVERT: J 1266 ILE cc_start: 0.8035 (mm) cc_final: 0.7808 (mt) REVERT: J 1275 LEU cc_start: 0.8821 (tp) cc_final: 0.8230 (tt) outliers start: 92 outliers final: 64 residues processed: 333 average time/residue: 0.6203 time to fit residues: 240.7091 Evaluate side-chains 326 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 251 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 677 ASN Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 124 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 314 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 193 ASN ** I1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.198065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124269 restraints weight = 34820.972| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.29 r_work: 0.3429 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26617 Z= 0.113 Angle : 0.538 11.235 36224 Z= 0.273 Chirality : 0.041 0.241 4150 Planarity : 0.004 0.076 4517 Dihedral : 13.201 124.853 4314 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.04 % Allowed : 18.52 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3148 helix: 1.86 (0.16), residues: 1100 sheet: 0.40 (0.25), residues: 448 loop : -0.68 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 88 TYR 0.018 0.001 TYR J1282 PHE 0.010 0.001 PHE J 62 TRP 0.024 0.001 TRP J1020 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (26609) covalent geometry : angle 0.53531 / 0.27 (36212) hydrogen bonds : bond 0.04100 / 2.56 ( 1108) hydrogen bonds : angle 4.04296 / 2.58 ( 3058) metal coordination : bond 0.00354 / 0.18 ( 8) metal coordination : angle 2.71469 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 258 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8147 (pt0) cc_final: 0.7809 (pm20) REVERT: G 72 GLU cc_start: 0.8244 (tt0) cc_final: 0.7832 (tm-30) REVERT: G 99 ILE cc_start: 0.7906 (mt) cc_final: 0.7643 (mp) REVERT: G 122 GLU cc_start: 0.6953 (tt0) cc_final: 0.6251 (tm-30) REVERT: G 127 GLN cc_start: 0.7779 (mp10) cc_final: 0.7420 (mp10) REVERT: H 38 THR cc_start: 0.6016 (OUTLIER) cc_final: 0.4942 (m) REVERT: H 66 HIS cc_start: 0.7616 (t-90) cc_final: 0.7123 (t70) REVERT: H 80 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7648 (mt-10) REVERT: H 114 ASP cc_start: 0.7680 (t0) cc_final: 0.7447 (t70) REVERT: H 150 ARG cc_start: 0.5981 (mpt180) cc_final: 0.5618 (mtm110) REVERT: H 176 CYS cc_start: 0.8693 (m) cc_final: 0.7618 (t) REVERT: H 197 ASP cc_start: 0.7431 (p0) cc_final: 0.6848 (t0) REVERT: H 200 LYS cc_start: 0.6746 (tttt) cc_final: 0.6525 (tttp) REVERT: H 204 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7200 (mp0) REVERT: I 77 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8119 (mm-30) REVERT: I 127 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.6999 (tt) REVERT: I 132 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (t0) REVERT: I 160 ASP cc_start: 0.5805 (m-30) cc_final: 0.5177 (p0) REVERT: I 200 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: I 201 ARG cc_start: 0.6218 (mtt-85) cc_final: 0.5807 (mtt180) REVERT: I 202 ARG cc_start: 0.7022 (ptm-80) cc_final: 0.6562 (ptt-90) REVERT: I 407 ARG cc_start: 0.8112 (ttt-90) cc_final: 0.7799 (tmm-80) REVERT: I 446 ASP cc_start: 0.7925 (m-30) cc_final: 0.7373 (m-30) REVERT: I 488 MET cc_start: 0.8710 (tpt) cc_final: 0.8503 (tpt) REVERT: I 546 GLU cc_start: 0.8526 (mp0) cc_final: 0.7779 (tt0) REVERT: I 602 GLU cc_start: 0.6781 (pt0) cc_final: 0.6310 (pm20) REVERT: I 632 ASP cc_start: 0.8012 (p0) cc_final: 0.7540 (m-30) REVERT: I 633 LEU cc_start: 0.7830 (mt) cc_final: 0.7463 (mp) REVERT: I 644 LEU cc_start: 0.8129 (mt) cc_final: 0.7827 (mt) REVERT: I 645 PHE cc_start: 0.7653 (m-80) cc_final: 0.7336 (m-80) REVERT: I 653 MET cc_start: 0.8226 (ttt) cc_final: 0.7997 (tpt) REVERT: I 696 ASP cc_start: 0.8137 (t0) cc_final: 0.7722 (t0) REVERT: I 835 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: I 882 ILE cc_start: 0.7806 (mp) cc_final: 0.7600 (tt) REVERT: I 1064 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6382 (OUTLIER) REVERT: I 1119 MET cc_start: 0.7094 (ttt) cc_final: 0.6557 (tpt) REVERT: I 1136 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7282 (mt0) REVERT: I 1154 ASP cc_start: 0.7999 (m-30) cc_final: 0.7466 (t0) REVERT: I 1168 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6758 (mt-10) REVERT: I 1230 MET cc_start: 0.8935 (ttp) cc_final: 0.8676 (ttp) REVERT: I 1265 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: J 60 ARG cc_start: 0.8647 (ttm170) cc_final: 0.7968 (ttm-80) REVERT: J 68 TYR cc_start: 0.8752 (m-80) cc_final: 0.8401 (m-80) REVERT: J 94 GLN cc_start: 0.7385 (mt0) cc_final: 0.7032 (mp10) REVERT: J 197 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8488 (tt0) REVERT: J 217 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8848 (pp) REVERT: J 227 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.5935 (t80) REVERT: J 329 ASP cc_start: 0.7657 (m-30) cc_final: 0.7332 (m-30) REVERT: J 348 ASP cc_start: 0.7550 (m-30) cc_final: 0.6748 (t0) REVERT: J 402 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8459 (tm-30) REVERT: J 404 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7377 (mp0) REVERT: J 413 ASP cc_start: 0.8091 (t70) cc_final: 0.7787 (t0) REVERT: J 606 ASN cc_start: 0.6234 (t0) cc_final: 0.5812 (m110) REVERT: J 709 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7859 (tmm-80) REVERT: J 712 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8423 (mm-40) REVERT: J 811 GLU cc_start: 0.7457 (tt0) cc_final: 0.7111 (mt-10) REVERT: J 857 LEU cc_start: 0.7686 (tm) cc_final: 0.7038 (mt) REVERT: J 860 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7620 (tpt-90) REVERT: J 862 THR cc_start: 0.8248 (m) cc_final: 0.7890 (p) REVERT: J 932 MET cc_start: 0.8340 (ttm) cc_final: 0.7760 (mtp) REVERT: J 1156 LEU cc_start: 0.9246 (mt) cc_final: 0.8967 (tp) REVERT: J 1243 LEU cc_start: 0.8110 (tt) cc_final: 0.7870 (mp) REVERT: J 1266 ILE cc_start: 0.8033 (mm) cc_final: 0.7812 (mt) REVERT: J 1275 LEU cc_start: 0.8811 (tp) cc_final: 0.8204 (tt) outliers start: 82 outliers final: 59 residues processed: 325 average time/residue: 0.6094 time to fit residues: 230.8966 Evaluate side-chains 317 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 677 ASN Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 89 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 316 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 284 optimal weight: 50.0000 chunk 197 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN H 186 ASN I 193 ASN ** I1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.196647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121100 restraints weight = 34767.140| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.20 r_work: 0.3412 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26617 Z= 0.150 Angle : 0.581 12.363 36224 Z= 0.294 Chirality : 0.042 0.221 4150 Planarity : 0.004 0.052 4517 Dihedral : 13.195 124.919 4311 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.08 % Allowed : 18.74 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3148 helix: 1.79 (0.16), residues: 1099 sheet: 0.54 (0.25), residues: 449 loop : -0.69 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 133 TYR 0.017 0.001 TYR J1282 PHE 0.018 0.001 PHE I 57 TRP 0.026 0.001 TRP J1020 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (26609) covalent geometry : angle 0.57905 / 0.29 (36212) hydrogen bonds : bond 0.04708 / 2.91 ( 1108) hydrogen bonds : angle 4.10159 / 2.62 ( 3058) metal coordination : bond 0.00472 / 0.24 ( 8) metal coordination : angle 2.70896 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 257 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8116 (pt0) cc_final: 0.7767 (pm20) REVERT: G 72 GLU cc_start: 0.8265 (tt0) cc_final: 0.7825 (tm-30) REVERT: G 99 ILE cc_start: 0.7908 (mt) cc_final: 0.7637 (mp) REVERT: G 122 GLU cc_start: 0.6946 (tt0) cc_final: 0.6283 (tm-30) REVERT: G 127 GLN cc_start: 0.7789 (mp10) cc_final: 0.7431 (mp10) REVERT: H 38 THR cc_start: 0.6013 (OUTLIER) cc_final: 0.5021 (m) REVERT: H 66 HIS cc_start: 0.7620 (t-90) cc_final: 0.7173 (t70) REVERT: H 114 ASP cc_start: 0.7821 (t0) cc_final: 0.7589 (t0) REVERT: H 150 ARG cc_start: 0.5970 (mpt180) cc_final: 0.5605 (mtm110) REVERT: H 176 CYS cc_start: 0.8732 (m) cc_final: 0.7637 (t) REVERT: H 197 ASP cc_start: 0.7427 (p0) cc_final: 0.6826 (t0) REVERT: H 200 LYS cc_start: 0.6694 (tttt) cc_final: 0.6471 (tttp) REVERT: H 204 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7179 (mp0) REVERT: I 40 GLU cc_start: 0.5604 (tt0) cc_final: 0.5385 (tp30) REVERT: I 77 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8142 (mm-30) REVERT: I 132 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7964 (t0) REVERT: I 160 ASP cc_start: 0.5849 (m-30) cc_final: 0.5223 (p0) REVERT: I 200 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7594 (mmm-85) REVERT: I 201 ARG cc_start: 0.6067 (mtt-85) cc_final: 0.5792 (mtt-85) REVERT: I 202 ARG cc_start: 0.7145 (ptm-80) cc_final: 0.6837 (ptt-90) REVERT: I 407 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7793 (tmm-80) REVERT: I 446 ASP cc_start: 0.7930 (m-30) cc_final: 0.7389 (m-30) REVERT: I 546 GLU cc_start: 0.8476 (mp0) cc_final: 0.7755 (tt0) REVERT: I 602 GLU cc_start: 0.6792 (pt0) cc_final: 0.6310 (pm20) REVERT: I 632 ASP cc_start: 0.8009 (p0) cc_final: 0.7520 (m-30) REVERT: I 633 LEU cc_start: 0.7816 (mt) cc_final: 0.7432 (mp) REVERT: I 644 LEU cc_start: 0.8066 (mt) cc_final: 0.7764 (mt) REVERT: I 645 PHE cc_start: 0.7617 (m-80) cc_final: 0.7252 (m-80) REVERT: I 653 MET cc_start: 0.8227 (ttt) cc_final: 0.7949 (tpt) REVERT: I 694 ARG cc_start: 0.6539 (mtm180) cc_final: 0.6173 (mtm180) REVERT: I 696 ASP cc_start: 0.8096 (t0) cc_final: 0.7681 (t0) REVERT: I 835 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: I 882 ILE cc_start: 0.7796 (mp) cc_final: 0.7584 (tt) REVERT: I 890 LYS cc_start: 0.5633 (OUTLIER) cc_final: 0.5067 (pmtt) REVERT: I 1064 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6292 (OUTLIER) REVERT: I 1119 MET cc_start: 0.7139 (ttt) cc_final: 0.6568 (tpt) REVERT: I 1136 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: I 1154 ASP cc_start: 0.7982 (m-30) cc_final: 0.7426 (t0) REVERT: I 1168 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6723 (mt-10) REVERT: I 1230 MET cc_start: 0.8880 (ttp) cc_final: 0.8613 (ttp) REVERT: I 1265 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: J 60 ARG cc_start: 0.8665 (ttm170) cc_final: 0.7947 (ttm-80) REVERT: J 94 GLN cc_start: 0.7399 (mt0) cc_final: 0.7025 (mp10) REVERT: J 197 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8464 (tt0) REVERT: J 217 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8863 (pp) REVERT: J 227 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5903 (t80) REVERT: J 329 ASP cc_start: 0.7604 (m-30) cc_final: 0.7284 (m-30) REVERT: J 348 ASP cc_start: 0.7617 (m-30) cc_final: 0.6648 (t0) REVERT: J 402 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8463 (tm-30) REVERT: J 404 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7351 (mp0) REVERT: J 413 ASP cc_start: 0.8070 (t70) cc_final: 0.7782 (t0) REVERT: J 709 ARG cc_start: 0.8096 (tmm-80) cc_final: 0.7823 (tmm-80) REVERT: J 712 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8426 (mm-40) REVERT: J 811 GLU cc_start: 0.7390 (tt0) cc_final: 0.7032 (mt-10) REVERT: J 857 LEU cc_start: 0.7752 (tm) cc_final: 0.7111 (mt) REVERT: J 860 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7621 (tpt-90) REVERT: J 862 THR cc_start: 0.8239 (m) cc_final: 0.7881 (p) REVERT: J 932 MET cc_start: 0.8411 (ttm) cc_final: 0.7671 (mtp) REVERT: J 1156 LEU cc_start: 0.9245 (mt) cc_final: 0.8982 (tp) REVERT: J 1222 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7179 (mpp80) REVERT: J 1243 LEU cc_start: 0.8103 (tt) cc_final: 0.7868 (mp) REVERT: J 1266 ILE cc_start: 0.8009 (mm) cc_final: 0.7779 (mt) REVERT: J 1275 LEU cc_start: 0.8799 (tp) cc_final: 0.8208 (tt) outliers start: 83 outliers final: 56 residues processed: 327 average time/residue: 0.6303 time to fit residues: 240.8292 Evaluate side-chains 316 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 250 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 890 LYS Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1222 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 95 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 251 optimal weight: 0.0270 chunk 166 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 193 ASN I 618 GLN I1134 GLN J1227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115964 restraints weight = 34429.556| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.42 r_work: 0.3205 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26617 Z= 0.129 Angle : 0.568 11.673 36224 Z= 0.287 Chirality : 0.042 0.221 4150 Planarity : 0.004 0.064 4517 Dihedral : 13.152 125.672 4311 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.67 % Allowed : 19.48 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3148 helix: 1.83 (0.16), residues: 1100 sheet: 0.54 (0.25), residues: 429 loop : -0.66 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 88 TYR 0.018 0.001 TYR J1282 PHE 0.013 0.001 PHE I 828 TRP 0.027 0.001 TRP J1020 HIS 0.004 0.001 HIS J 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (26609) covalent geometry : angle 0.56586 / 0.29 (36212) hydrogen bonds : bond 0.04325 / 2.70 ( 1108) hydrogen bonds : angle 4.06929 / 2.60 ( 3058) metal coordination : bond 0.00395 / 0.20 ( 8) metal coordination : angle 2.64525 / 1.76 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8001 (pt0) cc_final: 0.7618 (pm20) REVERT: G 72 GLU cc_start: 0.8215 (tt0) cc_final: 0.7762 (tm-30) REVERT: G 96 ASP cc_start: 0.6850 (p0) cc_final: 0.6455 (t0) REVERT: G 99 ILE cc_start: 0.7708 (mt) cc_final: 0.7453 (mp) REVERT: G 122 GLU cc_start: 0.6746 (tt0) cc_final: 0.6128 (tm-30) REVERT: G 127 GLN cc_start: 0.7643 (mp10) cc_final: 0.7291 (mp10) REVERT: H 38 THR cc_start: 0.5654 (OUTLIER) cc_final: 0.4699 (m) REVERT: H 66 HIS cc_start: 0.7501 (t-90) cc_final: 0.7057 (t70) REVERT: H 114 ASP cc_start: 0.7804 (t0) cc_final: 0.7588 (t0) REVERT: H 150 ARG cc_start: 0.5715 (mpt180) cc_final: 0.5352 (mtm110) REVERT: H 176 CYS cc_start: 0.8684 (m) cc_final: 0.7550 (t) REVERT: H 197 ASP cc_start: 0.7454 (p0) cc_final: 0.6836 (t0) REVERT: H 204 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6959 (mp0) REVERT: I 77 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8143 (mm-30) REVERT: I 132 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7870 (t0) REVERT: I 160 ASP cc_start: 0.5821 (m-30) cc_final: 0.5206 (p0) REVERT: I 201 ARG cc_start: 0.5971 (mtt-85) cc_final: 0.5608 (mtt180) REVERT: I 202 ARG cc_start: 0.6902 (ptm-80) cc_final: 0.6623 (ptt-90) REVERT: I 407 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7694 (tmm-80) REVERT: I 446 ASP cc_start: 0.7807 (m-30) cc_final: 0.7258 (m-30) REVERT: I 470 ARG cc_start: 0.6401 (tpp80) cc_final: 0.5812 (mpt180) REVERT: I 546 GLU cc_start: 0.8437 (mp0) cc_final: 0.7643 (tt0) REVERT: I 602 GLU cc_start: 0.6526 (pt0) cc_final: 0.6259 (pt0) REVERT: I 632 ASP cc_start: 0.8013 (p0) cc_final: 0.7498 (m-30) REVERT: I 633 LEU cc_start: 0.7652 (mt) cc_final: 0.7255 (mp) REVERT: I 644 LEU cc_start: 0.7988 (mt) cc_final: 0.7659 (mt) REVERT: I 645 PHE cc_start: 0.7345 (m-80) cc_final: 0.6961 (m-80) REVERT: I 653 MET cc_start: 0.7961 (ttt) cc_final: 0.7649 (tpt) REVERT: I 694 ARG cc_start: 0.6213 (mtm180) cc_final: 0.5965 (mtm-85) REVERT: I 696 ASP cc_start: 0.7960 (t0) cc_final: 0.7405 (t0) REVERT: I 835 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: I 1064 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6161 (p0) REVERT: I 1119 MET cc_start: 0.6812 (ttt) cc_final: 0.6255 (tpt) REVERT: I 1136 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: I 1154 ASP cc_start: 0.7922 (m-30) cc_final: 0.7323 (t0) REVERT: I 1168 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6622 (mt-10) REVERT: I 1230 MET cc_start: 0.8626 (ttp) cc_final: 0.8321 (ttp) REVERT: I 1265 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: J 60 ARG cc_start: 0.8651 (ttm170) cc_final: 0.7924 (ttm-80) REVERT: J 94 GLN cc_start: 0.7282 (mt0) cc_final: 0.6959 (mp10) REVERT: J 197 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8510 (tt0) REVERT: J 217 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8791 (pp) REVERT: J 227 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5625 (t80) REVERT: J 329 ASP cc_start: 0.7314 (m-30) cc_final: 0.7004 (m-30) REVERT: J 348 ASP cc_start: 0.7408 (m-30) cc_final: 0.6538 (t0) REVERT: J 413 ASP cc_start: 0.7947 (t70) cc_final: 0.7670 (t0) REVERT: J 709 ARG cc_start: 0.8040 (tmm-80) cc_final: 0.7737 (tmm-80) REVERT: J 712 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8387 (mm-40) REVERT: J 811 GLU cc_start: 0.7234 (tt0) cc_final: 0.6898 (mt-10) REVERT: J 857 LEU cc_start: 0.7637 (tm) cc_final: 0.7026 (mt) REVERT: J 860 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7556 (tpt-90) REVERT: J 862 THR cc_start: 0.8032 (m) cc_final: 0.7650 (p) REVERT: J 932 MET cc_start: 0.8383 (ttm) cc_final: 0.7673 (mtp) REVERT: J 1156 LEU cc_start: 0.9170 (mt) cc_final: 0.8929 (tp) REVERT: J 1243 LEU cc_start: 0.7929 (tt) cc_final: 0.7705 (mp) REVERT: J 1275 LEU cc_start: 0.8661 (tp) cc_final: 0.8171 (tt) REVERT: J 1290 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7440 (ptp90) outliers start: 72 outliers final: 55 residues processed: 308 average time/residue: 0.6560 time to fit residues: 234.8725 Evaluate side-chains 310 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 677 ASN Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 1134 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 180 optimal weight: 0.6980 chunk 143 optimal weight: 0.0770 chunk 287 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 318 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 283 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN I 193 ASN I 618 GLN ** I1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.192734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114481 restraints weight = 34156.548| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.58 r_work: 0.3215 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26617 Z= 0.114 Angle : 0.568 12.135 36224 Z= 0.284 Chirality : 0.041 0.222 4150 Planarity : 0.004 0.049 4517 Dihedral : 13.091 126.469 4311 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.71 % Allowed : 19.48 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3148 helix: 1.87 (0.16), residues: 1101 sheet: 0.76 (0.26), residues: 424 loop : -0.62 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 133 TYR 0.017 0.001 TYR J1282 PHE 0.017 0.001 PHE I 57 TRP 0.026 0.001 TRP J1020 HIS 0.007 0.001 HIS J1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (26609) covalent geometry : angle 0.56588 / 0.28 (36212) hydrogen bonds : bond 0.03999 / 2.50 ( 1108) hydrogen bonds : angle 4.01547 / 2.55 ( 3058) metal coordination : bond 0.00325 / 0.16 ( 8) metal coordination : angle 2.51881 / 1.68 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11973.42 seconds wall clock time: 203 minutes 26.75 seconds (12206.75 seconds total)