Starting phenix.real_space_refine on Sat Jun 6 08:34:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10md_75282/06_2026/10md_75282.cif Found real_map, /net/cci-nas-00/data/ceres_data/10md_75282/06_2026/10md_75282.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/10md_75282/06_2026/10md_75282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10md_75282/06_2026/10md_75282.map" model { file = "/net/cci-nas-00/data/ceres_data/10md_75282/06_2026/10md_75282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10md_75282/06_2026/10md_75282.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= 0.013 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 13 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 312 Classifications: {'water': 312} Link IDs: {None: 311} Chain: "J" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16109 SG CYS J 70 117.001 66.433 71.612 1.00133.27 S ATOM 16123 SG CYS J 72 117.500 63.083 69.630 1.00140.85 S ATOM 16231 SG CYS J 85 118.772 65.451 68.104 1.00133.34 S ATOM 16255 SG CYS J 88 115.810 66.107 67.842 1.00130.80 S ATOM 21943 SG CYS J 814 87.219 128.496 67.157 1.00 45.42 S ATOM 22508 SG CYS J 888 85.793 124.930 67.599 1.00 27.38 S ATOM 22559 SG CYS J 895 86.733 127.027 70.718 1.00 39.65 S ATOM 22580 SG CYS J 898 84.202 127.331 69.431 1.00 41.51 S Time building chain proxies: 6.58, per 1000 atoms: 0.25 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 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 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " 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 48 sheets defined 39.3% alpha, 18.2% beta 23 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 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: 3.574A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.878A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.577A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.949A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.522A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.838A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 4.017A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.650A 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: 3.994A 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: 3.761A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.558A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.528A 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: 4.120A 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 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.822A pdb=" N ARG I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 4.123A 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 Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.293A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 663 through 668 removed outlier: 3.759A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.842A 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 983 removed outlier: 4.601A pdb=" N ILE I 948 " --> pdb=" O ARG I 944 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 4.061A 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: 3.505A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.576A pdb=" N THR I1115 " --> pdb=" O GLN I1111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I1120 " --> pdb=" O HIS I1116 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.578A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.560A 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 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.533A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.935A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.871A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.579A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.680A 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 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.535A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.545A 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: 3.694A pdb=" N MET J 330 " --> pdb=" O LEU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 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 403 Processing helix chain 'J' and resid 406 through 416 removed outlier: 4.297A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.556A 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 539 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 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.717A pdb=" N ALA J 633 " --> pdb=" O PHE J 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.509A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.527A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.614A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) removed outlier: 4.263A 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: 3.741A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.216A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.782A 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 914 through 925 removed outlier: 3.673A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.734A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1037 through 1041 removed outlier: 3.726A pdb=" N ILE J1041 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.702A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.605A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.390A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.897A 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 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.640A 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: 3.561A 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: 8.674A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.692A 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: 4.029A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (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: 3.656A 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: 6.570A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU H 201 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.664A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (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: 6.731A 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: 4.232A pdb=" N ILE I 59 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 68 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.025A 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: 3.591A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.553A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.603A 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: 4.870A 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: 6.964A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.897A 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: 6.690A 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: 6.507A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (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: 7.347A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.693A 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 841 removed outlier: 3.938A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.826A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.684A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.726A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.542A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.571A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 254 through 255 Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.561A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.923A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.551A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN J1019 " --> pdb=" O VAL J1002 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.594A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS J 996 " --> pdb=" O THR J 980 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR J 980 " --> pdb=" O LYS J 996 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 3.703A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE9, first strand: chain 'J' and resid 1059 through 1060 Processing sheet with id=AF1, first strand: chain 'J' and resid 1089 through 1090 Processing sheet with id=AF2, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.826A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.068A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 3.20 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: 7814 1.33 - 1.45: 3607 1.45 - 1.57: 14883 1.57 - 1.69: 121 1.69 - 1.81: 184 Bond restraints: 26609 Sorted by residual: bond pdb=" P DC B 25 " pdb=" OP2 DC B 25 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C GLU J 925 " pdb=" N PRO J 926 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.39e+00 bond pdb=" P DG B 27 " pdb=" OP2 DG B 27 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" P DA B 26 " pdb=" OP1 DA B 26 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" P DG B 28 " pdb=" OP2 DG B 28 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 26604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 35768 1.76 - 3.52: 393 3.52 - 5.29: 40 5.29 - 7.05: 9 7.05 - 8.81: 2 Bond angle restraints: 36212 Sorted by residual: angle pdb=" O3' G R 10 " pdb=" C3' G R 10 " pdb=" C2' G R 10 " ideal model delta sigma weight residual 113.70 118.20 -4.50 1.50e+00 4.44e-01 9.02e+00 angle pdb=" N PRO H 30 " pdb=" CA PRO H 30 " pdb=" C PRO H 30 " ideal model delta sigma weight residual 112.47 118.01 -5.54 2.06e+00 2.36e-01 7.22e+00 angle pdb=" C3' G R 10 " pdb=" O3' G R 10 " pdb=" P A R 11 " ideal model delta sigma weight residual 120.20 124.22 -4.02 1.50e+00 4.44e-01 7.17e+00 angle pdb=" C3' DG B 28 " pdb=" O3' DG B 28 " pdb=" P DA B 29 " ideal model delta sigma weight residual 120.20 124.10 -3.90 1.50e+00 4.44e-01 6.75e+00 angle pdb=" C LEU G 9 " pdb=" N LYS G 10 " pdb=" CA LYS G 10 " ideal model delta sigma weight residual 122.15 113.34 8.81 3.47e+00 8.31e-02 6.45e+00 ... (remaining 36207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 15701 27.04 - 54.07: 515 54.07 - 81.11: 91 81.11 - 108.15: 6 108.15 - 135.18: 1 Dihedral angle restraints: 16314 sinusoidal: 7223 harmonic: 9091 Sorted by residual: 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 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU J 120 " pdb=" C LEU J 120 " pdb=" N PRO J 121 " pdb=" CA PRO J 121 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ALA I1263 " pdb=" C ALA I1263 " pdb=" N GLN I1264 " pdb=" CA GLN I1264 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 16311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4103 0.118 - 0.237: 43 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 8.77e+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 -2.86 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" P DA B 26 " pdb=" OP1 DA B 26 " pdb=" OP2 DA B 26 " pdb=" O5' DA B 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 4147 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO I 190 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO I 590 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J1184 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO J1185 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO J1185 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO J1185 " 0.023 5.00e-02 4.00e+02 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 33 2.62 - 3.19: 22072 3.19 - 3.76: 38753 3.76 - 4.33: 55561 4.33 - 4.90: 92177 Nonbonded interactions: 208596 Sorted by model distance: nonbonded pdb=" O3' U R 19 " pdb="MG MG J1501 " model vdw 2.049 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.253 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.261 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.321 2.170 nonbonded pdb=" O4 DT B 13 " pdb=" O6 DG A 19 " model vdw 2.541 2.432 ... (remaining 208591 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: 0.740 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.090 Find NCS groups from input model: 0.280 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 0.086 26617 Z= 0.126 Angle : 0.587 32.613 36224 Z= 0.281 Chirality : 0.044 0.592 4150 Planarity : 0.004 0.050 4517 Dihedral : 13.122 135.184 10466 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.04 % Allowed : 5.31 % Favored : 91.65 % 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: 0.70 (0.15), residues: 3148 helix: 1.70 (0.16), residues: 1079 sheet: 0.99 (0.24), residues: 440 loop : -0.53 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1246 TYR 0.010 0.001 TYR J 679 PHE 0.011 0.001 PHE I 514 TRP 0.008 0.001 TRP J1193 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (26609) covalent geometry : angle 0.50229 / 0.28 (36212) hydrogen bonds : bond 0.15004 / 8.90 ( 1137) hydrogen bonds : angle 5.51262 / 3.57 ( 3140) metal coordination : bond 0.05795 / 2.83 ( 8) metal coordination : angle 16.69029 / 11.13 ( 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 575 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 493 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8473 (mt) REVERT: G 114 ASP cc_start: 0.8600 (m-30) cc_final: 0.8336 (m-30) REVERT: G 136 GLU cc_start: 0.7974 (tp30) cc_final: 0.7625 (mp0) REVERT: G 181 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7602 (mp0) REVERT: G 219 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.6821 (tpt90) REVERT: G 226 GLU cc_start: 0.7657 (tt0) cc_final: 0.7185 (pt0) REVERT: H 32 GLU cc_start: 0.8536 (tp30) cc_final: 0.8331 (tp30) REVERT: H 38 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.6966 (t) REVERT: H 144 ILE cc_start: 0.7906 (pt) cc_final: 0.7566 (mt) REVERT: H 145 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7388 (ttmm) REVERT: H 188 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8186 (mp0) REVERT: H 204 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8133 (mp0) REVERT: H 218 ARG cc_start: 0.6250 (mtt-85) cc_final: 0.5998 (mtm-85) REVERT: I 11 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8253 (mt) REVERT: I 36 GLN cc_start: 0.8274 (tp-100) cc_final: 0.8043 (tt0) REVERT: I 185 ASP cc_start: 0.8575 (m-30) cc_final: 0.8313 (m-30) REVERT: I 187 GLU cc_start: 0.8420 (pt0) cc_final: 0.8101 (pt0) REVERT: I 204 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7648 (mt) REVERT: I 403 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8359 (tmm) REVERT: I 423 ASP cc_start: 0.7342 (t0) cc_final: 0.7067 (p0) REVERT: I 465 ARG cc_start: 0.6431 (ttm-80) cc_final: 0.6131 (ttp80) REVERT: I 518 ASN cc_start: 0.7239 (p0) cc_final: 0.6891 (p0) REVERT: I 529 ARG cc_start: 0.8486 (ttm170) cc_final: 0.7785 (ttm170) REVERT: I 538 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7692 (pp) REVERT: I 546 GLU cc_start: 0.8618 (mp0) cc_final: 0.8036 (mp0) REVERT: I 609 ILE cc_start: 0.8031 (mt) cc_final: 0.7652 (tp) REVERT: I 641 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7545 (mm-30) REVERT: I 648 ASP cc_start: 0.7611 (t70) cc_final: 0.7281 (t0) REVERT: I 775 GLU cc_start: 0.8215 (tt0) cc_final: 0.7911 (mt-10) REVERT: I 779 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.8311 (ttt-90) REVERT: I 1089 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7407 (mp0) REVERT: I 1119 MET cc_start: 0.7876 (ttt) cc_final: 0.7516 (tpt) REVERT: I 1171 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7052 (ttp-170) REVERT: I 1211 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7995 (mmt90) REVERT: I 1274 GLU cc_start: 0.8921 (mp0) cc_final: 0.8491 (mp0) REVERT: I 1321 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7948 (mm-30) REVERT: J 225 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7403 (mt-10) REVERT: J 298 MET cc_start: 0.7799 (mmt) cc_final: 0.7348 (mtp) REVERT: J 301 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7435 (mm-30) REVERT: J 363 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8867 (tp) REVERT: J 386 GLU cc_start: 0.7188 (tt0) cc_final: 0.6428 (mt-10) REVERT: J 407 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8075 (p) REVERT: J 552 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7566 (mp) REVERT: J 562 GLU cc_start: 0.7895 (tp30) cc_final: 0.6977 (pm20) REVERT: J 797 THR cc_start: 0.9123 (t) cc_final: 0.8863 (t) REVERT: J 833 GLU cc_start: 0.7215 (tt0) cc_final: 0.6952 (tt0) REVERT: J 867 GLN cc_start: 0.7238 (mp10) cc_final: 0.6732 (tm-30) REVERT: J 878 ASP cc_start: 0.7733 (t0) cc_final: 0.7163 (p0) REVERT: J 1025 MET cc_start: 0.7812 (mtm) cc_final: 0.6819 (mpt) REVERT: J 1219 ASP cc_start: 0.8473 (m-30) cc_final: 0.8227 (m-30) outliers start: 82 outliers final: 23 residues processed: 555 average time/residue: 0.8091 time to fit residues: 509.8081 Evaluate side-chains 350 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 317 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN H 186 ASN I 65 ASN I 276 GLN I 387 ASN I 618 GLN I 932 GLN J 277 ASN J 708 ASN J 817 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.196603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.160617 restraints weight = 27036.544| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.53 r_work: 0.3160 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26617 Z= 0.126 Angle : 0.528 11.733 36224 Z= 0.281 Chirality : 0.042 0.223 4150 Planarity : 0.004 0.051 4517 Dihedral : 13.439 133.615 4327 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.60 % Allowed : 11.87 % Favored : 84.53 % 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: 0.89 (0.15), residues: 3148 helix: 1.97 (0.16), residues: 1098 sheet: 1.08 (0.24), residues: 432 loop : -0.53 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1330 TYR 0.013 0.001 TYR J 140 PHE 0.013 0.001 PHE I 514 TRP 0.007 0.001 TRP J1193 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (26609) covalent geometry : angle 0.52046 / 0.28 (36212) hydrogen bonds : bond 0.05371 / 3.27 ( 1137) hydrogen bonds : angle 4.28182 / 2.81 ( 3140) metal coordination : bond 0.00537 / 0.26 ( 8) metal coordination : angle 4.82216 / 3.21 ( 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 405 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 308 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 157 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8266 (m) REVERT: G 219 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.7926 (tpt90) REVERT: H 38 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7823 (t) REVERT: I 11 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (mt) REVERT: I 18 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7985 (ptp90) REVERT: I 185 ASP cc_start: 0.8744 (m-30) cc_final: 0.8461 (m-30) REVERT: I 187 GLU cc_start: 0.8426 (pt0) cc_final: 0.8178 (pt0) REVERT: I 413 GLU cc_start: 0.8132 (pm20) cc_final: 0.7760 (pm20) REVERT: I 422 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7862 (ptpp) REVERT: I 518 ASN cc_start: 0.7601 (p0) cc_final: 0.7263 (p0) REVERT: I 529 ARG cc_start: 0.8697 (ttm170) cc_final: 0.8207 (ttm170) REVERT: I 546 GLU cc_start: 0.8782 (mp0) cc_final: 0.8381 (mp0) REVERT: I 609 ILE cc_start: 0.8338 (mt) cc_final: 0.8017 (tp) REVERT: I 648 ASP cc_start: 0.7295 (t70) cc_final: 0.7023 (t0) REVERT: I 1089 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7858 (mp0) REVERT: I 1171 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7707 (ttp-170) REVERT: J 29 MET cc_start: 0.8277 (ttp) cc_final: 0.7999 (ttm) REVERT: J 363 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9004 (tp) REVERT: J 386 GLU cc_start: 0.7154 (tt0) cc_final: 0.6828 (mt-10) REVERT: J 552 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.7966 (mt) REVERT: J 805 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: J 1219 ASP cc_start: 0.8685 (m-30) cc_final: 0.8466 (m-30) REVERT: J 1334 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7688 (mm-30) outliers start: 97 outliers final: 39 residues processed: 376 average time/residue: 0.7960 time to fit residues: 340.9465 Evaluate side-chains 332 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 407 ARG Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 292 optimal weight: 20.0000 chunk 250 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 193 optimal weight: 0.0670 chunk 235 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN H 186 ASN I 36 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 932 GLN J1049 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.193593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.154091 restraints weight = 26953.585| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.94 r_work: 0.2939 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26617 Z= 0.147 Angle : 0.545 9.509 36224 Z= 0.293 Chirality : 0.043 0.226 4150 Planarity : 0.004 0.047 4517 Dihedral : 13.408 134.704 4310 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.60 % Allowed : 13.40 % Favored : 83.01 % 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: 1.92 (0.16), residues: 1108 sheet: 0.95 (0.24), residues: 431 loop : -0.58 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 297 TYR 0.016 0.001 TYR J 140 PHE 0.011 0.001 PHE I 57 TRP 0.006 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (26609) covalent geometry : angle 0.54084 / 0.29 (36212) hydrogen bonds : bond 0.05932 / 3.60 ( 1137) hydrogen bonds : angle 4.22855 / 2.77 ( 3140) metal coordination : bond 0.00397 / 0.19 ( 8) metal coordination : angle 3.63207 / 2.42 ( 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 401 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 304 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8890 (mt) REVERT: G 181 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: G 219 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.7810 (tpt90) REVERT: H 6 THR cc_start: 0.8746 (t) cc_final: 0.8464 (m) REVERT: H 38 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (t) REVERT: H 170 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6723 (pmm-80) REVERT: H 219 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7990 (mpp80) REVERT: I 11 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8508 (mt) REVERT: I 18 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7982 (ptp90) REVERT: I 185 ASP cc_start: 0.8846 (m-30) cc_final: 0.8563 (m-30) REVERT: I 187 GLU cc_start: 0.8611 (pt0) cc_final: 0.8344 (pt0) REVERT: I 394 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7380 (mmm160) REVERT: I 413 GLU cc_start: 0.8087 (pm20) cc_final: 0.7712 (pm20) REVERT: I 518 ASN cc_start: 0.7767 (p0) cc_final: 0.7482 (p0) REVERT: I 529 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8253 (ttm170) REVERT: I 538 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8004 (pp) REVERT: I 546 GLU cc_start: 0.8944 (mp0) cc_final: 0.8463 (mp0) REVERT: I 565 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: I 609 ILE cc_start: 0.8355 (mt) cc_final: 0.8009 (tp) REVERT: I 618 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: I 672 GLU cc_start: 0.8789 (pm20) cc_final: 0.8265 (pm20) REVERT: I 1089 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7923 (mp0) REVERT: I 1171 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7752 (ttp-170) REVERT: I 1264 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: J 21 LYS cc_start: 0.8744 (tttm) cc_final: 0.8296 (tttm) REVERT: J 29 MET cc_start: 0.8455 (ttp) cc_final: 0.8098 (ttm) REVERT: J 275 ARG cc_start: 0.8001 (mmt-90) cc_final: 0.7765 (mmt90) REVERT: J 278 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7012 (ttp-110) REVERT: J 363 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9015 (tp) REVERT: J 386 GLU cc_start: 0.7334 (tt0) cc_final: 0.6719 (mt-10) REVERT: J 402 GLU cc_start: 0.8344 (tt0) cc_final: 0.8114 (tt0) REVERT: J 552 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.7987 (mt) REVERT: J 805 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: J 1189 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7388 (mmp) REVERT: J 1236 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: J 1334 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7845 (mm-30) outliers start: 97 outliers final: 43 residues processed: 372 average time/residue: 0.7760 time to fit residues: 329.4510 Evaluate side-chains 344 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL 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: 6.9990 chunk 45 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 256 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 261 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.195226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159121 restraints weight = 26781.544| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.48 r_work: 0.3156 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26617 Z= 0.148 Angle : 0.553 12.007 36224 Z= 0.296 Chirality : 0.043 0.226 4150 Planarity : 0.004 0.044 4517 Dihedral : 13.411 135.295 4310 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.78 % Allowed : 14.36 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.75 (0.15), residues: 3148 helix: 1.92 (0.16), residues: 1110 sheet: 0.75 (0.24), residues: 444 loop : -0.60 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 143 TYR 0.017 0.001 TYR J 140 PHE 0.011 0.001 PHE I 57 TRP 0.007 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (26609) covalent geometry : angle 0.55044 / 0.30 (36212) hydrogen bonds : bond 0.05864 / 3.58 ( 1137) hydrogen bonds : angle 4.20178 / 2.76 ( 3140) metal coordination : bond 0.00318 / 0.16 ( 8) metal coordination : angle 2.91425 / 1.94 ( 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 395 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 293 time to evaluate : 0.935 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 83 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8961 (mt) REVERT: G 118 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: G 157 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8223 (m) REVERT: G 181 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: G 219 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.8026 (tpt90) REVERT: H 38 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8124 (t) REVERT: H 219 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7994 (mpp80) REVERT: I 11 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8539 (mt) REVERT: I 185 ASP cc_start: 0.8826 (m-30) cc_final: 0.8548 (m-30) REVERT: I 187 GLU cc_start: 0.8541 (pt0) cc_final: 0.8295 (pt0) REVERT: I 413 GLU cc_start: 0.7866 (pm20) cc_final: 0.7610 (pm20) REVERT: I 423 ASP cc_start: 0.7706 (p0) cc_final: 0.7286 (p0) REVERT: I 427 ASP cc_start: 0.7981 (m-30) cc_final: 0.7685 (m-30) REVERT: I 518 ASN cc_start: 0.7915 (p0) cc_final: 0.7610 (p0) REVERT: I 529 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8266 (ttm170) REVERT: I 538 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8022 (pp) REVERT: I 546 GLU cc_start: 0.8800 (mp0) cc_final: 0.8342 (mp0) REVERT: I 565 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: I 609 ILE cc_start: 0.8395 (mt) cc_final: 0.8058 (tp) REVERT: I 672 GLU cc_start: 0.8861 (pm20) cc_final: 0.8376 (pm20) REVERT: I 1089 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7916 (mp0) REVERT: I 1264 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: J 21 LYS cc_start: 0.8640 (tttm) cc_final: 0.8341 (tttm) REVERT: J 29 MET cc_start: 0.8459 (ttp) cc_final: 0.8155 (ttm) REVERT: J 275 ARG cc_start: 0.7939 (mmt-90) cc_final: 0.7693 (mmt90) REVERT: J 278 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7157 (ttp-110) REVERT: J 386 GLU cc_start: 0.7157 (tt0) cc_final: 0.6737 (mt-10) REVERT: J 402 GLU cc_start: 0.8190 (tt0) cc_final: 0.7975 (tt0) REVERT: J 552 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8116 (mt) REVERT: J 805 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: J 1236 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: J 1334 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7722 (mm-30) outliers start: 102 outliers final: 49 residues processed: 365 average time/residue: 0.7948 time to fit residues: 330.2532 Evaluate side-chains 347 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 456 VAL 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 565 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL 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: 3.9990 chunk 57 optimal weight: 0.5980 chunk 259 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 932 GLN I1136 GLN J 430 HIS J 560 ASN J1249 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.194241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.157450 restraints weight = 26682.574| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.59 r_work: 0.3109 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26617 Z= 0.148 Angle : 0.551 10.084 36224 Z= 0.296 Chirality : 0.043 0.225 4150 Planarity : 0.005 0.045 4517 Dihedral : 13.418 135.739 4310 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.97 % Allowed : 14.25 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.74 (0.15), residues: 3148 helix: 1.92 (0.16), residues: 1110 sheet: 0.72 (0.24), residues: 444 loop : -0.62 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 143 TYR 0.016 0.001 TYR J 140 PHE 0.011 0.001 PHE J1319 TRP 0.007 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (26609) covalent geometry : angle 0.54919 / 0.30 (36212) hydrogen bonds : bond 0.05876 / 3.59 ( 1137) hydrogen bonds : angle 4.17293 / 2.74 ( 3140) metal coordination : bond 0.00282 / 0.14 ( 8) metal coordination : angle 2.60347 / 1.74 ( 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 401 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 294 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8925 (mt) REVERT: G 118 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: G 157 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8194 (m) REVERT: G 181 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: G 219 ARG cc_start: 0.8602 (mtt-85) cc_final: 0.7943 (tpt90) REVERT: H 38 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8076 (t) REVERT: H 183 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8671 (tp) REVERT: H 214 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: H 219 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7957 (mpp80) REVERT: I 11 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8527 (mt) REVERT: I 185 ASP cc_start: 0.8789 (m-30) cc_final: 0.8514 (m-30) REVERT: I 187 GLU cc_start: 0.8525 (pt0) cc_final: 0.8267 (pt0) REVERT: I 413 GLU cc_start: 0.7863 (pm20) cc_final: 0.7543 (pm20) REVERT: I 423 ASP cc_start: 0.7711 (p0) cc_final: 0.7495 (p0) REVERT: I 518 ASN cc_start: 0.7744 (p0) cc_final: 0.7509 (p0) REVERT: I 529 ARG cc_start: 0.8743 (ttm170) cc_final: 0.8240 (ttm170) REVERT: I 538 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7973 (pp) REVERT: I 546 GLU cc_start: 0.8787 (mp0) cc_final: 0.8319 (mp0) REVERT: I 565 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: I 609 ILE cc_start: 0.8358 (mt) cc_final: 0.8024 (tp) REVERT: I 693 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8621 (mt) REVERT: I 1089 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7918 (mp0) REVERT: I 1264 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: J 21 LYS cc_start: 0.8632 (tttm) cc_final: 0.8303 (tttm) REVERT: J 66 LYS cc_start: 0.7318 (mtpp) cc_final: 0.7099 (mptt) REVERT: J 275 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7710 (mmt90) REVERT: J 278 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7155 (ttp-110) REVERT: J 386 GLU cc_start: 0.7166 (tt0) cc_final: 0.6724 (mt-10) REVERT: J 402 GLU cc_start: 0.8216 (tt0) cc_final: 0.8003 (tt0) REVERT: J 552 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8203 (mt) REVERT: J 805 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: J 1334 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7690 (mm-30) outliers start: 107 outliers final: 54 residues processed: 372 average time/residue: 0.7889 time to fit residues: 334.4163 Evaluate side-chains 360 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 290 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL 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: 9.9990 chunk 65 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1136 GLN J 430 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.193398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.156414 restraints weight = 26708.057| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.60 r_work: 0.3075 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26617 Z= 0.164 Angle : 0.576 10.862 36224 Z= 0.309 Chirality : 0.044 0.226 4150 Planarity : 0.005 0.047 4517 Dihedral : 13.476 135.528 4310 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.64 % Allowed : 15.36 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.72 (0.15), residues: 3148 helix: 1.90 (0.16), residues: 1104 sheet: 0.80 (0.24), residues: 442 loop : -0.64 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 143 TYR 0.017 0.001 TYR J 140 PHE 0.012 0.002 PHE I 934 TRP 0.007 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (26609) covalent geometry : angle 0.57468 / 0.31 (36212) hydrogen bonds : bond 0.06273 / 3.82 ( 1137) hydrogen bonds : angle 4.21118 / 2.77 ( 3140) metal coordination : bond 0.00289 / 0.14 ( 8) metal coordination : angle 2.41392 / 1.61 ( 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 388 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 290 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8944 (mt) REVERT: G 118 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: G 157 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8197 (m) REVERT: G 181 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: G 219 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.7962 (tpt90) REVERT: H 38 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8108 (t) REVERT: H 183 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.8666 (tp) REVERT: H 214 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: H 215 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: H 219 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7801 (mpp80) REVERT: I 185 ASP cc_start: 0.8784 (m-30) cc_final: 0.8506 (m-30) REVERT: I 187 GLU cc_start: 0.8507 (pt0) cc_final: 0.8257 (pt0) REVERT: I 412 GLU cc_start: 0.7779 (pm20) cc_final: 0.7425 (pm20) REVERT: I 529 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8258 (ttm170) REVERT: I 538 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7965 (pp) REVERT: I 546 GLU cc_start: 0.8755 (mp0) cc_final: 0.8283 (mp0) REVERT: I 565 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: I 609 ILE cc_start: 0.8364 (mt) cc_final: 0.8021 (tp) REVERT: I 1089 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7911 (mp0) REVERT: I 1264 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: J 21 LYS cc_start: 0.8639 (tttm) cc_final: 0.8318 (tttm) REVERT: J 29 MET cc_start: 0.8435 (ttp) cc_final: 0.8122 (ttm) REVERT: J 66 LYS cc_start: 0.7317 (mtpp) cc_final: 0.7111 (mptt) REVERT: J 386 GLU cc_start: 0.7174 (tt0) cc_final: 0.6769 (mt-10) REVERT: J 552 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8242 (mt) REVERT: J 562 GLU cc_start: 0.7121 (pm20) cc_final: 0.6906 (pm20) REVERT: J 599 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7586 (mtmm) REVERT: J 805 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: J 1236 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: J 1334 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7665 (mm-30) outliers start: 98 outliers final: 56 residues processed: 367 average time/residue: 0.8189 time to fit residues: 341.2576 Evaluate side-chains 357 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 284 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 LYS Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 13 optimal weight: 0.0770 chunk 312 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1136 GLN J 430 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.196639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.161039 restraints weight = 26785.846| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.48 r_work: 0.3154 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26617 Z= 0.112 Angle : 0.511 11.206 36224 Z= 0.273 Chirality : 0.041 0.221 4150 Planarity : 0.004 0.050 4517 Dihedral : 13.315 136.629 4308 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.86 % Allowed : 16.40 % Favored : 80.74 % 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: 0.91 (0.15), residues: 3148 helix: 2.12 (0.16), residues: 1094 sheet: 0.73 (0.24), residues: 452 loop : -0.51 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 143 TYR 0.014 0.001 TYR J 140 PHE 0.013 0.001 PHE J1319 TRP 0.007 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (26609) covalent geometry : angle 0.50911 / 0.27 (36212) hydrogen bonds : bond 0.04781 / 2.94 ( 1137) hydrogen bonds : angle 4.03117 / 2.64 ( 3140) metal coordination : bond 0.00209 / 0.10 ( 8) metal coordination : angle 2.27406 / 1.52 ( 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 381 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 304 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 157 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8151 (m) REVERT: G 181 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: G 219 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.7985 (tpt90) REVERT: H 38 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7837 (t) REVERT: H 183 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.8707 (tp) REVERT: H 215 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: H 219 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7952 (mpp80) REVERT: I 185 ASP cc_start: 0.8836 (m-30) cc_final: 0.8533 (m-30) REVERT: I 187 GLU cc_start: 0.8512 (pt0) cc_final: 0.8248 (pt0) REVERT: I 529 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8252 (ttm170) REVERT: I 538 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8009 (pp) REVERT: I 546 GLU cc_start: 0.8764 (mp0) cc_final: 0.8335 (mp0) REVERT: I 609 ILE cc_start: 0.8433 (mt) cc_final: 0.8068 (tp) REVERT: I 672 GLU cc_start: 0.8824 (pm20) cc_final: 0.8423 (pm20) REVERT: I 741 MET cc_start: 0.8427 (ttp) cc_final: 0.8099 (ttt) REVERT: I 790 ASP cc_start: 0.8851 (t0) cc_final: 0.8636 (t70) REVERT: I 1089 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7909 (mp0) REVERT: J 21 LYS cc_start: 0.8648 (tttm) cc_final: 0.8347 (tttm) REVERT: J 29 MET cc_start: 0.8412 (ttp) cc_final: 0.8129 (ttm) REVERT: J 275 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.7605 (mmt90) REVERT: J 278 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7113 (ttp-110) REVERT: J 363 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9008 (tp) REVERT: J 386 GLU cc_start: 0.7093 (tt0) cc_final: 0.6701 (mt-10) REVERT: J 552 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8226 (mt) REVERT: J 562 GLU cc_start: 0.6983 (pm20) cc_final: 0.6769 (pm20) REVERT: J 599 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7585 (mtmm) REVERT: J 805 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: J 1334 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7658 (mm-30) outliers start: 77 outliers final: 40 residues processed: 362 average time/residue: 0.8112 time to fit residues: 334.3309 Evaluate side-chains 344 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 118 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 LYS Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1334 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 124 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN H 186 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1136 GLN J 430 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.194511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.157492 restraints weight = 26844.058| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.64 r_work: 0.3046 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26617 Z= 0.137 Angle : 0.545 11.586 36224 Z= 0.290 Chirality : 0.042 0.224 4150 Planarity : 0.004 0.060 4517 Dihedral : 13.332 136.469 4306 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.89 % Allowed : 16.73 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.87 (0.15), residues: 3148 helix: 2.10 (0.16), residues: 1092 sheet: 0.75 (0.24), residues: 445 loop : -0.54 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 143 TYR 0.016 0.001 TYR J 140 PHE 0.012 0.001 PHE J1319 TRP 0.007 0.001 TRP J1193 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (26609) covalent geometry : angle 0.54346 / 0.29 (36212) hydrogen bonds : bond 0.05478 / 3.35 ( 1137) hydrogen bonds : angle 4.07825 / 2.68 ( 3140) metal coordination : bond 0.00248 / 0.12 ( 8) metal coordination : angle 2.24347 / 1.50 ( 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 365 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 287 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8944 (mt) REVERT: G 157 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (m) REVERT: G 181 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: G 219 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.7901 (tpt90) REVERT: H 38 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7975 (t) REVERT: H 183 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.8663 (tp) REVERT: H 215 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: H 219 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7813 (mpp80) REVERT: I 185 ASP cc_start: 0.8802 (m-30) cc_final: 0.8513 (m-30) REVERT: I 187 GLU cc_start: 0.8537 (pt0) cc_final: 0.8318 (pt0) REVERT: I 529 ARG cc_start: 0.8742 (ttm170) cc_final: 0.8248 (ttm170) REVERT: I 538 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7938 (pp) REVERT: I 546 GLU cc_start: 0.8799 (mp0) cc_final: 0.8316 (mp0) REVERT: I 609 ILE cc_start: 0.8367 (mt) cc_final: 0.8026 (tp) REVERT: I 1089 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7916 (mp0) REVERT: J 21 LYS cc_start: 0.8662 (tttm) cc_final: 0.8321 (tttm) REVERT: J 29 MET cc_start: 0.8455 (ttp) cc_final: 0.8129 (ttm) REVERT: J 275 ARG cc_start: 0.7918 (mmt-90) cc_final: 0.7685 (mmt90) REVERT: J 278 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7231 (ttp-170) REVERT: J 386 GLU cc_start: 0.7179 (tt0) cc_final: 0.6755 (mt-10) REVERT: J 552 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8230 (mt) REVERT: J 805 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: J 1334 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7729 (mm-30) outliers start: 78 outliers final: 48 residues processed: 347 average time/residue: 0.8131 time to fit residues: 320.9057 Evaluate side-chains 344 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 456 VAL 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 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 89 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 284 optimal weight: 30.0000 chunk 197 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1134 GLN I1264 GLN J 430 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.194231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157917 restraints weight = 26766.719| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.54 r_work: 0.3103 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26617 Z= 0.152 Angle : 0.571 11.487 36224 Z= 0.305 Chirality : 0.043 0.224 4150 Planarity : 0.005 0.061 4517 Dihedral : 13.404 136.146 4306 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.82 % Allowed : 17.03 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.81 (0.15), residues: 3148 helix: 2.02 (0.16), residues: 1092 sheet: 0.74 (0.24), residues: 451 loop : -0.57 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 143 TYR 0.017 0.001 TYR J 140 PHE 0.012 0.001 PHE I 934 TRP 0.007 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (26609) covalent geometry : angle 0.56968 / 0.30 (36212) hydrogen bonds : bond 0.05959 / 3.64 ( 1137) hydrogen bonds : angle 4.13483 / 2.72 ( 3140) metal coordination : bond 0.00255 / 0.12 ( 8) metal coordination : angle 2.19620 / 1.46 ( 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 363 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 287 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8969 (mt) REVERT: G 157 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8159 (m) REVERT: G 181 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: G 219 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8008 (tpt90) REVERT: H 38 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8121 (t) REVERT: H 143 ARG cc_start: 0.6735 (ttm110) cc_final: 0.6522 (mtm-85) REVERT: H 183 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.8711 (tp) REVERT: H 219 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7989 (mpp80) REVERT: I 185 ASP cc_start: 0.8842 (m-30) cc_final: 0.8574 (m-30) REVERT: I 187 GLU cc_start: 0.8532 (pt0) cc_final: 0.8322 (pt0) REVERT: I 529 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8273 (ttm170) REVERT: I 538 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8016 (pp) REVERT: I 546 GLU cc_start: 0.8808 (mp0) cc_final: 0.8379 (mp0) REVERT: I 609 ILE cc_start: 0.8415 (mt) cc_final: 0.8058 (tp) REVERT: I 741 MET cc_start: 0.8469 (ttp) cc_final: 0.8130 (ttt) REVERT: I 1089 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7950 (mp0) REVERT: J 21 LYS cc_start: 0.8665 (tttm) cc_final: 0.8365 (tttm) REVERT: J 275 ARG cc_start: 0.7942 (mmt-90) cc_final: 0.7603 (mmt90) REVERT: J 386 GLU cc_start: 0.7153 (tt0) cc_final: 0.6779 (mt-10) REVERT: J 552 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8266 (mt) REVERT: J 599 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7724 (mtmm) REVERT: J 805 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: J 1334 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7721 (mm-30) outliers start: 76 outliers final: 52 residues processed: 346 average time/residue: 0.8012 time to fit residues: 314.8369 Evaluate side-chains 344 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 492 MET 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 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 LYS Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 95 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 251 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1134 GLN I1264 GLN J 430 HIS J 817 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.191953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.154452 restraints weight = 26679.723| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.66 r_work: 0.3049 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26617 Z= 0.170 Angle : 0.602 11.667 36224 Z= 0.321 Chirality : 0.044 0.226 4150 Planarity : 0.005 0.065 4517 Dihedral : 13.472 135.732 4306 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.67 % Allowed : 17.25 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: 0.71 (0.15), residues: 3148 helix: 1.91 (0.16), residues: 1099 sheet: 0.73 (0.24), residues: 452 loop : -0.63 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 143 TYR 0.017 0.001 TYR I1229 PHE 0.012 0.002 PHE I 934 TRP 0.007 0.001 TRP J1193 HIS 0.007 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (26609) covalent geometry : angle 0.60102 / 0.32 (36212) hydrogen bonds : bond 0.06332 / 3.86 ( 1137) hydrogen bonds : angle 4.20365 / 2.77 ( 3140) metal coordination : bond 0.00286 / 0.14 ( 8) metal coordination : angle 2.20504 / 1.47 ( 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 352 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8944 (mt) REVERT: G 157 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8139 (m) REVERT: G 181 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: G 219 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.7907 (tpt90) REVERT: H 38 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8105 (t) REVERT: H 143 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6575 (mtm-85) REVERT: H 145 LYS cc_start: 0.8515 (tptm) cc_final: 0.8169 (tttt) REVERT: H 183 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.8698 (tp) REVERT: H 219 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7945 (mpp80) REVERT: I 185 ASP cc_start: 0.8806 (m-30) cc_final: 0.8535 (m-30) REVERT: I 187 GLU cc_start: 0.8541 (pt0) cc_final: 0.8314 (pt0) REVERT: I 407 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8393 (tpp-160) REVERT: I 529 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8280 (ttm170) REVERT: I 538 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7963 (pp) REVERT: I 546 GLU cc_start: 0.8793 (mp0) cc_final: 0.8350 (mp0) REVERT: I 609 ILE cc_start: 0.8370 (mt) cc_final: 0.8023 (tp) REVERT: I 741 MET cc_start: 0.8491 (ttp) cc_final: 0.8125 (ttt) REVERT: I 1089 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7938 (mp0) REVERT: J 21 LYS cc_start: 0.8663 (tttm) cc_final: 0.8317 (tttm) REVERT: J 275 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.7640 (mmt90) REVERT: J 386 GLU cc_start: 0.7175 (tt0) cc_final: 0.6744 (mt-10) REVERT: J 552 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8255 (mt) REVERT: J 599 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7691 (mtmm) REVERT: J 805 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: J 1334 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7737 (mm-30) outliers start: 72 outliers final: 52 residues processed: 335 average time/residue: 0.8029 time to fit residues: 306.3335 Evaluate side-chains 339 residues out of total 2697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 492 MET 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 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 648 ASP Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 LYS Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1080 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 0.0970 chunk 287 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 318 optimal weight: 0.8980 chunk 302 optimal weight: 0.0070 chunk 98 optimal weight: 0.5980 chunk 283 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 GLN I1134 GLN I1264 GLN J 430 HIS J 667 GLN J 867 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.196279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.159874 restraints weight = 26715.655| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.57 r_work: 0.3121 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26617 Z= 0.108 Angle : 0.518 12.211 36224 Z= 0.276 Chirality : 0.041 0.220 4150 Planarity : 0.004 0.047 4517 Dihedral : 13.277 137.134 4306 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.37 % Allowed : 17.70 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.92 (0.15), residues: 3148 helix: 2.09 (0.16), residues: 1103 sheet: 0.81 (0.25), residues: 434 loop : -0.50 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 143 TYR 0.013 0.001 TYR J 140 PHE 0.012 0.001 PHE J1319 TRP 0.007 0.001 TRP J1193 HIS 0.003 0.000 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26609) covalent geometry : angle 0.51683 / 0.28 (36212) hydrogen bonds : bond 0.04457 / 2.74 ( 1137) hydrogen bonds : angle 4.00429 / 2.63 ( 3140) metal coordination : bond 0.00184 / 0.09 ( 8) metal coordination : angle 2.01988 / 1.35 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9723.87 seconds wall clock time: 165 minutes 58.66 seconds (9958.66 seconds total)