Starting phenix.real_space_refine on Thu Mar 5 22:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r9g_4770/03_2026/6r9g_4770.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r9g_4770/03_2026/6r9g_4770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r9g_4770/03_2026/6r9g_4770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r9g_4770/03_2026/6r9g_4770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r9g_4770/03_2026/6r9g_4770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r9g_4770/03_2026/6r9g_4770.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 16236 2.51 5 N 4498 2.21 5 O 5107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25944 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1765 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1743 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 221} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10112 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 6, 'ARG:plan': 24, 'GLU:plan': 11, 'ASP:plan': 7, 'PHE:plan': 7, 'HIS:plan': 3, 'GLN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 309 Chain: "D" Number of atoms: 10051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10051 Classifications: {'peptide': 1334} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 65} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1280} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 10, 'ARG:plan': 17, 'TYR:plan': 4, 'HIS:plan': 5, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 849 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 101} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 852 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 3} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.98, per 1000 atoms: 0.19 Number of scatterers: 25944 At special positions: 0 Unit cell: (141.37, 167.745, 152.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5107 8.00 N 4498 7.00 C 16236 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: 1.91 Conformation dependent library (CDL) restraints added in 878.5 milliseconds 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6342 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 28 sheets defined 36.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.512A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.597A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.778A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.016A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.791A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.751A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.358A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.688A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.905A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.611A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.514A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.842A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.613A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 4.125A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 4.168A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.333A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 899 through 907 removed outlier: 3.626A pdb=" N GLY C 907 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 979 removed outlier: 6.265A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 992 through 1000 removed outlier: 4.216A pdb=" N ARG C 996 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 removed outlier: 3.552A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.782A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1120 " --> pdb=" O HIS C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.587A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1176 removed outlier: 3.651A pdb=" N LEU C1172 " --> pdb=" O GLU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1200 Processing helix chain 'C' and resid 1201 through 1203 No H-bonds generated for 'chain 'C' and resid 1201 through 1203' Processing helix chain 'C' and resid 1273 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 3.661A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1331 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.510A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 192 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.064A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 285 removed outlier: 4.274A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.769A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.917A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.514A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.815A pdb=" N LEU D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.800A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.699A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.689A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 674 through 701 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.005A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 784 removed outlier: 4.297A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 784 " --> pdb=" O ARG D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.117A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 916 through 925 removed outlier: 3.673A pdb=" N GLN D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.581A pdb=" N ALA D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D1147 " --> pdb=" O ASP D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.911A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.373A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 4.261A pdb=" N GLU D1293 " --> pdb=" O ASN D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1322 removed outlier: 3.580A pdb=" N ALA D1322 " --> pdb=" O PHE D1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.542A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 3.939A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.293A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.538A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'G' and resid 6 through 26 removed outlier: 3.501A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.954A pdb=" N HIS G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.803A pdb=" N VAL G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 57 " --> pdb=" O PHE G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 108 removed outlier: 4.045A pdb=" N GLU G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL G 108 " --> pdb=" O TYR G 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 76 through 105 removed outlier: 3.966A pdb=" N ILE F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.206A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.635A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 60 removed outlier: 3.714A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 57 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.480A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 69 removed outlier: 4.257A pdb=" N GLN C 69 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 101 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 94 through 98 removed outlier: 5.127A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.926A pdb=" N PHE C 136 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.483A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AB3, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.698A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.869A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.656A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.514A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 724 through 727 removed outlier: 5.485A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC1, first strand: chain 'C' and resid 817 through 818 removed outlier: 8.605A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 830 through 837 removed outlier: 3.930A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 105 through 112 removed outlier: 11.646A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AC5, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.740A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 434 through 437 Processing sheet with id=AC7, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.624A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 821 through 822 removed outlier: 3.558A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.513A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1264 through 1265 895 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8335 1.34 - 1.46: 3224 1.46 - 1.57: 14567 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 26306 Sorted by residual: bond pdb=" C GLU D 925 " pdb=" N PRO D 926 " ideal model delta sigma weight residual 1.332 1.395 -0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.51e+00 bond pdb=" CA PHE D1165 " pdb=" C PHE D1165 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.32e-02 5.74e+03 4.47e+00 bond pdb=" CA ILE D 416 " pdb=" C ILE D 416 " ideal model delta sigma weight residual 1.519 1.543 -0.024 1.14e-02 7.69e+03 4.43e+00 bond pdb=" C LYS C 496 " pdb=" N PRO C 497 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.18e+00 ... (remaining 26301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 34999 2.66 - 5.32: 555 5.32 - 7.99: 105 7.99 - 10.65: 16 10.65 - 13.31: 2 Bond angle restraints: 35677 Sorted by residual: angle pdb=" N VAL D 885 " pdb=" CA VAL D 885 " pdb=" C VAL D 885 " ideal model delta sigma weight residual 109.34 122.65 -13.31 2.08e+00 2.31e-01 4.09e+01 angle pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" C GLU B 29 " ideal model delta sigma weight residual 109.81 121.95 -12.14 2.21e+00 2.05e-01 3.02e+01 angle pdb=" C ASP F 25 " pdb=" N ASP F 26 " pdb=" CA ASP F 26 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ARG D 933 " pdb=" N THR D 934 " pdb=" CA THR D 934 " ideal model delta sigma weight residual 122.61 130.23 -7.62 1.56e+00 4.11e-01 2.38e+01 angle pdb=" N LEU D 127 " pdb=" CA LEU D 127 " pdb=" C LEU D 127 " ideal model delta sigma weight residual 110.30 117.61 -7.31 1.50e+00 4.44e-01 2.37e+01 ... (remaining 35672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 15346 15.22 - 30.44: 576 30.44 - 45.65: 173 45.65 - 60.87: 14 60.87 - 76.09: 21 Dihedral angle restraints: 16130 sinusoidal: 6293 harmonic: 9837 Sorted by residual: dihedral pdb=" C GLU B 29 " pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " ideal model delta harmonic sigma weight residual -122.60 -147.50 24.90 0 2.50e+00 1.60e-01 9.92e+01 dihedral pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " ideal model delta harmonic sigma weight residual 122.80 146.60 -23.80 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 0.00 -29.45 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 16127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 4162 0.216 - 0.431: 17 0.431 - 0.647: 0 0.647 - 0.862: 0 0.862 - 1.078: 1 Chirality restraints: 4180 Sorted by residual: chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA LEU C1176 " pdb=" N LEU C1176 " pdb=" C LEU C1176 " pdb=" CB LEU C1176 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA LEU C 571 " pdb=" N LEU C 571 " pdb=" C LEU C 571 " pdb=" CB LEU C 571 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4177 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D1164 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.32e+00 pdb=" C SER D1164 " -0.050 2.00e-02 2.50e+03 pdb=" O SER D1164 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE D1165 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 488 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 489 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 489 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 489 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C1064 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C ASP C1064 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP C1064 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C1065 " -0.015 2.00e-02 2.50e+03 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7447 2.83 - 3.34: 22492 3.34 - 3.86: 39588 3.86 - 4.38: 43256 4.38 - 4.90: 75915 Nonbonded interactions: 188698 Sorted by model distance: nonbonded pdb=" OE1 GLN C 148 " pdb=" OG SER C 531 " model vdw 2.307 3.040 nonbonded pdb=" OG SER D1160 " pdb=" O VAL D1204 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR C 123 " pdb=" OE2 GLU C 126 " model vdw 2.328 3.040 nonbonded pdb=" O LYS C1328 " pdb=" OG SER C1332 " model vdw 2.335 3.040 nonbonded pdb=" OH TYR C1281 " pdb=" O ILE D 434 " model vdw 2.336 3.040 ... (remaining 188693 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 'A' and (resid 6 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 70 or (resid 71 and (name N or name \ CA or name C or name O or name CB )) or resid 72 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 142 or (resid 143 and (name N or name CA or name C or name O or name C \ B )) or resid 144 through 163 or (resid 164 and (name N or name CA or name C or \ name O or name CB )) or resid 165 or (resid 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N or n \ ame CA or name C or name O or name CB )) or resid 171 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 23 \ 5)) selection = (chain 'B' and (resid 6 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161 through 190 or (resid 191 a \ nd (name N or name CA or name C or name O or name CB )) or resid 192 through 235 \ )) } ncs_group { reference = (chain 'F' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 108)) selection = (chain 'G' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 23 or (resid 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 85 or (resid 86 and (name N or na \ me CA or name C or name O or name CB )) or resid 87 through 108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 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 0.063 26306 Z= 0.198 Angle : 0.868 13.310 35677 Z= 0.491 Chirality : 0.055 1.078 4180 Planarity : 0.006 0.066 4716 Dihedral : 9.851 76.091 9788 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.97 % Favored : 91.91 % Rotamer: Outliers : 0.33 % Allowed : 2.64 % Favored : 97.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.26 % 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: -4.32 (0.11), residues: 3399 helix: -2.71 (0.10), residues: 1162 sheet: -1.22 (0.31), residues: 237 loop : -3.34 (0.11), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 84 TYR 0.032 0.002 TYR D 360 PHE 0.028 0.002 PHE D 227 TRP 0.016 0.002 TRP D 236 HIS 0.007 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00338 (26306) covalent geometry : angle 0.86802 (35677) hydrogen bonds : bond 0.15821 ( 893) hydrogen bonds : angle 7.07403 ( 2598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 788 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8073 (tt) cc_final: 0.7708 (pt) REVERT: B 219 ARG cc_start: 0.6456 (mtp-110) cc_final: 0.5820 (ttt180) REVERT: C 40 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6160 (tp30) REVERT: C 685 MET cc_start: 0.5744 (mmp) cc_final: 0.5540 (mmp) REVERT: C 878 THR cc_start: 0.7393 (p) cc_final: 0.6965 (p) REVERT: C 1069 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6869 (mtm110) REVERT: D 17 PHE cc_start: 0.3209 (t80) cc_final: 0.1825 (t80) REVERT: D 240 THR cc_start: 0.8828 (m) cc_final: 0.8588 (p) REVERT: D 349 TYR cc_start: 0.3922 (m-80) cc_final: 0.3683 (m-80) REVERT: D 485 MET cc_start: 0.5412 (mmm) cc_final: 0.4573 (mmt) REVERT: D 634 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7184 (mtt-85) REVERT: D 661 VAL cc_start: 0.6476 (t) cc_final: 0.5970 (t) REVERT: G 52 ILE cc_start: 0.5767 (mt) cc_final: 0.5472 (mm) REVERT: F 17 MET cc_start: 0.7418 (mmm) cc_final: 0.6259 (ppp) REVERT: F 39 MET cc_start: 0.7336 (mmm) cc_final: 0.6895 (mmp) REVERT: F 53 PHE cc_start: 0.7446 (m-80) cc_final: 0.7199 (m-80) outliers start: 9 outliers final: 1 residues processed: 793 average time/residue: 0.1883 time to fit residues: 222.9171 Evaluate side-chains 424 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1176 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 147 GLN C 69 GLN C 165 HIS C 339 ASN C 437 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C 725 GLN C 952 GLN C 965 GLN C1072 ASN C1220 GLN C1236 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 196 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN D 341 ASN D 448 GLN D 504 GLN D 702 GLN D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS D1268 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.206100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.173200 restraints weight = 41634.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.173087 restraints weight = 38758.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.175423 restraints weight = 30564.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.175389 restraints weight = 19925.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.175807 restraints weight = 19248.653| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26306 Z= 0.123 Angle : 0.650 12.992 35677 Z= 0.330 Chirality : 0.044 0.237 4180 Planarity : 0.005 0.068 4716 Dihedral : 4.754 47.113 3687 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 2.42 % Allowed : 12.17 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.90 (0.12), residues: 3399 helix: -0.78 (0.14), residues: 1170 sheet: -1.09 (0.32), residues: 228 loop : -2.90 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 738 TYR 0.022 0.002 TYR D1282 PHE 0.015 0.002 PHE C 505 TRP 0.023 0.002 TRP D 236 HIS 0.014 0.001 HIS D 817 Details of bonding type rmsd covalent geometry : bond 0.00272 (26306) covalent geometry : angle 0.64982 (35677) hydrogen bonds : bond 0.03446 ( 893) hydrogen bonds : angle 4.76830 ( 2598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 471 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8042 (tt) cc_final: 0.7513 (pt) REVERT: C 407 ARG cc_start: 0.7496 (mmm160) cc_final: 0.6941 (mmt180) REVERT: C 771 VAL cc_start: 0.5944 (t) cc_final: 0.5656 (t) REVERT: C 965 GLN cc_start: 0.7891 (mt0) cc_final: 0.7443 (pt0) REVERT: C 1030 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5810 (mm-30) REVERT: C 1069 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7227 (mtm110) REVERT: C 1180 MET cc_start: 0.7127 (tpp) cc_final: 0.6561 (tpp) REVERT: C 1319 MET cc_start: 0.4467 (pmm) cc_final: 0.4064 (mpp) REVERT: D 17 PHE cc_start: 0.1917 (t80) cc_final: 0.1426 (t80) REVERT: D 349 TYR cc_start: 0.4322 (m-80) cc_final: 0.3699 (m-80) REVERT: D 634 ARG cc_start: 0.7557 (mtp85) cc_final: 0.7347 (mtt-85) REVERT: D 743 MET cc_start: 0.5985 (mtt) cc_final: 0.5581 (mtp) REVERT: D 915 ILE cc_start: 0.7191 (mm) cc_final: 0.6917 (mt) REVERT: G 17 MET cc_start: 0.6506 (ptm) cc_final: 0.5463 (ptp) REVERT: G 52 ILE cc_start: 0.5874 (mt) cc_final: 0.5596 (mm) REVERT: F 17 MET cc_start: 0.7736 (mmm) cc_final: 0.6204 (ppp) REVERT: F 39 MET cc_start: 0.6514 (mmm) cc_final: 0.6313 (mmt) REVERT: F 55 VAL cc_start: 0.6853 (t) cc_final: 0.6650 (m) outliers start: 66 outliers final: 27 residues processed: 511 average time/residue: 0.1645 time to fit residues: 130.5415 Evaluate side-chains 382 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 355 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 236 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 313 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1244 HIS C1307 ASN D 209 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 102 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.197895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.164005 restraints weight = 42113.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.162594 restraints weight = 49963.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.165479 restraints weight = 39680.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.165424 restraints weight = 25037.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.166392 restraints weight = 24874.003| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26306 Z= 0.143 Angle : 0.651 13.231 35677 Z= 0.330 Chirality : 0.044 0.203 4180 Planarity : 0.005 0.050 4716 Dihedral : 4.629 24.930 3685 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.27 % Favored : 92.70 % Rotamer: Outliers : 3.34 % Allowed : 13.42 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -2.28 (0.13), residues: 3399 helix: -0.09 (0.15), residues: 1191 sheet: -0.84 (0.32), residues: 235 loop : -2.66 (0.12), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 275 TYR 0.026 0.002 TYR C 614 PHE 0.022 0.002 PHE D 172 TRP 0.013 0.001 TRP D 580 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00328 (26306) covalent geometry : angle 0.65138 (35677) hydrogen bonds : bond 0.03493 ( 893) hydrogen bonds : angle 4.46636 ( 2598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 385 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8003 (tt) cc_final: 0.7494 (pt) REVERT: A 131 CYS cc_start: 0.4670 (OUTLIER) cc_final: 0.3993 (p) REVERT: C 407 ARG cc_start: 0.7529 (mmm160) cc_final: 0.6984 (mmt180) REVERT: C 629 PHE cc_start: 0.3352 (OUTLIER) cc_final: 0.2281 (t80) REVERT: C 738 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6361 (pp20) REVERT: C 781 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: C 1180 MET cc_start: 0.7422 (tpp) cc_final: 0.6866 (tpp) REVERT: C 1319 MET cc_start: 0.4571 (pmm) cc_final: 0.4196 (mpp) REVERT: D 17 PHE cc_start: 0.2521 (t80) cc_final: 0.1711 (t80) REVERT: D 115 TRP cc_start: 0.7045 (p90) cc_final: 0.6844 (p90) REVERT: D 349 TYR cc_start: 0.4206 (m-80) cc_final: 0.3573 (m-80) REVERT: D 363 LEU cc_start: 0.6873 (tp) cc_final: 0.6424 (tp) REVERT: D 698 MET cc_start: 0.5062 (mmm) cc_final: 0.4111 (mmm) REVERT: D 798 ARG cc_start: 0.6811 (mtp85) cc_final: 0.6540 (mtt180) REVERT: D 821 MET cc_start: 0.7540 (tpp) cc_final: 0.7171 (mmm) REVERT: G 5 MET cc_start: 0.4335 (ppp) cc_final: 0.3436 (ppp) REVERT: G 17 MET cc_start: 0.6337 (ptm) cc_final: 0.5503 (ptp) REVERT: G 38 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7186 (p-80) REVERT: F 16 GLU cc_start: 0.6850 (tp30) cc_final: 0.6247 (pt0) REVERT: F 17 MET cc_start: 0.7657 (mmm) cc_final: 0.6244 (ppp) REVERT: F 55 VAL cc_start: 0.7135 (t) cc_final: 0.6812 (m) outliers start: 91 outliers final: 53 residues processed: 437 average time/residue: 0.1731 time to fit residues: 120.0663 Evaluate side-chains 387 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 302 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 287 optimal weight: 40.0000 chunk 12 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN D1252 HIS D1326 GLN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.184422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.151879 restraints weight = 42936.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.153617 restraints weight = 71892.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.154638 restraints weight = 48676.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.154863 restraints weight = 33459.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.156463 restraints weight = 28307.432| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 26306 Z= 0.307 Angle : 0.865 15.510 35677 Z= 0.443 Chirality : 0.052 0.345 4180 Planarity : 0.007 0.124 4716 Dihedral : 5.686 33.356 3685 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.00 % Favored : 90.88 % Rotamer: Outliers : 4.58 % Allowed : 13.97 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.13), residues: 3399 helix: -0.31 (0.15), residues: 1197 sheet: -1.05 (0.31), residues: 258 loop : -2.69 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 431 TYR 0.047 0.003 TYR C 26 PHE 0.034 0.003 PHE C 828 TRP 0.015 0.002 TRP D 686 HIS 0.017 0.002 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00704 (26306) covalent geometry : angle 0.86543 (35677) hydrogen bonds : bond 0.04694 ( 893) hydrogen bonds : angle 5.05089 ( 2598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 370 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8030 (tt) cc_final: 0.7462 (pt) REVERT: B 219 ARG cc_start: 0.6895 (mtp-110) cc_final: 0.6642 (ttp-170) REVERT: C 269 ILE cc_start: -0.0702 (OUTLIER) cc_final: -0.0939 (mp) REVERT: C 450 ASN cc_start: 0.6676 (m-40) cc_final: 0.6462 (m110) REVERT: C 629 PHE cc_start: 0.3865 (OUTLIER) cc_final: 0.2704 (t80) REVERT: C 654 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6057 (m-30) REVERT: C 681 MET cc_start: 0.6560 (ttm) cc_final: 0.5979 (ttm) REVERT: C 684 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7652 (t0) REVERT: C 741 MET cc_start: 0.3656 (mmt) cc_final: 0.3424 (mmm) REVERT: C 750 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7466 (mm) REVERT: C 813 GLU cc_start: 0.6264 (mt-10) cc_final: 0.4662 (mm-30) REVERT: C 1065 LYS cc_start: 0.8417 (tppt) cc_final: 0.8179 (tppp) REVERT: C 1119 MET cc_start: 0.7804 (tpt) cc_final: 0.7601 (tpt) REVERT: C 1131 MET cc_start: 0.7871 (ppp) cc_final: 0.7632 (ppp) REVERT: C 1180 MET cc_start: 0.7606 (tpp) cc_final: 0.7181 (tpp) REVERT: C 1198 LEU cc_start: 0.8118 (tp) cc_final: 0.7637 (tt) REVERT: C 1335 ILE cc_start: 0.5980 (OUTLIER) cc_final: 0.5628 (pt) REVERT: D 17 PHE cc_start: 0.2791 (t80) cc_final: 0.1964 (t80) REVERT: D 361 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6256 (mt) REVERT: D 381 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.6010 (mt) REVERT: D 445 LYS cc_start: 0.4805 (mmtp) cc_final: 0.4502 (mmmt) REVERT: D 1263 LYS cc_start: 0.4287 (tptp) cc_final: 0.3573 (mtmt) REVERT: D 1349 GLU cc_start: 0.6199 (tt0) cc_final: 0.5425 (mp0) REVERT: E 1 MET cc_start: -0.0383 (ppp) cc_final: -0.0769 (ptt) REVERT: G 5 MET cc_start: 0.4404 (ppp) cc_final: 0.3557 (ppp) REVERT: G 17 MET cc_start: 0.6120 (ptm) cc_final: 0.5745 (ptm) REVERT: G 38 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7518 (p-80) REVERT: F 17 MET cc_start: 0.7741 (mmm) cc_final: 0.6169 (ppp) outliers start: 125 outliers final: 75 residues processed: 464 average time/residue: 0.1759 time to fit residues: 126.9605 Evaluate side-chains 393 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 309 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 47 HIS Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 330 optimal weight: 9.9990 chunk 283 optimal weight: 30.0000 chunk 191 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 226 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN D 276 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D1197 ASN F 47 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.185745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.144114 restraints weight = 42479.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.140943 restraints weight = 46224.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.142746 restraints weight = 37536.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143116 restraints weight = 26610.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.143231 restraints weight = 26164.866| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26306 Z= 0.197 Angle : 0.724 13.509 35677 Z= 0.367 Chirality : 0.047 0.281 4180 Planarity : 0.005 0.058 4716 Dihedral : 5.301 32.299 3685 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.22 % Allowed : 16.13 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.13), residues: 3399 helix: -0.01 (0.15), residues: 1193 sheet: -1.08 (0.32), residues: 253 loop : -2.55 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 218 TYR 0.034 0.002 TYR D 631 PHE 0.028 0.002 PHE D 172 TRP 0.023 0.002 TRP D 580 HIS 0.010 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00461 (26306) covalent geometry : angle 0.72395 (35677) hydrogen bonds : bond 0.03807 ( 893) hydrogen bonds : angle 4.77880 ( 2598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 337 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8035 (tt) cc_final: 0.7464 (pt) REVERT: A 131 CYS cc_start: 0.6940 (p) cc_final: 0.6358 (p) REVERT: C 138 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6877 (mp) REVERT: C 407 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7156 (mmt180) REVERT: C 629 PHE cc_start: 0.3734 (OUTLIER) cc_final: 0.2743 (t80) REVERT: C 681 MET cc_start: 0.6349 (ttm) cc_final: 0.5800 (ttm) REVERT: C 684 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7616 (t0) REVERT: C 782 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8418 (t) REVERT: C 1131 MET cc_start: 0.7559 (ppp) cc_final: 0.7173 (ppp) REVERT: C 1180 MET cc_start: 0.7517 (tpp) cc_final: 0.7153 (tpp) REVERT: C 1198 LEU cc_start: 0.8206 (tp) cc_final: 0.7704 (tt) REVERT: D 17 PHE cc_start: 0.3164 (t80) cc_final: 0.2468 (t80) REVERT: D 119 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7276 (p) REVERT: D 180 MET cc_start: 0.4687 (tpt) cc_final: 0.4183 (tpt) REVERT: D 235 GLU cc_start: 0.5768 (mt-10) cc_final: 0.5553 (mt-10) REVERT: D 361 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6256 (mt) REVERT: D 1263 LYS cc_start: 0.4274 (tptp) cc_final: 0.3569 (mtmt) REVERT: D 1349 GLU cc_start: 0.6466 (tt0) cc_final: 0.5754 (mp0) REVERT: F 17 MET cc_start: 0.7658 (mmm) cc_final: 0.6123 (ppp) outliers start: 115 outliers final: 71 residues processed: 414 average time/residue: 0.1737 time to fit residues: 114.9284 Evaluate side-chains 379 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 302 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 67 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 305 optimal weight: 40.0000 chunk 160 optimal weight: 2.9990 chunk 334 optimal weight: 9.9990 chunk 136 optimal weight: 40.0000 chunk 29 optimal weight: 50.0000 chunk 247 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS D 340 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN F 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.182552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.148994 restraints weight = 43364.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.150811 restraints weight = 73400.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.152352 restraints weight = 47631.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.152278 restraints weight = 34325.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.153468 restraints weight = 28897.547| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26306 Z= 0.218 Angle : 0.757 12.221 35677 Z= 0.383 Chirality : 0.048 0.321 4180 Planarity : 0.005 0.076 4716 Dihedral : 5.460 32.412 3685 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.50 % Favored : 90.44 % Rotamer: Outliers : 4.77 % Allowed : 17.19 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3399 helix: 0.04 (0.15), residues: 1192 sheet: -1.35 (0.31), residues: 265 loop : -2.46 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 860 TYR 0.048 0.002 TYR D 631 PHE 0.032 0.002 PHE C 828 TRP 0.019 0.002 TRP D 580 HIS 0.011 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00510 (26306) covalent geometry : angle 0.75684 (35677) hydrogen bonds : bond 0.04048 ( 893) hydrogen bonds : angle 4.83579 ( 2598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 322 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7370 (pt0) cc_final: 0.7061 (mt-10) REVERT: A 99 ILE cc_start: 0.8079 (tt) cc_final: 0.7450 (pt) REVERT: C 138 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7091 (mp) REVERT: C 629 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.3556 (t80) REVERT: C 684 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7665 (t0) REVERT: C 710 VAL cc_start: 0.7619 (p) cc_final: 0.7337 (m) REVERT: C 1131 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7019 (ppp) REVERT: C 1180 MET cc_start: 0.7393 (tpp) cc_final: 0.7117 (tpp) REVERT: C 1198 LEU cc_start: 0.8218 (tp) cc_final: 0.7818 (tt) REVERT: C 1238 LEU cc_start: 0.6837 (mm) cc_final: 0.6630 (mm) REVERT: D 17 PHE cc_start: 0.2707 (t80) cc_final: 0.1854 (t80) REVERT: D 119 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6989 (p) REVERT: D 180 MET cc_start: 0.4738 (tpt) cc_final: 0.3724 (tpt) REVERT: D 361 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6342 (mt) REVERT: D 798 ARG cc_start: 0.7225 (mtp85) cc_final: 0.7006 (mtp85) REVERT: D 872 LEU cc_start: 0.8281 (mt) cc_final: 0.7952 (tp) REVERT: D 1263 LYS cc_start: 0.4417 (tptp) cc_final: 0.3739 (mtmt) REVERT: D 1349 GLU cc_start: 0.6424 (tt0) cc_final: 0.5880 (mp0) REVERT: F 17 MET cc_start: 0.7727 (mmm) cc_final: 0.6204 (ppp) outliers start: 130 outliers final: 92 residues processed: 416 average time/residue: 0.1608 time to fit residues: 107.7505 Evaluate side-chains 395 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 297 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 32 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 294 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 255 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.182013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.148549 restraints weight = 43091.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.149950 restraints weight = 69007.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.151118 restraints weight = 48768.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.151424 restraints weight = 32430.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.153022 restraints weight = 27263.846| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26306 Z= 0.204 Angle : 0.748 12.593 35677 Z= 0.378 Chirality : 0.047 0.309 4180 Planarity : 0.005 0.058 4716 Dihedral : 5.385 32.892 3685 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 4.47 % Allowed : 18.66 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.14), residues: 3399 helix: 0.14 (0.15), residues: 1188 sheet: -1.27 (0.32), residues: 258 loop : -2.42 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 860 TYR 0.038 0.002 TYR D 631 PHE 0.029 0.002 PHE C 828 TRP 0.020 0.002 TRP D 580 HIS 0.009 0.001 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00481 (26306) covalent geometry : angle 0.74818 (35677) hydrogen bonds : bond 0.03894 ( 893) hydrogen bonds : angle 4.79845 ( 2598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 314 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8067 (tt) cc_final: 0.7472 (pt) REVERT: A 130 ILE cc_start: 0.7786 (pt) cc_final: 0.7384 (pt) REVERT: B 200 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4855 (tttt) REVERT: C 138 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7084 (mp) REVERT: C 565 GLU cc_start: 0.6086 (pp20) cc_final: 0.5782 (pp20) REVERT: C 629 PHE cc_start: 0.5092 (OUTLIER) cc_final: 0.4368 (t80) REVERT: C 681 MET cc_start: 0.6321 (ttm) cc_final: 0.5984 (ttm) REVERT: C 684 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7462 (t0) REVERT: C 1180 MET cc_start: 0.7401 (tpp) cc_final: 0.7127 (tpp) REVERT: C 1198 LEU cc_start: 0.8190 (tp) cc_final: 0.7776 (tt) REVERT: C 1323 PHE cc_start: 0.8151 (t80) cc_final: 0.7908 (t80) REVERT: D 17 PHE cc_start: 0.2542 (t80) cc_final: 0.1970 (t80) REVERT: D 119 SER cc_start: 0.7152 (OUTLIER) cc_final: 0.6895 (p) REVERT: D 130 MET cc_start: 0.4847 (pmm) cc_final: 0.4577 (pmm) REVERT: D 872 LEU cc_start: 0.8200 (mt) cc_final: 0.7858 (tp) REVERT: D 1263 LYS cc_start: 0.4399 (tptp) cc_final: 0.3745 (mtmt) REVERT: D 1349 GLU cc_start: 0.6351 (tt0) cc_final: 0.5674 (mp0) REVERT: F 17 MET cc_start: 0.7714 (mmm) cc_final: 0.6206 (ppp) outliers start: 122 outliers final: 103 residues processed: 405 average time/residue: 0.1555 time to fit residues: 101.5958 Evaluate side-chains 401 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 293 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 29 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 274 optimal weight: 30.0000 chunk 308 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 144 optimal weight: 50.0000 chunk 264 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 337 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.182987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.150365 restraints weight = 43071.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.152314 restraints weight = 70323.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.153109 restraints weight = 48356.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.153195 restraints weight = 34401.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.154752 restraints weight = 28197.995| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 26306 Z= 0.170 Angle : 0.720 12.474 35677 Z= 0.363 Chirality : 0.046 0.311 4180 Planarity : 0.005 0.059 4716 Dihedral : 5.218 33.203 3685 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.33 % Allowed : 19.24 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 3399 helix: 0.29 (0.15), residues: 1184 sheet: -1.32 (0.31), residues: 272 loop : -2.36 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 407 TYR 0.030 0.002 TYR D 631 PHE 0.025 0.002 PHE C 828 TRP 0.022 0.002 TRP D 580 HIS 0.007 0.001 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00407 (26306) covalent geometry : angle 0.71996 (35677) hydrogen bonds : bond 0.03706 ( 893) hydrogen bonds : angle 4.70423 ( 2598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 310 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7454 (pt0) cc_final: 0.7224 (mt-10) REVERT: B 200 LYS cc_start: 0.5032 (OUTLIER) cc_final: 0.4791 (tttt) REVERT: C 565 GLU cc_start: 0.6081 (pp20) cc_final: 0.5751 (pp20) REVERT: C 629 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4211 (t80) REVERT: C 684 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7354 (t0) REVERT: C 685 MET cc_start: 0.6227 (mmt) cc_final: 0.5826 (mmt) REVERT: C 741 MET cc_start: 0.3980 (mmt) cc_final: 0.3675 (mmt) REVERT: C 755 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8554 (tppt) REVERT: C 782 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8467 (t) REVERT: C 955 GLN cc_start: 0.6293 (tt0) cc_final: 0.5941 (tt0) REVERT: C 1131 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7384 (ppp) REVERT: C 1180 MET cc_start: 0.7392 (tpp) cc_final: 0.7099 (tpp) REVERT: C 1198 LEU cc_start: 0.8146 (tp) cc_final: 0.7708 (tt) REVERT: D 17 PHE cc_start: 0.2523 (t80) cc_final: 0.2045 (t80) REVERT: D 119 SER cc_start: 0.7236 (OUTLIER) cc_final: 0.6977 (p) REVERT: D 349 TYR cc_start: 0.4987 (m-10) cc_final: 0.4517 (m-80) REVERT: D 472 LEU cc_start: 0.8517 (mt) cc_final: 0.7996 (mt) REVERT: D 872 LEU cc_start: 0.8116 (mt) cc_final: 0.7730 (tp) REVERT: D 1263 LYS cc_start: 0.4219 (tptp) cc_final: 0.3543 (mtmt) REVERT: D 1349 GLU cc_start: 0.6325 (tt0) cc_final: 0.5699 (mp0) REVERT: F 17 MET cc_start: 0.7680 (mmm) cc_final: 0.6360 (ptm) outliers start: 118 outliers final: 88 residues processed: 391 average time/residue: 0.1615 time to fit residues: 102.1200 Evaluate side-chains 392 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 297 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 PHE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 49 optimal weight: 0.9990 chunk 188 optimal weight: 20.0000 chunk 339 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 329 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.183616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.141576 restraints weight = 42887.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140328 restraints weight = 38293.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.141396 restraints weight = 32220.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.141745 restraints weight = 24418.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.141689 restraints weight = 23283.065| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26306 Z= 0.154 Angle : 0.714 12.569 35677 Z= 0.358 Chirality : 0.046 0.310 4180 Planarity : 0.004 0.056 4716 Dihedral : 5.088 33.243 3685 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.81 % Allowed : 20.05 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3399 helix: 0.37 (0.15), residues: 1189 sheet: -1.29 (0.31), residues: 275 loop : -2.31 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 860 TYR 0.041 0.002 TYR G 48 PHE 0.032 0.002 PHE D 172 TRP 0.033 0.002 TRP D 236 HIS 0.007 0.001 HIS D 897 Details of bonding type rmsd covalent geometry : bond 0.00367 (26306) covalent geometry : angle 0.71384 (35677) hydrogen bonds : bond 0.03560 ( 893) hydrogen bonds : angle 4.59562 ( 2598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 320 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7828 (pt0) cc_final: 0.7312 (mt-10) REVERT: B 200 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.4658 (tttt) REVERT: C 239 MET cc_start: 0.2377 (ppp) cc_final: 0.1521 (pmm) REVERT: C 684 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7568 (t0) REVERT: C 685 MET cc_start: 0.5950 (mmt) cc_final: 0.5745 (mmt) REVERT: C 755 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8575 (tppt) REVERT: C 782 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8548 (t) REVERT: C 955 GLN cc_start: 0.6551 (tt0) cc_final: 0.6198 (tt0) REVERT: C 1180 MET cc_start: 0.7603 (tpp) cc_final: 0.7285 (tpp) REVERT: C 1198 LEU cc_start: 0.8118 (tp) cc_final: 0.7660 (tt) REVERT: D 17 PHE cc_start: 0.3094 (t80) cc_final: 0.2632 (t80) REVERT: D 119 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7429 (p) REVERT: D 349 TYR cc_start: 0.5359 (m-10) cc_final: 0.4833 (m-80) REVERT: D 472 LEU cc_start: 0.8717 (mt) cc_final: 0.8310 (mt) REVERT: D 743 MET cc_start: 0.7117 (mmt) cc_final: 0.6908 (mmt) REVERT: D 872 LEU cc_start: 0.8246 (mt) cc_final: 0.7771 (tp) REVERT: D 1263 LYS cc_start: 0.4505 (tptp) cc_final: 0.3561 (mtmt) REVERT: D 1349 GLU cc_start: 0.6303 (tt0) cc_final: 0.5877 (mp0) REVERT: F 17 MET cc_start: 0.7697 (mmm) cc_final: 0.6340 (ptm) outliers start: 104 outliers final: 85 residues processed: 393 average time/residue: 0.1693 time to fit residues: 106.6268 Evaluate side-chains 390 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 300 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 177 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 171 optimal weight: 0.0870 chunk 280 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 287 optimal weight: 50.0000 overall best weight: 3.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 274 ASN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.179125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.145804 restraints weight = 43067.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.148361 restraints weight = 69489.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.148766 restraints weight = 44159.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.149115 restraints weight = 31387.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.151314 restraints weight = 25481.319| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 26306 Z= 0.254 Angle : 0.825 12.250 35677 Z= 0.419 Chirality : 0.050 0.374 4180 Planarity : 0.006 0.094 4716 Dihedral : 5.654 34.376 3685 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.39 % Favored : 89.50 % Rotamer: Outliers : 4.18 % Allowed : 20.34 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.14), residues: 3399 helix: 0.03 (0.15), residues: 1206 sheet: -1.36 (0.33), residues: 251 loop : -2.42 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 860 TYR 0.047 0.002 TYR D 631 PHE 0.048 0.003 PHE C 156 TRP 0.038 0.003 TRP D1193 HIS 0.010 0.002 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00599 (26306) covalent geometry : angle 0.82510 (35677) hydrogen bonds : bond 0.04293 ( 893) hydrogen bonds : angle 4.90526 ( 2598) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 319 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7471 (pt0) cc_final: 0.7250 (mt-10) REVERT: C 138 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7154 (mp) REVERT: C 239 MET cc_start: 0.2895 (ppp) cc_final: 0.1945 (pmm) REVERT: C 681 MET cc_start: 0.5773 (ttm) cc_final: 0.5410 (ttm) REVERT: C 684 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7290 (t0) REVERT: C 685 MET cc_start: 0.6236 (mmt) cc_final: 0.5992 (mmt) REVERT: C 755 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8805 (tppt) REVERT: C 955 GLN cc_start: 0.6270 (tt0) cc_final: 0.5941 (tt0) REVERT: C 966 ILE cc_start: 0.7489 (mt) cc_final: 0.7268 (mt) REVERT: C 1198 LEU cc_start: 0.8191 (tp) cc_final: 0.7793 (tt) REVERT: D 119 SER cc_start: 0.7393 (OUTLIER) cc_final: 0.7152 (p) REVERT: D 269 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6296 (t80) REVERT: D 276 ASN cc_start: 0.8075 (t0) cc_final: 0.7831 (t0) REVERT: D 472 LEU cc_start: 0.8912 (mt) cc_final: 0.8663 (mt) REVERT: D 872 LEU cc_start: 0.8171 (mt) cc_final: 0.7829 (tp) REVERT: D 1263 LYS cc_start: 0.4569 (tptp) cc_final: 0.3913 (mtmt) REVERT: D 1349 GLU cc_start: 0.6362 (tt0) cc_final: 0.5677 (mp0) REVERT: E 1 MET cc_start: -0.1631 (ptt) cc_final: -0.3943 (ttt) REVERT: F 17 MET cc_start: 0.7803 (mmm) cc_final: 0.6277 (ppp) outliers start: 114 outliers final: 91 residues processed: 401 average time/residue: 0.1635 time to fit residues: 105.5850 Evaluate side-chains 396 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 300 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 405 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 755 LYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1291 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 124 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 239 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 269 optimal weight: 0.0470 chunk 157 optimal weight: 1.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.183274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.149340 restraints weight = 42565.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.152328 restraints weight = 54452.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.152547 restraints weight = 39173.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.152757 restraints weight = 27699.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.153765 restraints weight = 23425.532| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26306 Z= 0.150 Angle : 0.738 13.005 35677 Z= 0.371 Chirality : 0.047 0.326 4180 Planarity : 0.005 0.061 4716 Dihedral : 5.210 33.471 3685 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.01 % Allowed : 21.88 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3399 helix: 0.31 (0.15), residues: 1195 sheet: -1.17 (0.32), residues: 267 loop : -2.32 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 860 TYR 0.032 0.002 TYR G 48 PHE 0.041 0.002 PHE C 156 TRP 0.035 0.003 TRP D1193 HIS 0.026 0.001 HIS C1313 Details of bonding type rmsd covalent geometry : bond 0.00346 (26306) covalent geometry : angle 0.73818 (35677) hydrogen bonds : bond 0.03549 ( 893) hydrogen bonds : angle 4.61557 ( 2598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.24 seconds wall clock time: 76 minutes 25.46 seconds (4585.46 seconds total)